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Zhang W, Liu K, Kong F, Ye T, Wang T. Multiple Functions of Compatible Solute Ectoine and Strategies for Constructing Overproducers for Biobased Production. Mol Biotechnol 2024; 66:1772-1785. [PMID: 37488320 DOI: 10.1007/s12033-023-00827-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023]
Abstract
Ectoine and its derivative 5-hydroxyectoine are compatible solutes initially found in the hyperhalophilic bacterium Ectothiorhodospira halochloris, which inhabits the desert in Egypt. The habitat of ectoine producers implies the primary function of ectoine as a cytoprotectant against harsh conditions such as high salinity, drought, and high radiation. More extensive and in-depth studies have revealed the multiple functions of ectoine in its native producer bacterial cells and other types of cells and its biomolecular components (such as proteins and DNA) as a general protective agent. Its chemical properties as a bio-based amino acid derivative make it attractive for basic scientific research and related industries, such as the food/agricultural industry, cosmetic manufacturing, biologics, and therapeutic agent preparation. This article first discusses the functions and applications of ectoine and 5-hydroxyectoine. Subsequently, more emphasis was placed on advances in bio-based ectoine and/or 5-hydroxyectoine production. Strategies for developing more robust cell factories for highly efficient ectoine and/or 5-hydroxyectoine production are further discussed. We hope this review will provide a valuable reference for studies on the bio-based production of ectoine and 5-hydroxyectoine.
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Affiliation(s)
- Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, People's Republic of China
| | - Kun Liu
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Fang Kong
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Tao Ye
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China
| | - Tianwen Wang
- College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, People's Republic of China.
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2
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Azevedo LG, Sosa E, de Queiroz ATL, Barral A, Wheeler RJ, Nicolás MF, Farias LP, Do Porto DF, Ramos PIP. High-throughput prioritization of target proteins for development of new antileishmanial compounds. Int J Parasitol Drugs Drug Resist 2024; 25:100538. [PMID: 38669848 PMCID: PMC11068527 DOI: 10.1016/j.ijpddr.2024.100538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/11/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Leishmaniasis, a vector-borne disease, is caused by the infection of Leishmania spp., obligate intracellular protozoan parasites. Presently, human vaccines are unavailable, and the primary treatment relies heavily on systemic drugs, often presenting with suboptimal formulations and substantial toxicity, making new drugs a high priority for LMIC countries burdened by the disease, but a low priority in the agenda of most pharmaceutical companies due to unattractive profit margins. New ways to accelerate the discovery of new, or the repositioning of existing drugs, are needed. To address this challenge, our study aimed to identify potential protein targets shared among clinically-relevant Leishmania species. We employed a subtractive proteomics and comparative genomics approach, integrating high-throughput multi-omics data to classify these targets based on different druggability metrics. This effort resulted in the ranking of 6502 ortholog groups of protein targets across 14 pathogenic Leishmania species. Among the top 20 highly ranked groups, metabolic processes known to be attractive drug targets, including the ubiquitination pathway, aminoacyl-tRNA synthetases, and purine synthesis, were rediscovered. Additionally, we unveiled novel promising targets such as the nicotinate phosphoribosyltransferase enzyme and dihydrolipoamide succinyltransferases. These groups exhibited appealing druggability features, including less than 40% sequence identity to the human host proteome, predicted essentiality, structural classification as highly druggable or druggable, and expression levels above the 50th percentile in the amastigote form. The resources presented in this work also represent a comprehensive collection of integrated data regarding trypanosomatid biology.
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Affiliation(s)
- Lucas G Azevedo
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
| | - Ezequiel Sosa
- Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Artur T L de Queiroz
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
| | - Aldina Barral
- Laboratório de Medicina e Saúde Pública de Precisão (MeSP2), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil.
| | - Richard J Wheeler
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom.
| | - Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil.
| | - Leonardo P Farias
- Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil; Laboratório de Medicina e Saúde Pública de Precisão (MeSP2), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil.
| | | | - Pablo Ivan P Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Instituto Gonçalo Moniz, Fundação Oswaldo Cruz (Fiocruz Bahia), Salvador, Bahia, Brazil; Post-graduate Program in Biotechnology and Investigative Medicine, Instituto Gonçalo Moniz, Salvador, Bahia, Brazil.
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3
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Faridi R, Yousaf R, Inagaki S, Olszewski R, Gu S, Morell RJ, Wilson E, Xia Y, Qaiser TA, Rashid M, Fenollar-Ferrer C, Hoa M, Riazuddin S, Friedman TB. Deafness DFNB128 Associated with a Recessive Variant of Human MAP3K1 Recapitulates Hearing Loss of Map3k1-Deficient Mice. Genes (Basel) 2024; 15:845. [PMID: 39062623 PMCID: PMC11276321 DOI: 10.3390/genes15070845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/20/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Deafness in vertebrates is associated with variants of hundreds of genes. Yet, many mutant genes causing rare forms of deafness remain to be discovered. A consanguineous Pakistani family segregating nonsyndromic deafness in two sibships were studied using microarrays and exome sequencing. A 1.2 Mb locus (DFNB128) on chromosome 5q11.2 encompassing six genes was identified. In one of the two sibships of this family, a novel homozygous recessive variant NM_005921.2:c.4460G>A p.(Arg1487His) in the kinase domain of MAP3K1 co-segregated with nonsyndromic deafness. There are two previously reported Map3k1-kinase-deficient mouse models that are associated with recessively inherited syndromic deafness. MAP3K1 phosphorylates serine and threonine and functions in a signaling pathway where pathogenic variants of HGF, MET, and GAB1 were previously reported to be associated with human deafness DFNB39, DFNB97, and DFNB26, respectively. Our single-cell transcriptome data of mouse cochlea mRNA show expression of Map3k1 and its signaling partners in several inner ear cell types suggesting a requirement of wild-type MAP3K1 for normal hearing. In contrast to dominant variants of MAP3K1 associated with Disorders of Sex Development 46,XY sex-reversal, our computational modeling of the recessive substitution p.(Arg1487His) predicts a subtle structural alteration in MAP3K1, consistent with the limited phenotype of nonsyndromic deafness.
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Affiliation(s)
- Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rizwan Yousaf
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Sayaka Inagaki
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Rafal Olszewski
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Shoujun Gu
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Robert J. Morell
- Genomics and Computational Biology Core, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA;
| | - Elizabeth Wilson
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Ying Xia
- Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Tanveer Ahmed Qaiser
- Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Sector G-8/3, Ravi Road, Islamabad 44000, Pakistan;
| | - Muhammad Rashid
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Cristina Fenollar-Ferrer
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
| | - Michael Hoa
- Auditory Development and Restoration Program, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.O.); (S.G.); (M.H.)
| | - Sheikh Riazuddin
- Allama Iqbal Medical Research Center, Jinnah Burn and Reconstructive Surgery Center, University of Health Sciences, Lahore 54550, Pakistan;
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders (NIDCD), National Institutes of Health (NIH), Bethesda, MD 20892, USA; (R.F.); (R.Y.); (S.I.); (E.W.); (C.F.-F.)
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4
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Hu L, An K, Zhang Y, Bai C. Exploring the Activation Mechanism of the GPR183 Receptor. J Phys Chem B 2024; 128:6071-6081. [PMID: 38877985 DOI: 10.1021/acs.jpcb.4c02812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
The G protein-coupled receptors (GPCRs) play a pivotal role in numerous biological processes as crucial cell membrane receptors. However, the dynamic mechanisms underlying the activation of GPR183, a specific GPCR, remain largely elusive. To address this, we employed computational simulation techniques to elucidate the activation process and key events associated with GPR183, including conformational changes from inactive to active state, binding interactions with the Gi protein complex, and GDP release. Our findings demonstrate that the association between GPR183 and the Gi protein involves the formation of receptor-specific conformations, the gradual proximity of the Gi protein to the binding pocket, and fine adjustments of the protein conformation, ultimately leading to a stable GPR183-Gi complex characterized by a high energy barrier. The presence of Gi protein partially promotes GPR183 activation, which is consistent with the observation of GPCR constitutive activity test experiments, thus illustrating the reliability of our calculations. Moreover, our study suggests the existence of a stable partially activated state preceding complete activation, providing novel avenues for future investigations. In addition, the relevance of GPR183 for various diseases, such as colitis, the response of eosinophils to Mycobacterium tuberculosis infection, antiviral properties, and pulmonary inflammation, has been emphasized, underscoring its therapeutic potential. Consequently, understanding the activation process of GPR183 through molecular dynamic simulations offers valuable kinetic insights that can aid in the development of targeted therapies.
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Affiliation(s)
- Linfeng Hu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, PR China
- Warshel Institute for Computational Biology, Shenzhen, Guangdong 518172, PR China
| | - Ke An
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang 310005, PR China
| | - Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, PR China
- Warshel Institute for Computational Biology, Shenzhen, Guangdong 518172, PR China
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, PR China
- Warshel Institute for Computational Biology, Shenzhen, Guangdong 518172, PR China
- Chenzhu (MoMeD) Biotechnology Co., Ltd, Hangzhou, Zhejiang 310005, PR China
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5
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Kaneko H, Korenaga R, Nakamura R, Kawai S, Ando T, Shiroishi M. Binding characteristics of the doxepin E/Z-isomers to the histamine H 1 receptor revealed by receptor-bound ligand analysis and molecular dynamics study. J Mol Recognit 2024:e3098. [PMID: 38924170 DOI: 10.1002/jmr.3098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/14/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Doxepin is an antihistamine and tricyclic antidepressant that binds to the histamine H1 receptor (H1R) with high affinity. Doxepin is an 85:15 mixture of the E- and Z-isomers. The Z-isomer is well known to be more effective than the E-isomer, whereas based on the crystal structure of the H1R/doxepin complex, the hydroxyl group of Thr1123.37 is close enough to form a hydrogen bond with the oxygen atom of the E-isomer. The detailed binding characteristics and reasons for the differences remain unclear. In this study, we analyzed doxepin isomers bound to the receptor following extraction from a purified H1R protein complexed with doxepin. The ratio of the E- and Z-isomers bound to wild-type (WT) H1R was 55:45, indicating that the Z-isomer was bound to WT H1R with an approximately 5.2-fold higher affinity than the E-isomer. For the T1123.37V mutant, the E/Z ratio was 89:11, indicating that both isomers have similar affinities. Free energy calculations using molecular dynamics (MD) simulations also reproduced the experimental results of the relative binding free energy differences between the isomers for WT and T1123.37V. Furthermore, MD simulations revealed that the hydroxyl group of T1123.37 did not form hydrogen bonds with the E-isomer, but with the adjacent residues in the binding pocket. Analysis of the receptor-bound doxepin and MD simulations suggested that the hydroxyl group of T1123.37 contributes to the formation of a chemical environment in the binding pocket, which is slightly more favorable for the Z-isomer without hydrogen bonding with doxepin.
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Affiliation(s)
- Hiroto Kaneko
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryunosuke Korenaga
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
| | - Ryota Nakamura
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Shinnosuke Kawai
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
| | - Tadashi Ando
- Department of Applied Electronics, Tokyo University of Science, Tokyo, Japan
- Research Institute for Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Mitsunori Shiroishi
- Department of Biological Science and Technology, Tokyo University of Science, Tokyo, Japan
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6
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Zhekova HR, Ramirez Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. Biophys J 2024; 123:1705-1721. [PMID: 38760929 PMCID: PMC11214021 DOI: 10.1016/j.bpj.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 04/09/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024] Open
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO3-, CO32-, Cl-, Na+, K+, NH3, and H+, which are necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl-/HCO3- exchanger) and NBCe1 (Na+-CO32-cotransporter). Previous computational studies of the outward-facing state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed coarse-grained and atomistic molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1, and NDCBE (an Na+-CO32-/Cl- exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin. The recently resolved inward-facing state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, phosphatidylcholine, and sphingomyelin in the three studied proteins, and their potential roles in the SLC4 transport function, conformational transition, and protein dimerization are discussed.
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Affiliation(s)
- Hristina R Zhekova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Daniel P Ramirez Echemendía
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Besian I Sejdiu
- Department of Structural Biology and Center of Excellence for Data Driven Discovery, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Alexander Pushkin
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - D Peter Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Ira Kurtz
- Department of Medicine, Division of Nephrology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Brain Research Institute, University of California, Los Angeles, Los Angeles, California.
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7
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Maharana J, Hwang SK, Singha DL, Panda D, Singh S, Okita TW, Modi MK. Exploring the structural assembly of rice ADP-glucose pyrophosphorylase subunits using MD simulation. J Mol Graph Model 2024; 129:108761. [PMID: 38552302 DOI: 10.1016/j.jmgm.2024.108761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
ADP-glucose pyrophosphorylase plays a pivotal role as an allosteric enzyme, essential for starch biosynthesis in plants. The higher plant AGPase comparises of a pair of large and a pair of small subunits to form a heterotetrameric complex. Growing evidence indicates that each subunit plays a distinct role in regulating the underlying mechanism of starch biosynthesis. In the rice genome, there are four large subunit genes (OsL1-L4) and three small subunit genes (OsS1, OsS2a, and OsS2b). While the structural assembly of cytosolic rice AGPase subunits (OsL2:OsS2b) has been elucidated, there is currently no such documented research available for plastidial rice AGPases (OsL1:OsS1). In this study, we employed protein modeling and MD simulation approaches to gain insights into the structural association of plastidial rice AGPase subunits. Our results demonstrate that the heterotetrameric association of OsL1:OsS1 is very similar to that of cytosolic OsL2:OsS2b and potato AGPase heterotetramer (StLS:StSS). Moreover, the yeast-two-hybrid results on OsL1:OsS1, which resemble StLS:StSS, suggest a differential protein assembly for OsL2:OsS2b. Thus, the regulatory and catalytic mechanisms for plastidial AGPases (OsL1:OsS1) could be different in rice culm and developing endosperm compared to those of OsL2:OsS2b, which are predominantly found in rice endosperm.
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Affiliation(s)
- Jitendra Maharana
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
| | - Seon-Kap Hwang
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Dhanawantari L Singha
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India; Department of Botany, Rabindranath Tagore University, Hojai, Assam, 782435, India
| | - Debashis Panda
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Salvinder Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Thomas W Okita
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Oliva B, Velasco J, Leila Berto G, Polikarpov I, Cristante de Oliveira L, Segato F. Recombinant cellobiose dehydrogenase from Thermothelomyces thermophilus: Its functional characterization and applicability in cellobionic acid production. BIORESOURCE TECHNOLOGY 2024; 402:130763. [PMID: 38692377 DOI: 10.1016/j.biortech.2024.130763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/10/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
The fungus Thermothelomyces thermophilus is a thermotolerant microorganism that has been explored as a reservoir for enzymes (hydrolytic enzymes and oxidoreductases). The functional analysis of a recombinant cellobiose dehydrogenase (MtCDHB) from T. thermophilus demonstrated a thermophilic behavior, an optimal pH in alkaline conditions for inter-domain electron transfer, and catalytic activity on cellooligosaccharides with different degree of polymerization. Its applicability was evaluated to the sustainable production of cellobionic acid (CBA), a potential pharmaceutical and cosmetic ingredient rarely commercialized. Dissolving pulp was used as a disaccharide source for MtCDHB. Initially, recombinant exoglucanases (MtCBHI and MtCBHII) from T. thermophilus hydrolyzed the dissolving pulp, resulting in 87% cellobiose yield, which was subsequently converted into CBA by MtCDHB, achieving a 66% CBA yield after 24 h. These findings highlight the potential of MtCDHB as a novel approach to obtaining CBA through the bioconversion of a plant-based source.
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Affiliation(s)
- Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil; Biological Sciences Department, Universidad de los Andes, Bogotá DC, Colombia
| | - Gabriela Leila Berto
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leandro Cristante de Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences (IBILCE) São Paulo State University "Júlio de Mesquita Filho" - Unesp - São José do Rio Preto, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil.
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9
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Pan D, Luo QJ, O Reilly AO, Yuan GR, Wang JJ, Dou W. Mutations of voltage-gated sodium channel contribute to pyrethroid resistance in Panonychus citri. INSECT SCIENCE 2024; 31:803-816. [PMID: 37650774 DOI: 10.1111/1744-7917.13266] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/25/2023] [Indexed: 09/01/2023]
Abstract
Insecticide resistance in Panonychus citri is a major obstacle to mite control in citrus orchards. Pyrethroid insecticides are continually used to control mites in China, although resistance to pyrethroids has evolved in some populations. Here, the resistance to the pyrethroid fenpropathrin was investigated and 7 out of 8 field-collected populations of P. citri exhibited a high level of resistance, ranging from 171-fold to 15 391-fold higher than the susceptible (SS) comparison strain. Three voltage-gated sodium channel (VGSC) mutations were identified in the tested populations: L1031V, F1747L, and F1751I. Amplicon sequencing was used to evaluate the frequency of these mutations in the 19 field populations. L1031V and F1751I were present in all populations at frequencies of 11.6%-82.1% and 0.5%-31.8%, respectively, whereas the F1747L mutation was only present in 12 populations from Chongqing, Sichuan, Guangxi, and Yunnan provinces. Introduction of these mutations singly or in combination into transgenic flies significantly increased their resistance to fenpropathrin and these flies also exhibited reduced mortality after exposure to the pyrethroids permethrin and β-cypermethrin. Panonychus citri VGSC homology modeling and ligand docking indicate that F1747 and F1751 form direct binding contacts with pyrethroids, which are lost with mutation, whereas L1031 mutation may diminish pyrethroid effects through an allosteric mechanism. Overall, the results provide molecular markers for monitoring pest resistance to pyrethroids and offer new insights into the basis of pyrethroid actions on sodium channels.
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Affiliation(s)
- Deng Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qiu-Juan Luo
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Andrias O O Reilly
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, UK
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), Academy of Agricultural Sciences, Southwest University, Chongqing, China
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10
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Ito S, Matsunaga R, Nakakido M, Komura D, Katoh H, Ishikawa S, Tsumoto K. High-throughput system for the thermostability analysis of proteins. Protein Sci 2024; 33:e5029. [PMID: 38801228 PMCID: PMC11129621 DOI: 10.1002/pro.5029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024]
Abstract
Thermal stability of proteins is a primary metric for evaluating their physical properties. Although researchers attempted to predict it using machine learning frameworks, their performance has been dependent on the quality and quantity of published data. This is due to the technical limitation that thermodynamic characterization of protein denaturation by fluorescence or calorimetry in a high-throughput manner has been challenging. Obtaining a melting curve that derives solely from the target protein requires laborious purification, making it far from practical to prepare a hundred or more samples in a single workflow. Here, we aimed to overcome this throughput limitation by leveraging the high protein secretion efficacy of Brevibacillus and consecutive treatment with plate-scale purification methodologies. By handling the entire process of expression, purification, and analysis on a per-plate basis, we enabled the direct observation of protein denaturation in 384 samples within 4 days. To demonstrate a practical application of the system, we conducted a comprehensive analysis of 186 single mutants of a single-chain variable fragment of nivolumab, harvesting the melting temperature (Tm) ranging from -9.3 up to +10.8°C compared to the wild-type sequence. Our findings will allow for data-driven stabilization in protein design and streamlining the rational approaches.
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Affiliation(s)
- Sae Ito
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
| | - Ryo Matsunaga
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of EngineeringThe University of TokyoTokyoJapan
- Department of Chemistry and Biotechnology, School of EngineeringThe University of TokyoTokyoJapan
- The Institute of Medical ScienceThe University of TokyoTokyoJapan
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11
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Juliá-Palacios N, Olivella M, Sigatullina Bondarenko M, Ibáñez-Micó S, Muñoz-Cabello B, Alonso-Luengo O, Soto-Insuga V, García-Navas D, Cuesta-Herraiz L, Andreo-Lillo P, Aguilera-Albesa S, Hedrera-Fernández A, González Alguacil E, Sánchez-Carpintero R, Martín Del Valle F, Jiménez González E, Cean Cabrera L, Medina-Rivera I, Perez-Ordoñez M, Colomé R, Lopez L, Engracia Cazorla M, Fornaguera M, Ormazabal A, Alonso-Colmenero I, Illescas KS, Balsells-Mejía S, Mari-Vico R, Duffo Viñas M, Cappuccio G, Terrone G, Romano R, Manti F, Mastrangelo M, Alfonsi C, de Siqueira Barros B, Nizon M, Gjerulfsen CE, Muro VL, Karall D, Zeiner F, Masnada S, Peterlongo I, Oyarzábal A, Santos-Gómez A, Altafaj X, García-Cazorla Á. L-serine treatment in patients with GRIN-related encephalopathy: a phase 2A, non-randomized study. Brain 2024; 147:1653-1666. [PMID: 38380699 DOI: 10.1093/brain/awae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/20/2023] [Accepted: 01/21/2024] [Indexed: 02/22/2024] Open
Abstract
GRIN-related disorders are rare developmental encephalopathies with variable manifestations and limited therapeutic options. Here, we present the first non-randomized, open-label, single-arm trial (NCT04646447) designed to evaluate the tolerability and efficacy of L-serine in children with GRIN genetic variants leading to loss-of-function. In this phase 2A trial, patients aged 2-18 years with GRIN loss-of-function pathogenic variants received L-serine for 52 weeks. Primary end points included safety and efficacy by measuring changes in the Vineland Adaptive Behavior Scales, Bayley Scales, age-appropriate Wechsler Scales, Gross Motor Function-88, Sleep Disturbance Scale for Children, Pediatric Quality of Life Inventory, Child Behavior Checklist and the Caregiver-Teacher Report Form following 12 months of treatment. Secondary outcomes included seizure frequency and intensity reduction and EEG improvement. Assessments were performed 3 months and 1 day before starting treatment and 1, 3, 6 and 12 months after beginning the supplement. Twenty-four participants were enrolled (13 males/11 females, mean age 9.8 years, SD 4.8), 23 of whom completed the study. Patients had GRIN2B, GRIN1 and GRIN2A variants (12, 6 and 5 cases, respectively). Their clinical phenotypes showed 91% had intellectual disability (61% severe), 83% had behavioural problems, 78% had movement disorders and 58% had epilepsy. Based on the Vineland Adaptive Behavior Composite standard scores, nine children were classified as mildly impaired (cut-off score > 55), whereas 14 were assigned to the clinically severe group. An improvement was detected in the Daily Living Skills domain (P = 0035) from the Vineland Scales within the mild group. Expressive (P = 0.005), Personal (P = 0.003), Community (P = 0.009), Interpersonal (P = 0.005) and Fine Motor (P = 0.031) subdomains improved for the whole cohort, although improvement was mostly found in the mild group. The Growth Scale Values in the Cognitive subdomain of the Bayley-III Scale showed a significant improvement in the severe group (P = 0.016), with a mean increase of 21.6 points. L-serine treatment was associated with significant improvement in the median Gross Motor Function-88 total score (P = 0.002) and the mean Pediatric Quality of Life total score (P = 0.00068), regardless of severity. L-serine normalized the EEG pattern in five children and the frequency of seizures in one clinically affected child. One patient discontinued treatment due to irritability and insomnia. The trial provides evidence that L-serine is a safe treatment for children with GRIN loss-of-function variants, having the potential to improve adaptive behaviour, motor function and quality of life, with a better response to the treatment in mild phenotypes.
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Affiliation(s)
- Natalia Juliá-Palacios
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Mireia Olivella
- Bioinformatics and Bioimaging Group. Faculty of Science, Technology and Engineering, University of Vic-Central University of Catalonia, 08500 Vic, Spain
- Institute for Research and Innovation in Life and Health Sciences (IRIS-CC), University of Vic-Central University of Catalonia, 08500 Vic, Spain
| | - Mariya Sigatullina Bondarenko
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | | | - Beatriz Muñoz-Cabello
- Department of Pediatrics, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | - Olga Alonso-Luengo
- Department of Pediatrics, Hospital Universitario Virgen del Rocío, 41013 Sevilla, Spain
| | | | - Deyanira García-Navas
- Department of Pediatric Neurology, Complejo Hospitalario Universitario de Cáceres, 10003 Cáceres, Spain
| | | | - Patricia Andreo-Lillo
- Neuropediatric Unit, Pediatric Department, University Hospital of Sant Joan d'Alacant, 03550 Sant Joan d'Alacant, Spain
| | - Sergio Aguilera-Albesa
- Paediatric Neurology Unit, Department of Pediatrics, Hospital Universitario de Navarra, 31008, Pamplona, Spain
| | - Antonio Hedrera-Fernández
- Child Neurology Unit, Pediatrics Department, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | | | | | | | | | | | - Ines Medina-Rivera
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Marta Perez-Ordoñez
- Child and Adolescent Mental Health Area, Psychiatry and Psychology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Roser Colomé
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Laura Lopez
- Department of Rehabilitation, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - María Engracia Cazorla
- Department of Rehabilitation, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Montserrat Fornaguera
- Department of Rehabilitation, Institut de Recerca Sant Joan de Déu, 08950 Barcelona, Spain
| | - Aida Ormazabal
- Department of Clinical Biochemistry, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
- European Reference Network for Hereditary Metabolic Diseases (MetabERN), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Itziar Alonso-Colmenero
- Pediatric Neurology Department, Hospital Sant Joan de Déu, Full Member of ERN EpiCare, Barcelona University, 08950 Barcelona, Spain
| | - Katia Sofía Illescas
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Sol Balsells-Mejía
- Department of Research Promotion and Management. Statistical Support, Hospital Sant Joan de Déu (HSJD), 08950 Barcelona, Spain
| | - Rosanna Mari-Vico
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Maria Duffo Viñas
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
- Child and Adolescent Mental Health Area, Psychiatry and Psychology, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Gerarda Cappuccio
- Department of Translational Medical Sciences, Università degli Studi di Napoli 'Federico II', 80125 Naples, Italy
- Telethon Institute of Genetics and Medicine, Department of Pediatrics, Pozzuoli, 80131 Naples, Italy
| | - Gaetano Terrone
- Department of Translational Medical Sciences, Università degli Studi di Napoli 'Federico II', 80125 Naples, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Università degli Studi di Napoli 'Federico II', 80125 Naples, Italy
| | - Filippo Manti
- Department of Human Neuroscience, University of Rome La Sapienza, 00185 Roma, Lazio, Italy
| | - Mario Mastrangelo
- Department of Women and Child Health and Uroginecological Sciences, Sapienza University of Rome, 00185 Rome, Italy
- Child Neurology and Psychiatry Unit, Department of Neuroscience/Mental Health, Azienda Ospedaliero-Universitaria Policlinico Umberto I, 00161 Rome, Italy
| | - Chiara Alfonsi
- Department of Human Neuroscience, University of Rome La Sapienza, 00185 Roma, Lazio, Italy
| | - Bruna de Siqueira Barros
- Núcleo de Estudos da Saúde do Adolescente, Programa de Pós-Graduação em Ciências Médicas, Universidade do Estado do Rio de Janeiro, Faculdade de Ciência Médicas, 56066 Rio de Janeiro, RJ, Brazil
| | - Mathilde Nizon
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France
| | | | - Valeria L Muro
- Pediatric Neurology Unit, Hospital Britanico Buenos Aires, C1280AEB Buenos Aires, Argentina
| | - Daniela Karall
- Clinic for Paediatrics, Division of Inherited Metabolic Disorders, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Fiona Zeiner
- Clinic for Paediatrics, Division of Inherited Metabolic Disorders, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Silvia Masnada
- Department of Child Neurology, V. Buzzi Children's Hospital, 20125 Milan, Italy
| | - Irene Peterlongo
- Department of Child Neurology, V. Buzzi Children's Hospital, 20125 Milan, Italy
| | - Alfonso Oyarzábal
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
| | - Ana Santos-Gómez
- Department of Biomedicine, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Xavier Altafaj
- Department of Biomedicine, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
| | - Ángeles García-Cazorla
- Neurometabolic Unit and Synaptic Metabolism Lab, Department of Neurology, Hospital Sant Joan de Déu-IRSJD, CIBERER and MetabERN, 08950 Barcelona, Spain
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12
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Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Bhat V, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. Nat Genet 2024; 56:925-937. [PMID: 38658794 DOI: 10.1038/s41588-024-01726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/21/2024] [Indexed: 04/26/2024]
Abstract
CRISPR base editing screens enable analysis of disease-associated variants at scale; however, variable efficiency and precision confounds the assessment of variant-induced phenotypes. Here, we provide an integrated experimental and computational pipeline that improves estimation of variant effects in base editing screens. We use a reporter construct to measure guide RNA (gRNA) editing outcomes alongside their phenotypic consequences and introduce base editor screen analysis with activity normalization (BEAN), a Bayesian network that uses per-guide editing outcomes provided by the reporter and target site chromatin accessibility to estimate variant impacts. BEAN outperforms existing tools in variant effect quantification. We use BEAN to pinpoint common regulatory variants that alter low-density lipoprotein (LDL) uptake, implicating previously unreported genes. Additionally, through saturation base editing of LDLR, we accurately quantify missense variant pathogenicity that is consistent with measurements in UK Biobank patients and identify underlying structural mechanisms. This work provides a widely applicable approach to improve the power of base editing screens for disease-associated variant characterization.
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Affiliation(s)
- Jayoung Ryu
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sam Barkal
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Martin Jankowiak
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Yunzhuo Zhou
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matthew Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Quang Vinh Phan
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhijian Li
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Manuel Tognon
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computer Science Department, University of Verona, Verona, Italy
| | - Lara Brown
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael I Love
- Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vineel Bhat
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, Quebec, Canada
- Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
| | - David B Ascher
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Christopher A Cassa
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Luca Pinello
- Molecular Pathology Unit, Krantz Family Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
- Gene Regulation Observatory, The Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Pathology, Harvard Medical School, Boston, MA, USA.
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13
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Zhang Q, Fan S, Tang M, Wang C, Li X, Jin Y, Yang Z. Computation-Guided Rational Design of Cysteine-Less Protein Variants in Engineered hCGL. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9937-9946. [PMID: 38651303 DOI: 10.1021/acs.jafc.3c06821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The engineered human cystathionine-γ-lyase (hCGL) resulting in enhanced activity toward both cysteine and cystine unveils a potential robust antitumor activity. However, the presence of cysteine residues has the potential to induce oligomerization or incorrect disulfide bonding, which may decrease the bioavailability of biopharmaceuticals. Through a meticulous design process targeting the cysteine residues within engineered hCGL, a set of potential beneficial mutants were obtained by virtual screening employing Rosetta and ABACUS. Experimental measurements have revealed that most of the mutants showed increased activity toward both substrates l-Cys and CSSC. Furthermore, mutants C109V and C229D demonstrated Tm value increases of 8.2 and 1.8 °C, respectively. After an 80 min incubation at 60 °C, mutant C229D still maintained high residual activity. Unexpectedly, mutant C109V, displaying activity approximately 2-fold higher than the activity of wild type (WT) for both substrates, showed disappointing instability in plasma, which suggests that computational design still requires further consideration. Analysis of their structure and molecular dynamics (MD) simulation revealed the impact of hydrophobic interaction, hydrogen bonds, and near-attack conformation (NAC) stability on activity and stability. This study acquired information about mutants that exhibit enhanced activity or thermal resistance and serve as valuable guidance for subsequent specific cysteine modifications.
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Affiliation(s)
- Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mengjia Tang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Chenyu Wang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaoxiao Li
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Maurici N, Phan TM, Henty-Ridilla JL, Kim YC, Mittal J, Bah A. Uncovering the molecular interactions underlying MBD2 and MBD3 phase separation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591564. [PMID: 38746378 PMCID: PMC11092444 DOI: 10.1101/2024.04.29.591564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Chromatin organization controls DNA's accessibility to regulatory factors to influence gene expression. Heterochromatin, or transcriptionally silent chromatin enriched in methylated DNA and methylated histone tails, self-assembles through multivalent interactions with its associated proteins into a condensed, but dynamic state. Liquid-liquid phase separation (LLPS) of key heterochromatin regulators, such as heterochromatin protein 1 (HP1), plays an essential role in heterochromatin assembly and function. Methyl-CpG-binding protein 2 (MeCP2), the most studied member of the methyl-CpG-binding domain (MBD) family of proteins, has been recently shown to undergo LLPS in the absence and presence of methylated DNA. These studies provide a new mechanistic framework for understanding the role of methylated DNA and its readers in heterochromatin formation. However, the details of the molecular interactions by which other MBD family members undergo LLPS to mediate genome organization and transcriptional regulation are not fully understood. Here, we focus on two MBD proteins, MBD2 and MBD3, that have distinct but interdependent roles in gene regulation. Using an integrated computational and experimental approach, we uncover the homotypic and heterotypic interactions governing MBD2 and MBD3 phase separation and DNA's influence on this process. We show that despite sharing the highest sequence identity and structural homology among all the MBD protein family members, MBD2 and MBD3 exhibit differing residue patterns resulting in distinct phase separation mechanisms. Understanding the molecular underpinnings of MBD protein condensation offers insights into the higher-order, LLPS-mediated organization of heterochromatin.
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15
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Bernardes GPMDA, Serra GM, Silva LDSE, Martins MP, Perez LN, de Molfetta FA, Santos AV, Schneider MPC. Potential Involvement of the South American Lungfish Intelectin-2 in Innate-Associated Immune Modulation. Int J Mol Sci 2024; 25:4798. [PMID: 38732017 PMCID: PMC11084424 DOI: 10.3390/ijms25094798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
Intelectins belong to a family of lectins with specific and transitory carbohydrate interaction capabilities. These interactions are related to the activity of agglutinating pathogens, as intelectins play a significant role in immunity. Despite the prominent immune defense function of intelectins, limited information about its structural characteristics and carbohydrate interaction properties is available. This study investigated an intelectin transcript identified in RNA-seq data obtained from the South American lungfish (Lepidosiren paradoxa), namely LpITLN2-B. The structural analyses predicted LpITLN2-B to be a homo-trimeric globular protein with the fibrinogen-like functional domain (FReD), exhibiting a molecular mass of 57 kDa. The quaternary structure is subdivided into three monomers, A, B, and C, and each domain comprises 11 β-sheets: an anti-parallel β-sheet, a β-hairpin, and a disordered β-sheet structure. Molecular docking demonstrates a significant interaction with disaccharides rather than monosaccharides. The preferential interaction with disaccharides highlights the potential interaction with pathogen molecules, such as LPS and Poly(I:C). The hemagglutination assay inhibited lectins activity, especially maltose and sucrose, highlighting lectin activity in L. paradoxa samples. Overall, our results show the potential relevance of LpITLN2-B in L. paradoxa immune defense against pathogens.
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Affiliation(s)
| | - Gustavo Marques Serra
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Lucas da Silva e Silva
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
| | - Maíra Pompeu Martins
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
| | - Louise Neiva Perez
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Fábio Alberto de Molfetta
- Laboratory of Molecular Modeling, Exact and Natural Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Agenor Valadares Santos
- Laboratory of Biotechnology of Enzymes and Biotransformation, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil;
| | - Maria Paula Cruz Schneider
- Laboratory of Genomics and Biotechnology, Biological Sciences Institute, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (G.P.M.d.A.B.); (L.d.S.e.S.); (M.P.C.S.)
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16
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Hutchinson K, Schlessinger A. Comprehensive Characterization of LAT1 Cholesterol-Binding Sites. J Chem Theory Comput 2024; 20:3349-3358. [PMID: 38597304 DOI: 10.1021/acs.jctc.3c01391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The human L-type amino acid transporter 1 (LAT1; SLC7A5), is an amino acid exchanger protein, primarily found in the blood-brain barrier, placenta, and testis, where it plays a key role in amino acid homeostasis. Cholesterol is an essential lipid that has been highlighted to play a role in regulating the activity of membrane transporters, such as LAT1, yet little is known about the molecular mechanisms driving this phenomenon. Here we perform a comprehensive computational analysis to investigate cholesterol's role in LAT1 structure and function, focusing on four cholesterol-binding sites (CHOL1-4) identified in a recent LAT1-apo inward-open conformation cryo-EM structure. Through a series of independent molecular dynamics (MD) simulations, molecular docking, MM/GBSA free energy calculations, and other analysis tools, we explored the interactions between LAT1 and cholesterol. Our findings suggest that CHOL3 forms the most stable and favorable interactions with LAT1. Principal component analysis (PCA) and center of mass (COM) distance assessments show that CHOL3 binding stabilizes the inward-open state of LAT1 by preserving the spatial arrangement of the hash and bundle domains. Additionally, we propose an alternative cholesterol-binding site for originally assigned CHOL1. Overall, this study improves the understanding of cholesterol's modulatory effect on LAT1 and proposes candidate sites for the discovery of future allosteric ligands with rational design.
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Affiliation(s)
- Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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17
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Yamagata A, Ito K, Suzuki T, Dohmae N, Terada T, Shirouzu M. Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Nat Commun 2024; 15:3027. [PMID: 38637505 PMCID: PMC11026379 DOI: 10.1038/s41467-024-47322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 HC, and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 HC through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers.
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Affiliation(s)
- Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Kaori Ito
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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18
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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19
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Tandiana R, Barletta GP, Soler MA, Fortuna S, Rocchia W. Computational Mutagenesis of Antibody Fragments: Disentangling Side Chains from ΔΔ G Predictions. J Chem Theory Comput 2024; 20:2630-2642. [PMID: 38445482 DOI: 10.1021/acs.jctc.3c01225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The development of highly potent antibodies and antibody fragments as binding agents holds significant implications in fields such as biosensing and biotherapeutics. Their binding strength is intricately linked to the arrangement and composition of residues at the binding interface. Computational techniques offer a robust means to predict the three-dimensional structure of these complexes and to assess the affinity changes resulting from mutations. Given the interdependence of structure and affinity prediction, our objective here is to disentangle their roles. We aim to evaluate independently six side-chain reconstruction methods and ten binding affinity estimation techniques. This evaluation was pivotal in predicting affinity alterations due to single mutations, a key step in computational affinity maturation protocols. Our analysis focuses on a data set comprising 27 distinct antibody/hen egg white lysozyme complexes, each with crystal structures and experimentally determined binding affinities. Using six different side-chain reconstruction methods, we transformed each structure into its corresponding mutant via in silico single-point mutations. Subsequently, these structures undergo minimization and molecular dynamics simulation. We therefore estimate ΔΔG values based on the original crystal structure, its energy-minimized form, and the ensuing molecular dynamics trajectories. Our research underscores the critical importance of selecting reliable side-chain reconstruction methods and conducting thorough molecular dynamics simulations to accurately predict the impact of mutations. In summary, our study demonstrates that the integration of conformational sampling and scoring is a potent approach to precisely characterizing mutation processes in single-point mutagenesis protocols and crucial for computational antibody design.
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Affiliation(s)
- Rika Tandiana
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - German P Barletta
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
- The Abdus Salam International Centre for Theoretical Physics─ICTP, Strada Costiera 11, 34151 Trieste, Italy
| | - Miguel Angel Soler
- Dipartimento di Scienze Matematiche, Informatiche e Fisiche, Universita' di Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Sara Fortuna
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
| | - Walter Rocchia
- Computational MOdelling of NanosCalE and BioPhysical SysTems─CONCEPT Lab Istituto Italiano di Tecnologia (IIT), Via Melen-83, B Block, 16152 Genoa, Italy
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20
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Nishio S, Emori C, Wiseman B, Fahrenkamp D, Dioguardi E, Zamora-Caballero S, Bokhove M, Han L, Stsiapanava A, Algarra B, Lu Y, Kodani M, Bainbridge RE, Komondor KM, Carlson AE, Landreh M, de Sanctis D, Yasumasu S, Ikawa M, Jovine L. ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat. Cell 2024; 187:1440-1459.e24. [PMID: 38490181 DOI: 10.1016/j.cell.2024.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
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Affiliation(s)
- Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Benjamin Wiseman
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisa Dioguardi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Marcel Bokhove
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Blanca Algarra
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Yonggang Lu
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Mayo Kodani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Rachel E Bainbridge
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kayla M Komondor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | | | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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21
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Gerovac M, Chihara K, Wicke L, Böttcher B, Lavigne R, Vogel J. Phage proteins target and co-opt host ribosomes immediately upon infection. Nat Microbiol 2024; 9:787-800. [PMID: 38443577 PMCID: PMC10914614 DOI: 10.1038/s41564-024-01616-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024]
Abstract
Bacteriophages must seize control of the host gene expression machinery to replicate. To bypass bacterial anti-phage defence systems, this host takeover occurs immediately upon infection. A general understanding of phage mechanisms for immediate targeting of host transcription and translation processes is lacking. Here we introduce an integrative high-throughput approach to uncover phage-encoded proteins that target the gene expression machinery of Pseudomonas aeruginosa immediately upon infection with the jumbo phage ΦKZ. By integrating biochemical, genetic and structural analyses, we identify an abundant and conserved phage factor ΦKZ014 that targets the large ribosomal subunit by binding the 5S ribosomal RNA, and rapidly promotes replication in several clinical isolates. ΦKZ014 is among the earliest ΦKZ proteins expressed after infection and remains bound to ribosomes during the entire translation cycle. Our study provides a strategy to decipher molecular components of phage-mediated host takeover and argues that phage genomes represent an untapped discovery space for proteins that modulate the host gene expression machinery.
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Affiliation(s)
- Milan Gerovac
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Kotaro Chihara
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Laura Wicke
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Bettina Böttcher
- Biocenter and Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Jörg Vogel
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany.
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
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22
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Zhang Y, Wu K, Li Y, Wu S, Warshel A, Bai C. Predicting Mutational Effects on Ca 2+-Activated Chloride Conduction of TMEM16A Based on a Simulation Study. J Am Chem Soc 2024; 146:4665-4679. [PMID: 38319142 DOI: 10.1021/jacs.3c11940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The dysfunction and defects of ion channels are associated with many human diseases, especially for loss-of-function mutations in ion channels such as cystic fibrosis transmembrane conductance regulator mutations in cystic fibrosis. Understanding ion channels is of great current importance for both medical and fundamental purposes. Such an understanding should include the ability to predict mutational effects and describe functional and mechanistic effects. In this work, we introduce an approach to predict mutational effects based on kinetic information (including reaction barriers and transition state locations) obtained by studying the working mechanism of target proteins. Specifically, we take the Ca2+-activated chloride channel TMEM16A as an example and utilize the computational biology model to predict the mutational effects of key residues. Encouragingly, we verified our predictions through electrophysiological experiments, demonstrating a 94% prediction accuracy regarding mutational directions. The mutational strength assessed by Pearson's correlation coefficient is -0.80 between our calculations and the experimental results. These findings suggest that the proposed methodology is reliable and can provide valuable guidance for revealing functional mechanisms and identifying key residues of the TMEM16A channel. The proposed approach can be extended to a broad scope of biophysical systems.
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Affiliation(s)
- Yue Zhang
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
| | - Kang Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Yuqing Li
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Chen Bai
- Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
- Chenzhu Biotechnology Co., Ltd., Hangzhou 310005, China
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23
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. eLife 2024; 12:RP92462. [PMID: 38381130 PMCID: PMC10942615 DOI: 10.7554/elife.92462] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Yuqi Shi
- Thermo Fisher ScientificSan JoseUnited States
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Katleen Willibal
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Nathan D Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - H Ronald Kaback
- Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech UniversityLubbockUnited States
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
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24
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Kenny S, Lai CH, Chiang TS, Brown K, Hewitt CS, Krabill AD, Chang HT, Wang YS, Flaherty DP, Hsu STD, Das C. Altered Protein Dynamics and a More Reactive Catalytic Cysteine in a Neurodegeneration-associated UCHL1 Mutant. J Mol Biol 2024; 436:168438. [PMID: 38185323 DOI: 10.1016/j.jmb.2024.168438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 12/31/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
A mutant of ubiquitin C-terminal hydrolase L1 (UCHL1) detected in early-onset neurodegenerative patients, UCHL1R178Q, showed higher catalytic activity than wild-type UCHL1 (UCHL1WT). Lying within the active-site pocket, the arginine is part of an interaction network that holds the catalytic histidine in an inactive arrangement. However, the structural basis and mechanism of enzymatic activation upon glutamine substitution was not understood. We combined X-ray crystallography, protein nuclear magnetic resonance (NMR) analysis, enzyme kinetics, covalent inhibition analysis, and biophysical measurements to delineate activating factors in the mutant. While the crystal structure of UCHL1R178Q showed nearly the same arrangement of the catalytic residues and active-site pocket, the mutation caused extensive alteration in the chemical environment and dynamics of more than 30 residues, some as far as 15 Å away from the site of mutation. Significant broadening of backbone amide resonances in the HSQC spectra indicates considerable backbone dynamics changes in several residues, in agreement with solution small-angle X-ray scattering (SAXS) analyses which indicate an overall increase in protein flexibility. Enzyme kinetics show the activation is due to a kcat effect despite a slightly weakened substrate affinity. In line with this, the mutant shows a higher second-order rate constant (kinact/Ki) in a reaction with a substrate-derived irreversible inhibitor, Ub-VME, compared to the wild-type enzyme, an observation indicative of a more reactive catalytic cysteine in the mutant. Together, the observations underscore structural plasticity as a factor contributing to enzyme kinetic behavior which can be modulated through mutational effects.
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Affiliation(s)
- Sebastian Kenny
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chih-Hsuan Lai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Tsung-Sheng Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Kwame Brown
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States
| | - Chad S Hewitt
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Aaron D Krabill
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Hao-Ting Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Yong-Sheng Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
| | - Daniel P Flaherty
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47906, United States
| | - Shang-Te Danny Hsu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan; International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)), Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan.
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, United States.
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25
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Mai M, Zazubovich V, Mansbach RA. Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations. J Phys Chem B 2024; 128:1371-1384. [PMID: 38299975 PMCID: PMC10876061 DOI: 10.1021/acs.jpcb.3c06889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
Reversible light and thermally induced spectral shifts are universally observed in a wide variety of pigment-protein complexes at temperatures ranging from cryogenic to ambient. In this paper, we employed large-scale molecular dynamics (MD) simulations of a prototypical pigment-protein complex to better understand these shifts at a molecular scale. Although multiple mechanisms have been proposed over the years, no verification of these proposals via MD simulations has thus far been performed; our work represents the first step in this direction. From simulations of the water-soluble chlorophyll-binding protein complex, we determined that rearrangements of long hydrogen bonds were unlikely to be the origin of the multiwell landscape features necessary to explain observed spectral shifts. We also assessed small motions of amino acid residues and identified side chain rotations of some of these residues as likely candidates for the origin of relevant multiwell landscape features. The protein free-energy landscapes associated with side chain rotations feature energy barriers of around 1100-1600 cm-1, in agreement with optical spectroscopy results, with the most promising residue type associated with experimental signatures being serine, which possesses a symmetric triple-well landscape and moment of inertia of a relevant magnitude.
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Affiliation(s)
- Martina Mai
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
| | - Rachael A. Mansbach
- Department of Physics, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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26
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Knight IS, Mailhot O, Tang KG, Irwin JJ. DockOpt: A Tool for Automatic Optimization of Docking Models. J Chem Inf Model 2024; 64:1004-1016. [PMID: 38206771 PMCID: PMC10865354 DOI: 10.1021/acs.jcim.3c01406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024]
Abstract
Molecular docking is a widely used technique for leveraging protein structure for ligand discovery, but it remains difficult to utilize due to limitations that have not been adequately addressed. Despite some progress toward automation, docking still requires expert guidance, hindering its adoption by a broader range of investigators. To make docking more accessible, we developed a new utility called DockOpt, which automates the creation, evaluation, and optimization of docking models prior to their deployment in large-scale prospective screens. DockOpt outperforms our previous automated pipeline across all 43 targets in the DUDE-Z benchmark data set, and the generated models for 84% of targets demonstrate sufficient enrichment to warrant their use in prospective screens, with normalized LogAUC values of at least 15%. DockOpt is available as part of the Python package Pydock3 included in the UCSF DOCK 3.8 distribution, which is available for free to academic researchers at https://dock.compbio.ucsf.edu and free for everyone upon registration at https://tldr.docking.org.
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Affiliation(s)
- Ian S. Knight
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Olivier Mailhot
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - Khanh G. Tang
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, UCSF, 1700 Fourth Street, San Francisco, California 94158-2330, United States
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27
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Kim J, Qin S, Zhou HX, Rosen MK. Surface Charge Can Modulate Phase Separation of Multidomain Proteins. J Am Chem Soc 2024; 146:3383-3395. [PMID: 38262618 PMCID: PMC10859935 DOI: 10.1021/jacs.3c12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/25/2024]
Abstract
Phase separation has emerged as an important mechanism explaining the formation of certain biomolecular condensates. Biological phase separation is often driven by the multivalent interactions of modular protein domains. Beyond valency, the physical features of folded domains that promote phase separation are poorly understood. We used a model system─the small ubiquitin modifier (SUMO) and its peptide ligand, the SUMO interaction motif (SIM)─to examine how domain surface charge influences multivalency-driven phase separation. Phase separation of polySUMO and polySIM was altered by pH via a change in the protonation state of SUMO surface histidines. These effects were recapitulated by histidine mutations, which modulated SUMO solubility and polySUMO-polySIM phase separation in parallel and were quantitatively explained by atomistic modeling of weak interactions among proteins in the system. Thus, surface charge can tune the phase separation of multivalent proteins, suggesting a means of controlling phase separation biologically, evolutionarily, and therapeutically.
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Affiliation(s)
- Jonggul Kim
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
| | - Sanbo Qin
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Huan-Xiang Zhou
- Department
of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
- Department
of Physics, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Michael K. Rosen
- Department
of Biophysics, University of Texas Southwestern
Medical Center, Dallas, Texas 75390, United States
- Howard
Hughes Medical Institute, Dallas, Texas 75390, United States
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28
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Min J, Rong X, Zhang J, Su R, Wang Y, Qi W. Computational Design of Peptide Assemblies. J Chem Theory Comput 2024; 20:532-550. [PMID: 38206800 DOI: 10.1021/acs.jctc.3c01054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
With the ongoing development of peptide self-assembling materials, there is growing interest in exploring novel functional peptide sequences. From short peptides to long polypeptides, as the functionality increases, the sequence space is also expanding exponentially. Consequently, attempting to explore all functional sequences comprehensively through experience and experiments alone has become impractical. By utilizing computational methods, especially artificial intelligence enhanced molecular dynamics (MD) simulation and de novo peptide design, there has been a significant expansion in the exploration of sequence space. Through these methods, a variety of supramolecular functional materials, including fibers, two-dimensional arrays, nanocages, etc., have been designed by meticulously controlling the inter- and intramolecular interactions. In this review, we first provide a brief overview of the current main computational methods and then focus on the computational design methods for various self-assembled peptide materials. Additionally, we introduce some representative protein self-assemblies to offer guidance for the design of self-assembling peptides.
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Affiliation(s)
- Jiwei Min
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Xi Rong
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Jiaxing Zhang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Rongxin Su
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Yuefei Wang
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
| | - Wei Qi
- State Key Laboratory of Chemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, P. R. China
- Tianjin Key Laboratory of Membrane Science and Desalination Technology, Tianjin 300072, P. R. China
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29
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Aarthy M, Pandiyan GN, Paramasivan R, Kumar A, Gupta B. Identification and prioritisation of potential vaccine candidates using subtractive proteomics and designing of a multi-epitope vaccine against Wuchereria bancrofti. Sci Rep 2024; 14:1970. [PMID: 38263422 PMCID: PMC10806236 DOI: 10.1038/s41598-024-52457-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/18/2024] [Indexed: 01/25/2024] Open
Abstract
This study employed subtractive proteomics and immunoinformatics to analyze the Wuchereria bancrofti proteome and identify potential therapeutic targets, with a focus on designing a vaccine against the parasite species. A comprehensive bioinformatics analysis of the parasite's proteome identified 51 probable therapeutic targets, among which "Kunitz/bovine pancreatic trypsin inhibitor domain-containing protein" was identified as the most promising vaccine candidate. The candidate protein was used to design a multi-epitope vaccine, incorporating B-cell and T-cell epitopes identified through various tools. The vaccine construct underwent extensive analysis of its antigenic, physical, and chemical features, including the determination of secondary and tertiary structures. Docking and molecular dynamics simulations were performed with HLA alleles, Toll-like receptor 4 (TLR4), and TLR3 to assess its potential to elicit the human immune response. Immune simulation analysis confirmed the predicted vaccine's strong binding affinity with immunoglobulins, indicating its potential efficacy in generating an immune response. However, experimental validation and testing of this multi-epitope vaccine construct would be needed to assess its potential against W. bancrofti and even for a broader range of lymphatic filarial infections given the similarities between W. bancrofti and Brugia.
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Affiliation(s)
- Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - G Navaneetha Pandiyan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - R Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
- Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Tandhalam, Chennai, Tamil Nadu, 602105, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, Madurai, Tamil Nadu, 625002, India.
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Boujemaa M, Nouira F, Jandoubi N, Mejri N, Bouaziz H, Charfeddine C, Ben Nasr S, Labidi S, El Benna H, Berrazega Y, Rachdi H, Daoud N, Benna F, Haddaoui A, Abdelhak S, Samir Boubaker M, Boussen H, Hamdi Y. Uncovering the clinical relevance of unclassified variants in DNA repair genes: a focus on BRCA negative Tunisian cancer families. Front Genet 2024; 15:1327894. [PMID: 38313678 PMCID: PMC10834681 DOI: 10.3389/fgene.2024.1327894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/02/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction: Recent advances in sequencing technologies have significantly increased our capability to acquire large amounts of genetic data. However, the clinical relevance of the generated data continues to be challenging particularly with the identification of Variants of Uncertain Significance (VUSs) whose pathogenicity remains unclear. In the current report, we aim to evaluate the clinical relevance and the pathogenicity of VUSs in DNA repair genes among Tunisian breast cancer families. Methods: A total of 67 unsolved breast cancer cases have been investigated. The pathogenicity of VUSs identified within 26 DNA repair genes was assessed using different in silico prediction tools including SIFT, PolyPhen2, Align-GVGD and VarSEAK. Effects on the 3D structure were evaluated using the stability predictor DynaMut and molecular dynamics simulation with NAMD. Family segregation analysis was also performed. Results: Among a total of 37 VUSs identified, 11 variants are likely deleterious affecting ATM, BLM, CHEK2, ERCC3, FANCC, FANCG, MSH2, PMS2 and RAD50 genes. The BLM variant, c.3254dupT, is novel and seems to be associated with increased risk of breast, endometrial and colon cancer. Moreover, c.6115G>A in ATM and c.592+3A>T in CHEK2 were of keen interest identified in families with multiple breast cancer cases and their familial cosegregation with disease has been also confirmed. In addition, functional in silico analyses revealed that the ATM variant may lead to protein immobilization and rigidification thus decreasing its activity. We have also shown that FANCC and FANCG variants may lead to protein destabilization and alteration of the structure compactness which may affect FANCC and FANCG protein activity. Conclusion: Our findings revealed that VUSs in DNA repair genes might be associated with increased cancer risk and highlight the need for variant reclassification for better disease management. This will help to improve the genetic diagnosis and therapeutic strategies of cancer patients not only in Tunisia but also in neighboring countries.
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Affiliation(s)
- Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fatma Nouira
- Laboratory of Bioactive Substances, Center of Biotechnology of Borj Cedria, University of Tunis El Manar, Hamam, Tunisia
| | - Nouha Jandoubi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Nesrine Mejri
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hanen Bouaziz
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Surgical Oncology Department, Salah Azaiez Institute of Cancer, Tunis, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- High Institute of Biotechnology of Sidi Thabet, Biotechpole of Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Sonia Ben Nasr
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Department of Medical Oncology, Military Hospital of Tunis, Tunis, Tunisia
| | - Soumaya Labidi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Houda El Benna
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosra Berrazega
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Haifa Rachdi
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Nouha Daoud
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Farouk Benna
- Radiation Oncology Department, Salah Azaiez Institute, Tunis, Tunisia
| | | | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Mohamed Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hamouda Boussen
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Medical Oncology Department, Abderrahman Mami Hospital, Faculty of Medicine Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR20IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
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31
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Suleman M, Ishaq I, Khan H, Ullah khan S, Masood R, Albekairi NA, Alshammari A, Crovella S. Elucidating the binding mechanism of SARS-CoV-2 NSP6-TBK1 and structure-based designing of phytocompounds inhibitors for instigating the host immune response. Front Chem 2024; 11:1346796. [PMID: 38293247 PMCID: PMC10824840 DOI: 10.3389/fchem.2023.1346796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/31/2023] [Indexed: 02/01/2024] Open
Abstract
SARS-CoV-2, also referred to as severe acute respiratory syndrome coronavirus 2, is the virus responsible for causing COVID-19, an infectious disease that emerged in Wuhan, China, in December 2019. Among its crucial functions, NSP6 plays a vital role in evading the human immune system by directly interacting with a receptor called TANK-binding kinase (TBK1), leading to the suppression of IFNβ production. Consequently, in the present study we used the structural and biophysical approaches to analyze the effect of newly emerged mutations on the binding of NSP6 and TBK1. Among the identified mutations, four (F35G, L37F, L125F, and I162T) were found to significantly destabilize the structure of NSP6. Furthermore, the molecular docking analysis highlighted that the mutant NSP6 displayed its highest binding affinity with TBK1, exhibiting docking scores of -1436.2 for the wildtype and -1723.2, -1788.6, -1510.2, and -1551.7 for the F35G, L37F, L125F, and I162T mutants, respectively. This suggests the potential for an enhanced immune system evasion capability of NSP6. Particularly, the F35G mutation exhibited the strongest binding affinity, supported by a calculated binding free energy of -172.19 kcal/mol. To disrupt the binding between NSP6 and TBK1, we conducted virtual drug screening to develop a novel inhibitor derived from natural products. From this screening, we identified the top 5 hit compounds as the most promising candidates with a docking score of -6.59 kcal/mol, -6.52 kcal/mol, -6.32 kcal/mol, -6.22 kcal/mol, and -6.21 kcal/mol. The molecular dynamic simulation of top 3 hits further verified the dynamic stability of drugs-NSP6 complexes. In conclusion, this study provides valuable insight into the higher infectivity of the SARS-CoV-2 new variants and a strong rationale for the development of novel drugs against NSP6.
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Affiliation(s)
- Muhammad Suleman
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Iqra Ishaq
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Haji Khan
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Safir Ullah khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Rehana Masood
- Department of Biochemistry, Shaheed Benazir Bhutto Women University, Peshawar, Pakistan
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Sergio Crovella
- Laboratory of Animal Research Center (LARC), Qatar University, Doha, Qatar
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32
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Palumbo R, Knutson B. Remote homology identification of the Drosophila melanogaster ortholog of the RNA Polymerase I subunit Rpa34/POLR1G. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001107. [PMID: 38287926 PMCID: PMC10823793 DOI: 10.17912/micropub.biology.001107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/08/2024] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
Highly conserved orthologous proteins are easily identified by sequence homology alone, whereas poorly conserved orthologs require additional structural information to be identified. All Drosophila orthologs of RNA polymerase I, II, and III subunits-except one-have been identified by sequence homology. Here, we identified CG11076 as the missing Rpa34/POLR1G ortholog in Drosophila . Remote homology detection and secondary structure analysis showed that CG11076 is predicted to have high structural conservation with Rpa34/POLR1G, and phylogenetic analysis demonstrated that these proteins are closely related. Our work underscores the importance of utilizing both sequence and structure to identify highly divergent orthologous proteins in different species.
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Affiliation(s)
- Ryan Palumbo
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, United States
| | - Bruce Knutson
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, New York, United States
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33
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Maharana J, Sano FK, Sarma P, Yadav MK, Duan L, Stepniewski TM, Chaturvedi M, Ranjan A, Singh V, Saha S, Mahajan G, Chami M, Shihoya W, Selent J, Chung KY, Banerjee R, Nureki O, Shukla AK. Molecular insights into atypical modes of β-arrestin interaction with seven transmembrane receptors. Science 2024; 383:101-108. [PMID: 38175886 PMCID: PMC7615931 DOI: 10.1126/science.adj3347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/29/2023] [Indexed: 01/06/2024]
Abstract
β-arrestins (βarrs) are multifunctional proteins involved in signaling and regulation of seven transmembrane receptors (7TMRs), and their interaction is driven primarily by agonist-induced receptor activation and phosphorylation. Here, we present seven cryo-electron microscopy structures of βarrs either in the basal state, activated by the muscarinic receptor subtype 2 (M2R) through its third intracellular loop, or activated by the βarr-biased decoy D6 receptor (D6R). Combined with biochemical, cellular, and biophysical experiments, these structural snapshots allow the visualization of atypical engagement of βarrs with 7TMRs and also reveal a structural transition in the carboxyl terminus of βarr2 from a β strand to an α helix upon activation by D6R. Our study provides previously unanticipated molecular insights into the structural and functional diversity encoded in 7TMR-βarr complexes with direct implications for exploring novel therapeutic avenues.
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Affiliation(s)
- Jagannath Maharana
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Fumiya K. Sano
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Parishmita Sarma
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Manish K. Yadav
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Longhan Duan
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Tomasz M. Stepniewski
- Research Program on Biomedical Informatics, Hospital del Mar Research Institute and Pompeu Fabra University, Barcelona, Spain
| | - Madhu Chaturvedi
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Ashutosh Ranjan
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Vinay Singh
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Sayantan Saha
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Gargi Mahajan
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland
| | - Wataru Shihoya
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Jana Selent
- Research Program on Biomedical Informatics, Hospital del Mar Research Institute and Pompeu Fabra University, Barcelona, Spain
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ramanuj Banerjee
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
| | - Osamu Nureki
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Arun K. Shukla
- Department of Biological Sciences, Indian Institute of Technology Kanpur, Kanpur, India
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34
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Banerjee P, Voth GA. Conformational transitions of the HIV-1 Gag polyprotein upon multimerization and gRNA binding. Biophys J 2024; 123:42-56. [PMID: 37978800 PMCID: PMC10808027 DOI: 10.1016/j.bpj.2023.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 11/19/2023] Open
Abstract
During the HIV-1 assembly process, the Gag polyprotein multimerizes at the producer cell plasma membrane, resulting in the formation of spherical immature virus particles. Gag-genomic RNA (gRNA) interactions play a crucial role in the multimerization process, which is yet to be fully understood. We performed large-scale all-atom molecular dynamics simulations of membrane-bound full-length Gag dimer, hexamer, and 18-mer. The inter-domain dynamic correlation of Gag, quantified by the heterogeneous elastic network model applied to the simulated trajectories, is observed to be altered by implicit gRNA binding, as well as the multimerization state of the Gag. The lateral dynamics of our simulated membrane-bound Gag proteins, with and without gRNA binding, agree with prior experimental data and help to validate our simulation models and methods. The gRNA binding is observed to affect mainly the SP1 domain of the 18-mer and the matrix-capsid linker domain of the hexamer. In the absence of gRNA binding, the independent dynamical motion of the nucleocapsid domain results in a collapsed state of the dimeric Gag. Unlike stable SP1 helices in the six-helix bundle, without IP6 binding, the SP1 domain undergoes a spontaneous helix-to-coil transition in the dimeric Gag. Together, our findings reveal conformational switches of Gag at different stages of the multimerization process and predict that the gRNA binding reinforces an efficient binding surface of Gag for multimerization, and also regulates the dynamic organization of the local membrane region itself.
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Affiliation(s)
- Puja Banerjee
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois.
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35
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Firdaus ARR, Baroroh U, Ramdani Tohari T, Hardianto A, Subroto T, Yusuf M. Computational design of scFv anti-receptor binding domain of SARS-CoV-2 spike protein based on antibody S230 anti-SARS-CoV-1. J Biomol Struct Dyn 2024; 42:22-33. [PMID: 37880854 DOI: 10.1080/07391102.2023.2265485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/28/2023] [Indexed: 10/27/2023]
Abstract
Developing therapeutics such as neutralizing antibodies targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is essential to halt the Covid-19 infection. However, antibody production is expensive and relatively inaccessible to many low-income countries. Therefore, a more efficient and smaller antibody fragment, such as a single-chain variable fragment (scFv), derived from a known neutralizing antibody structure, is of interest due to the lower cost of recombinant protein production and the ability to tailor scFvs against circulating viruses. In this study, we used computational design to create an scFv based on the structure of a known neutralizing antibody, S230, for SARS-CoV-1. By analyzing the interaction of S230 with the RBD of both SARS-CoV-1 and SARS-CoV-2, five mutations were introduced to improve the binding of the scFv to the RBD of SARS-CoV-2. These mutations were Ser32Thr, Trp99Val, Asn57Val, Lys65Glu, and Tyr106Ile. Molecular dynamics simulations were used to evaluate the stability and affinity of the designed scFv. Our results showed that the designed scFv improved binding to the RBD of SARS-CoV-2 compared to the original S230, as indicated by principal component analysis, distance analysis, and MM/GBSA interaction energy. Furthermore, a positive result in a spot test lateral flow assay of the expressed scFv against the RBD indicated that the mutations did not alter the protein's structure. The designed scFv showed a negative result when tested against human serum albumin as a negative control, indicating reasonable specificity. We hope that this study will be useful in designing a specific and low-cost therapeutic agent, particularly during early outbreaks when information on neutralizing antibodies is limited.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ade R R Firdaus
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Biotechnology Master Program, Postgraduate School, Universitas Padjadjaran, Bandung, Indonesia
| | - Umi Baroroh
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Pharmacy, Sekolah Tinggi Farmasi Indonesia, Bandung, Indonesia
| | - Taufik Ramdani Tohari
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
| | - Ari Hardianto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Toto Subroto
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
| | - Muhammad Yusuf
- Research Center for Molecular Biotechnology and Bioinformatics, Universitas Padjadjaran, Bandung, Indonesia
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Sumedang, Indonesia
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Li M, Zhang X, Chen S, Liu H, Zhang YW. Unique Substrate Recognition and Sodium-Substrate Binding Stoichiometry in a Bacterial Serotonin Transporter, TuriSERT. Int J Mol Sci 2023; 24:17112. [PMID: 38069433 PMCID: PMC10707687 DOI: 10.3390/ijms242317112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/27/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
All resolved high-resolution structures of the transporters in the neurotransmitter sodium symporter (NSS) family revealed that the NSS members share common structural and mechanistic features for substrate and ion binding and transport. However, a recently reported bacterial orthologue of the human serotonin transporter (hSERT), TuriSERT, possesses a structural characteristic specific for amino acid substrate binding but does transport a biogenic amine. The unique structural feature of TuriSERT requires a novel configuration for coordinating its substrate and ions. In the present study, we characterized TuriSERT expressed in Escherichia coli cells with a fluorescent substrate by biochemical, structural, and pharmacological approaches. Substrate transport by TuriSERT requires Na+ but not Cl-. Replacement of Asp262 by asparagine renders TuriSERT Cl--dependent. Substitutions of the corresponding Na1 residues did not alter Na+ dependence on substrate transport, whereas the mutation of a Na2 site residue led to a loss of transport activity, suggesting that Na+ binds only to the Na2 site in TuriSERT. In addition, substitutions of several residues essential for recognizing 5-hydroxytryptamine (5-HT) in hSERT had little effect on 5-HT displacement potency in transport assay for TuriSERT. In contrast, mutations of the residues that are proposed to coordinate with 5-HT in our docking model dramatically reduced 5-HT displacement. Furthermore, our results indicated that all tested antidepressants showed a weak inhibitory effect on TuriSERT. The present study demonstrated the existence of a unique substrate binding site and 1:1 stoichiometry of sodium-substrate binding in TuriSERT, a novel structural finding for the NSS transporters.
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Affiliation(s)
| | | | | | | | - Yuan-Wei Zhang
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China; (M.L.); (X.Z.); (S.C.); (H.L.)
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37
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Borges TJ, Lima K, Murshid A, Lape IT, Zhao Y, Rigo MM, Lang BJ, Siddiqui SS, Hui E, Riella LV, Bonorino C, Calderwood SK. Innate extracellular Hsp70 inflammatory properties are mediated by the interaction of Siglec-E and LOX-1 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569623. [PMID: 38106019 PMCID: PMC10723335 DOI: 10.1101/2023.12.01.569623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Innate immune responses to cell damage-associated molecular patterns induce a controlled degree of inflammation, ideally avoiding the promotion of intense unwanted inflammatory adverse events. When released by damaged cells, Hsp70 can stimulate different responses that range from immune activation to immune suppression. The effects of Hsp70 are mediated through innate receptors expressed primarily by myeloid cells, such as dendritic cells (DCs). The regulatory innate receptors that bind to extracellular mouse Hsp70 (mHsp70) are not fully characterized, and neither are their potential interactions with activating innate receptors. Here, we describe that extracellular mHsp70 interacts with a receptor complex formed by inhibitory Siglec-E and activating LOX-1 on DCs. We also find that this interaction takes place within lipid microdomains, and Siglec-E acts as a negative regulator of LOX-1-mediated innate activation upon mHsp70 or oxidized LDL binding. Thus, HSP70 can both bind to and modulate the interaction of inhibitory and activating innate receptors on the cell surface. These findings add another dimension of regulatory mechanism to how self-molecules contribute to dampening of exacerbated inflammatory responses.
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38
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558283. [PMID: 37790566 PMCID: PMC10542114 DOI: 10.1101/2023.09.18.558283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of the Na+-coupled major facilitator superfamily transporters. With a conformational nanobody (Nb), we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. Collectively with the available outward-facing sugar-bound structures, both the outer and inner barriers were localized. The N- and C-terminal residues of the inner barrier contribute to the sugar selectivity pocket. When the inner barrier is broken as shown in the inward-open conformation, the sugar selectivity pocket is also broken. The binding assays by isothermal titration calorimetry revealed that this inward-facing conformation trapped by the conformation-selective Nb exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for the substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is also supported by molecular dynamics simulations. Furthermore, the use of this Nb in combination with the hydron/deuterium exchange mass spectrometry allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | | | - Nathan D. Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Els Pardon
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - H. Ronald Kaback
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
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Vaissier Welborn V. Understanding Cysteine Reactivity in Protein Environments with Electric Fields. J Phys Chem B 2023; 127:9936-9942. [PMID: 37962274 DOI: 10.1021/acs.jpcb.3c05749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The role cysteine residues play in proteins is mediated by their protonation state, whereby the thiolate form of the side chain is highly reactive while the thiol form is more inert. However, the pKa of cysteine residues is hard to predict as it can differ widely from its reference value in solution, an effect that is accentuated by local effects in the heterogeneous protein environment. Here, we present a new approach to the prediction of cysteine reactivity based on electric field calculations at the thiol/thiolate group. We validated our approach by predicting the protonation state of cysteine residues in different protein environments (in the active site, at the protein surface, and buried within the protein interior), including Cys-25 in papaya protease omega, which was proven problematic for the more traditional constant pH molecular dynamics (MD) technique. We predict pKa shifts consistent with experimental observations, and the decomposition of the electric fields into contributions from molecular fragments provides a direct handle to rationalize local pH and pKa effects in proteins without introducing parameters other than those of the force field used for MD simulations.
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Affiliation(s)
- Valerie Vaissier Welborn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24060, United States
- Macromolecules Innovation Institute (MII),Virginia Tech, Blacksburg, Virginia 24060, United States
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Miranda-Sánchez D, Escalante CH, Andrade-Pavón D, Gómez-García O, Barrera E, Villa-Tanaca L, Delgado F, Tamariz J. Pyrrole-Based Enaminones as Building Blocks for the Synthesis of Indolizines and Pyrrolo[1,2- a]pyrazines Showing Potent Antifungal Activity. Molecules 2023; 28:7223. [PMID: 37894702 PMCID: PMC10608852 DOI: 10.3390/molecules28207223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
As a new approach, pyrrolo[1,2-a]pyrazines were synthesized through the cyclization of 2-formylpyrrole-based enaminones in the presence of ammonium acetate. The enaminones were prepared with a straightforward method, reacting the corresponding alkyl 2-(2-formyl-1H-pyrrol-1-yl)acetates, 2-(2-formyl-1H-pyrrol-1-yl)acetonitrile, and 2-(2-formyl-1H-pyrrol-1-yl)acetophenones with DMFDMA. Analogous enaminones elaborated from alkyl (E)-3-(1H-pyrrol-2-yl)acrylates were treated with a Lewis acid to afford indolizines. The antifungal activity of the series of substituted pyrroles, pyrrole-based enaminones, pyrrolo[1,2-a]pyrazines, and indolizines was evaluated on six Candida spp., including two multidrug-resistant ones. Compared to the reference drugs, most test compounds produced a more robust antifungal effect. Docking analysis suggests that the inhibition of yeast growth was probably mediated by the interaction of the compounds with the catalytic site of HMGR of the Candida species.
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Affiliation(s)
- Diter Miranda-Sánchez
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
| | - Carlos H. Escalante
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
| | - Dulce Andrade-Pavón
- Departamento de Fisiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Av. Wilfrido Massieu S/N, Mexico City 07738, Mexico;
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico;
| | - Omar Gómez-García
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
| | - Edson Barrera
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico;
| | - Francisco Delgado
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
| | - Joaquín Tamariz
- Departamento de Química Orgánica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Mexico City 11340, Mexico; (D.M.-S.); (C.H.E.); (O.G.-G.); (E.B.); (F.D.)
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Jian T, Su Q, Liu Y, Seoh HK, Houghton JE, Tai PC, Huang X. Structure-Based Virtual Screening of Helicobacter pylori SecA Inhibitors. IEEE Trans Nanobioscience 2023; 22:933-942. [PMID: 37030876 DOI: 10.1109/tnb.2023.3259946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
The human bacterial pathogen Helicobacter pylori causes a range of gastric diseases. The killing rate of Helicobacter pylori is declining year by year because of high antibiotics resistance. It is urgent to develop new target and novel anti- Helicobacter pylori drugs. As an "energy pump" for bacterial cells, SecA is essential for bacterial growth and drives bacterial protein transmembrane transport, moreover SecA is absent in mammals, all of which nominate SecA as an attractive antimicrobial target. Here, we provided a structure-based virtual screening method to screen the 3D-diversity natural-product-like screening library against SecA for novel anti- Helicobacter pylori inhibitors with novel scaffolds. In this study, homology modeling was used to construct the three-dimensional structure of Helicobacter pylori SecA. Two rounds of molecular docking were then used to find new small-molecule inhibitors of SecA, identifying six lead candidates that maintained key interactions with the binding pocket. After that, molecular dynamics simulations were used to explore more accurate ligand-receptor binding modes in states close to natural conditions. Encouragingly, all six compounds were relatively stable during the simulation. Apart from that the binding free energy calculation based on MM/PBSA demonstrated favorable results of < -13.642 kcal/mol. Finally, ADME-T analysis indicated that these compounds were also sufficiently druggable. All six compounds can be well combined with the crystal structure, which further facilitate the development of SecA inhibitors and lead compounds against Helicobacter pylori.
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42
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Zhou J, Wang A, Song Y, Liu N, Wang J, Li Y, Liang X, Li G, Chu H, Wang HW. Structural insights into the mechanism of GTP initiation of microtubule assembly. Nat Commun 2023; 14:5980. [PMID: 37749104 PMCID: PMC10519996 DOI: 10.1038/s41467-023-41615-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/08/2023] [Indexed: 09/27/2023] Open
Abstract
In eukaryotes, the dynamic assembly of microtubules (MT) plays an important role in numerous cellular processes. The underlying mechanism of GTP triggering MT assembly is still unknown. Here, we present cryo-EM structures of tubulin heterodimer at their GTP- and GDP-bound states, intermediate assembly states of GTP-tubulin, and final assembly stages of MT. Both GTP- and GDP-tubulin heterodimers adopt similar curved conformations with subtle flexibility differences. In head-to-tail oligomers of tubulin heterodimers, the inter-dimer interface of GDP-tubulin exhibits greater flexibility, particularly in tangential bending. Cryo-EM of the intermediate assembly states reveals two types of tubulin lateral contacts, "Tube-bond" and "MT-bond". Further, molecular dynamics (MD) simulations show that GTP triggers lateral contact formation in MT assembly in multiple sequential steps, gradually straightening the curved tubulin heterodimers. Therefore, we propose a flexible model of GTP-initiated MT assembly, including the formation of longitudinal and lateral contacts, to explain the nucleation and assembly of MT.
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Affiliation(s)
- Ju Zhou
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
- University of California Berkeley, Berkeley, CA, USA
| | - Anhui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Yinlong Song
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nan Liu
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Xin Liang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China
| | - Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian, 116023, China.
| | - Hong-Wei Wang
- State Key Laboratory of Membrane Biology, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing, 100084, China.
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Ryu J, Barkal S, Yu T, Jankowiak M, Zhou Y, Francoeur M, Phan QV, Li Z, Tognon M, Brown L, Love MI, Lettre G, Ascher DB, Cassa CA, Sherwood RI, Pinello L. Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantification. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.08.23295253. [PMID: 37732177 PMCID: PMC10508837 DOI: 10.1101/2023.09.08.23295253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
CRISPR base editing screens are powerful tools for studying disease-associated variants at scale. However, the efficiency and precision of base editing perturbations vary, confounding the assessment of variant-induced phenotypic effects. Here, we provide an integrated pipeline that improves the estimation of variant impact in base editing screens. We perform high-throughput ABE8e-SpRY base editing screens with an integrated reporter construct to measure the editing efficiency and outcomes of each gRNA alongside their phenotypic consequences. We introduce BEAN, a Bayesian network that accounts for per-guide editing outcomes and target site chromatin accessibility to estimate variant impacts. We show this pipeline attains superior performance compared to existing tools in variant classification and effect size quantification. We use BEAN to pinpoint common variants that alter LDL uptake, implicating novel genes. Additionally, through saturation base editing of LDLR, we enable accurate quantitative prediction of the effects of missense variants on LDL-C levels, which aligns with measurements in UK Biobank individuals, and identify structural mechanisms underlying variant pathogenicity. This work provides a widely applicable approach to improve the power of base editor screens for disease-associated variant characterization.
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Affiliation(s)
- Jayoung Ryu
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sam Barkal
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Tian Yu
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Yunzhuo Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matthew Francoeur
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Quang Vinh Phan
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Zhijian Li
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Manuel Tognon
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Computer Science Department, University of Verona, Verona, Italy
| | - Lara Brown
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael I. Love
- Department of Genetics, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Guillaume Lettre
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
- Faculté de Médecine, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - David B. Ascher
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Christopher A. Cassa
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Richard I. Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Luca Pinello
- Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
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Bae CH, Kim HY, Seo JE, Lee H, Kim S. In Silico Analysis of Pyeongwi-San Involved in Inflammatory Bowel Disease Treatment Using Network Pharmacology, Molecular Docking, and Molecular Dynamics. Biomolecules 2023; 13:1322. [PMID: 37759722 PMCID: PMC10526905 DOI: 10.3390/biom13091322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGOUND Pyeongwi-san (PWS) is a widely used formula for treating digestive disorders in Korea and China. Inflammatory bowel disease (IBD) is characterized by progressive inflammation of the gastrointestinal tract. Emerging evidence supports the protective effect of PWS against IBD, but specific mechanisms are still elusive. METHODS Active compounds of PWS were screened from the medicinal materials and chemical compounds in Northeast Asian traditional medicine (TM-MC) in the consideration of drug-likeness and oral bioavailability. Target candidates of active compounds were predicted using the ChEMBL database. IBD-related targets were obtained from the GeneCards and DisGeNET databases. The network of composition-targets-disease was constructed. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were analyzed. Molecular docking was used to simulate the binding affinity of active compounds on target proteins and molecular dynamics was used to validate the molecular docking result. RESULTS A total of 26 core target proteins of PWS were related to IBD. Enrichment analysis suggested that PWS is highly associated with tumor necrosis factor signaling pathway, apoptosis, and the collapse of tight junctions. Moreover, molecular docking and molecular dynamics simulation proposed β-eudesmol and (3R,6R,7S)-1,10-bisaboladien-3-ol to ameliorate IBD through the binding to TNF and MMP9, respectively. CONCLUSION Present in silico analysis revealed potential pathways and insight of PWS to regulate IBD. These results imply that the therapeutic effect of PWS might be achieved via an inhibitory effect.
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Affiliation(s)
- Chang-Hwan Bae
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea; (C.-H.B.); (J.E.S.); (H.L.)
| | - Hee-Young Kim
- Korean Medicine Research Center for Healthy Aging, Pusan National University, Yangsan 50612, Republic of Korea;
| | - Ji Eun Seo
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea; (C.-H.B.); (J.E.S.); (H.L.)
| | - Hanul Lee
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea; (C.-H.B.); (J.E.S.); (H.L.)
| | - Seungtae Kim
- Department of Korean Medical Science, School of Korean Medicine, Pusan National University, Yangsan 50612, Republic of Korea; (C.-H.B.); (J.E.S.); (H.L.)
- Korean Medicine Research Center for Healthy Aging, Pusan National University, Yangsan 50612, Republic of Korea;
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Singh H, Almaazmi SY, Dutta T, Keyzers RA, Blatch GL. In silico identification of modulators of J domain protein-Hsp70 interactions in Plasmodium falciparum: a drug repurposing strategy against malaria. Front Mol Biosci 2023; 10:1158912. [PMID: 37621993 PMCID: PMC10445141 DOI: 10.3389/fmolb.2023.1158912] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Plasmodium falciparum is a unicellular, intracellular protozoan parasite, and the causative agent of malaria in humans, a deadly vector borne infectious disease. A key phase of malaria pathology, is the invasion of human erythrocytes, resulting in drastic remodeling by exported parasite proteins, including molecular chaperones and co-chaperones. The survival of the parasite within the human host is mediated by P. falciparum heat shock protein 70s (PfHsp70s) and J domain proteins (PfJDPs), functioning as chaperones-co-chaperones partnerships. Two complexes have been shown to be important for survival and pathology of the malaria parasite: PfHsp70-x-PFE0055c (exported); and PfHsp70-2-PfSec63 (endoplasmic reticulum). Virtual screening was conducted on the drug repurposing library, the Pandemic Response Box, to identify small-molecules that could specifically disrupt these chaperone complexes. Five top ranked compounds possessing preferential binding affinity for the malarial chaperone system compared to the human system, were identified; three top PfHsp70-PfJDP binders, MBX 1641, zoliflodacin and itraconazole; and two top J domain binders, ezetimibe and a benzo-diazepinone. These compounds were validated by repeat molecular dockings and molecular dynamics simulation, resulting in all the compounds, except for MBX 1461, being confirmed to bind preferentially to the malarial chaperone system. A detailed contact analysis of the PfHsp70-PfJDP binders identified two different types of modulators, those that potentially inhibit complex formation (MBX 1461), and those that potentially stabilize the complex (zoliflodacin and itraconazole). These data suggested that zoliflodacin and itraconazole are potential novel modulators specific to the malarial system. A detailed contact analysis of the J domain binders (ezetimibe and the benzo-diazepinone), revealed that they bound with not only greater affinity but also a better pose to the malarial J domain compared to that of the human system. These data suggested that ezetimibe and the benzo-diazepinone are potential specific inhibitors of the malarial chaperone system. Both itraconazole and ezetimibe are FDA-approved drugs, possess anti-malarial activity and have recently been repurposed for the treatment of cancer. This is the first time that such drug-like compounds have been identified as potential modulators of PfHsp70-PfJDP complexes, and they represent novel candidates for validation and development into anti-malarial drugs.
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Affiliation(s)
- Harpreet Singh
- Department of Bioinformatics, Hans Raj Mahila Maha Vidyalaya, Jalandhar, India
| | - Shaikha Y. Almaazmi
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
| | - Tanima Dutta
- Department of Diagnostic Genomics, Path West Nedlands, QEII Medical Centre, Nedlands, WA, Australia
| | - Robert A. Keyzers
- Centre for Biodiscovery & School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Gregory L. Blatch
- Biomedical Research and Drug Discovery Research Group, Faculty of Health Sciences, Higher Colleges of Technology, Sharjah, United Arab Emirates
- Biomedical Biotechnology Research Unit, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
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Mitsui Y, Suzuki T, Kuniyoshi K, Inamo J, Yamaguchi K, Komuro M, Watanabe J, Edamoto M, Li S, Kouno T, Oba S, Hosoya T, Masuhiro K, Naito Y, Koyama S, Sakaguchi N, Standley DM, Shin JW, Akira S, Yasuda S, Miyazaki Y, Kochi Y, Kumanogoh A, Okamoto T, Satoh T. Expression of the readthrough transcript CiDRE in alveolar macrophages boosts SARS-CoV-2 susceptibility and promotes COVID-19 severity. Immunity 2023; 56:1939-1954.e12. [PMID: 37442134 DOI: 10.1016/j.immuni.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/25/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023]
Abstract
Lung infection during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via the angiotensin-I-converting enzyme 2 (ACE2) receptor induces a cytokine storm. However, the precise mechanisms involved in severe COVID-19 pneumonia are unknown. Here, we showed that interleukin-10 (IL-10) induced the expression of ACE2 in normal alveolar macrophages, causing them to become vectors for SARS-CoV-2. The inhibition of this system in hamster models attenuated SARS-CoV-2 pathogenicity. Genome-wide association and quantitative trait locus analyses identified a IFNAR2-IL10RB readthrough transcript, COVID-19 infectivity-enhancing dual receptor (CiDRE), which was highly expressed in patients harboring COVID-19 risk variants at the IFNAR2 locus. We showed that CiDRE exerted synergistic effects via the IL-10-ACE2 axis in alveolar macrophages and functioned as a decoy receptor for type I interferons. Collectively, our data show that high IL-10 and CiDRE expression are potential risk factors for severe COVID-19. Thus, IL-10R and CiDRE inhibitors might be useful COVID-19 therapies.
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Affiliation(s)
- Yuichi Mitsui
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Tatsuya Suzuki
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Department of Microbiology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Kanako Kuniyoshi
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Jun Inamo
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Mariko Komuro
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Junya Watanabe
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Mio Edamoto
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Songling Li
- Laboratory of Systems Immunology, World Premier Institute Immunology Frontier Research Center, WPI-IFReC, Osaka University, Osaka 565-0871, Japan
| | - Tsukasa Kouno
- RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Seiya Oba
- Department of Rheumatology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Tadashi Hosoya
- Department of Rheumatology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | | | - Daron M Standley
- Laboratory of Systems Immunology, World Premier Institute Immunology Frontier Research Center, WPI-IFReC, Osaka University, Osaka 565-0871, Japan
| | - Jay W Shin
- RIKEN Center for Integrative Medical Sciences, Kanagawa 230-0045, Japan
| | - Shizuo Akira
- Innate Cell Therapy Inc., Osaka 530-0017, Japan; Laboratory of Host Defense, World Premier Institute Immunology Frontier Research Center, WPI-IFReC, Osaka University, Osaka 565-0871, Japan
| | - Shinsuke Yasuda
- Department of Rheumatology, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan; Department of Microbiology, Juntendo University School of Medicine, Tokyo 113-8421, Japan
| | - Takashi Satoh
- Department of Immunology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; Innate Cell Therapy Inc., Osaka 530-0017, Japan.
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Jayaraj A, Thayer KM, Beveridge DL, Hingorani MM. Molecular dynamics of mismatch detection-How MutS uses indirect readout to find errors in DNA. Biophys J 2023; 122:3031-3043. [PMID: 37329136 PMCID: PMC10432192 DOI: 10.1016/j.bpj.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 04/30/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023] Open
Abstract
The mismatch repair protein MutS safeguards genomic integrity by finding and initiating repair of basepairing errors in DNA. Single-molecule studies show MutS diffusing on DNA, presumably scanning for mispaired/unpaired bases, and crystal structures show a characteristic "mismatch-recognition" complex with DNA enclosed within MutS and kinked at the site of error. But how MutS goes from scanning thousands of Watson-Crick basepairs to recognizing rare mismatches remains unanswered, largely because atomic-resolution data on the search process are lacking. Here, 10 μs all-atom molecular dynamics simulations of Thermus aquaticus MutS bound to homoduplex DNA and T-bulge DNA illuminate the structural dynamics underlying the search mechanism. MutS-DNA interactions constitute a multistep mechanism to check DNA over two helical turns for its 1) shape, through contacts with the sugar-phosphate backbone, 2) conformational flexibility, through bending/unbending engineered by large-scale motions of the clamp domain, and 3) local deformability, through basepair destabilizing contacts. Thus, MutS can localize a potential target by indirect readout due to lower energetic costs of bending mismatched DNA and identify a site that distorts easily due to weaker base stacking and pairing as a mismatch. The MutS signature Phe-X-Glu motif can then lock in the mismatch-recognition complex to initiate repair.
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Affiliation(s)
- Abhilash Jayaraj
- Chemistry Department, Wesleyan University, Middletown, Connecticut.
| | - Kelly M Thayer
- Chemistry Department, Wesleyan University, Middletown, Connecticut
| | | | - Manju M Hingorani
- Molecular Biology and Biochemistry Department, Wesleyan University, Middletown, Connecticut.
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Jensen M, Chandrasekaran V, García-Bonete MJ, Li S, Anindya AL, Andersson K, Erlandsson MC, Oparina NY, Burmann BM, Brath U, Panchenko AR, Bokarewa I. M, Katona G. Survivin prevents the polycomb repressor complex 2 from methylating histone 3 lysine 27. iScience 2023; 26:106976. [PMID: 37534134 PMCID: PMC10391610 DOI: 10.1016/j.isci.2023.106976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/27/2023] [Accepted: 04/17/2023] [Indexed: 08/04/2023] Open
Abstract
This study investigates the role of survivin in epigenetic control of gene transcription through interaction with the polycomb repressive complex 2 (PRC2). PRC2 is responsible for silencing gene expression by trimethylating lysine 27 on histone 3. We observed differential expression of PRC2 subunits in CD4+ T cells with varying levels of survivin expression, and ChIP-seq results indicated that survivin colocalizes with PRC2 along DNA. Inhibition of survivin resulted in a significant increase in H3K27 trimethylation, implying that survivin prevents PRC2 from functioning. Peptide microarray showed that survivin interacts with peptides from PRC2 subunits, and machine learning revealed that amino acid composition contains relevant information for predicting survivin interaction. NMR and BLI experiments supported the interaction of survivin with PRC2 subunit EZH2. Finally, protein-protein docking revealed that the survivin-EZH2 interaction interface overlaps with catalytic residues of EZH2, potentially inhibiting its H3K27 methylation activity. These findings suggest that survivin inhibits PRC2 function.
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Affiliation(s)
- Maja Jensen
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Venkataragavan Chandrasekaran
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - María-José García-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Atsarina Larasati Anindya
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
| | - Karin Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Malin C. Erlandsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Nina Y. Oparina
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
| | - Björn M. Burmann
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Ulrika Brath
- Department of Chemistry and Molecular Biology and the Swedish NMR Centre, University of Gothenburg, 412 96 Gothenburg, Sweden
| | - Anna R. Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Maria Bokarewa I.
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Box 480, 40530 Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gröna stråket 16, 41346 Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Box 462, 405 30 Gothenburg, Sweden
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49
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Liu N, Konuma T, Sharma R, Wang D, Zhao N, Cao L, Ju Y, Liu D, Wang S, Bosch A, Sun Y, Zhang S, Ji D, Nagatoishi S, Suzuki N, Kikuchi M, Wakamori M, Zhao C, Ren C, Zhou TJ, Xu Y, Meslamani J, Fu S, Umehara T, Tsumoto K, Akashi S, Zeng L, Roeder RG, Walsh MJ, Zhang Q, Zhou MM. Histone H3 lysine 27 crotonylation mediates gene transcriptional repression in chromatin. Mol Cell 2023; 83:2206-2221.e11. [PMID: 37311463 PMCID: PMC11138481 DOI: 10.1016/j.molcel.2023.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/22/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023]
Abstract
Histone lysine acylation, including acetylation and crotonylation, plays a pivotal role in gene transcription in health and diseases. However, our understanding of histone lysine acylation has been limited to gene transcriptional activation. Here, we report that histone H3 lysine 27 crotonylation (H3K27cr) directs gene transcriptional repression rather than activation. Specifically, H3K27cr in chromatin is selectively recognized by the YEATS domain of GAS41 in complex with SIN3A-HDAC1 co-repressors. Proto-oncogenic transcription factor MYC recruits GAS41/SIN3A-HDAC1 complex to repress genes in chromatin, including cell-cycle inhibitor p21. GAS41 knockout or H3K27cr-binding depletion results in p21 de-repression, cell-cycle arrest, and tumor growth inhibition in mice, explaining a causal relationship between GAS41 and MYC gene amplification and p21 downregulation in colorectal cancer. Our study suggests that H3K27 crotonylation signifies a previously unrecognized, distinct chromatin state for gene transcriptional repression in contrast to H3K27 trimethylation for transcriptional silencing and H3K27 acetylation for transcriptional activation.
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Affiliation(s)
- Nan Liu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China.
| | - Tsuyoshi Konuma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Rajal Sharma
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deyu Wang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Nan Zhao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Lingling Cao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Ying Ju
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Di Liu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Shuai Wang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Almudena Bosch
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yifei Sun
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Donglei Ji
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Satoru Nagatoishi
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Noa Suzuki
- School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Masaki Kikuchi
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | | | - Chengcheng Zhao
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Chunyan Ren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Thomas Jiachi Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yaoyao Xu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Jamel Meslamani
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shibo Fu
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China
| | - Takashi Umehara
- RIKEN Center for Biosystems Dynamics Research, Yokohama 230-0045, Japan
| | - Kouhei Tsumoto
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, the Rockefeller University, New Nork, NY 10065, USA
| | - Martin J Walsh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Qiang Zhang
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China; International Center of Future Science, Jilin University, Changchun 130012, China.
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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50
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Zhekova HR, Ramirez-Echemendía DP, Sejdiu BI, Pushkin A, Tieleman DP, Kurtz I. Coarse-grained molecular dynamics simulations of lipid-protein interactions in SLC4 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546592. [PMID: 37425774 PMCID: PMC10327080 DOI: 10.1101/2023.06.26.546592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The SLC4 family of secondary bicarbonate transporters is responsible for the transport of HCO 3 -, CO 3 2- , Cl - , Na + , K + , NH 3 and H + necessary for regulation of pH and ion homeostasis. They are widely expressed in numerous tissues throughout the body and function in different cell types with different membrane properties. Potential lipid roles in SLC4 function have been reported in experimental studies, focusing mostly on two members of the family: AE1 (Cl - /HCO 3 - exchanger) and NBCe1 (Na + -CO 3 2- cotransporter). Previous computational studies of the outward facing (OF) state of AE1 with model lipid membranes revealed enhanced protein-lipid interactions between cholesterol (CHOL) and phosphatidylinositol bisphosphate (PIP2). However, the protein-lipid interactions in other members of the family and other conformation states are still poorly understood and this precludes the detailed studies of a potential regulatory role for lipids in the SLC4 family. In this work, we performed multiple 50 µs coarse-grained molecular dynamics simulations on three members of the SLC4 family with different transport modes: AE1, NBCe1 and NDCBE (a Na + -CO 3 2- /Cl - exchanger), in model HEK293 membranes consisting of CHOL, PIP2, phosphatidylcholine (POPC), phosphatidylethanolamine (POPE), phosphatidylserine (POPS), and sphingomyelin (POSM). The recently resolved inward-facing (IF) state of AE1 was also included in the simulations. Lipid-protein contact analysis of the simulated trajectories was performed with the ProLint server, which provides a multitude of visualization tools for illustration of areas of enhanced lipid-protein contact and identification of putative lipid binding sites within the protein matrix. We observed enrichment of CHOL and PIP2 around all proteins with subtle differences in their distribution depending on the protein type and conformation state. Putative binding sites were identified for CHOL, PIP2, POPC, and POSM in the three studied proteins and their potential roles in the SLC4 transport function, conformational transition and protein dimerization were discussed. Statement of significance The SLC4 protein family is involved in critical physiological processes like pH and blood pressure regulation and maintenance of ion homeostasis. Its members can be found in various tissues. A number of studies suggest possible lipid regulation of the SLC4 function. However, the protein-lipid interactions in the SLC4 family are still poorly understood. Here we make use of long coarse-grained molecular dynamics simulations to assess the protein-lipid interactions in three SLC4 proteins with different transport modes, AE1, NBCe1, and NDCBE. We identify putative lipid binding sites for several lipid types of potential mechanistic importance, discuss them in the framework of the known experimental data and provide a necessary basis for further studies on lipid regulation of SLC4 function.
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