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Kumar S, Behera SK, Gururaj K, Chaurasia A, Murmu S, Prabha R, Angadi UB, Pawaiya RS, Rai A. In silico mutation of aromatic with aliphatic amino acid residues in Clostridium perfringens epsilon toxin (ETX) reduces its binding efficiency to Caprine Myelin and lymphocyte (MAL) protein receptors. J Biomol Struct Dyn 2024; 42:2257-2269. [PMID: 37129165 DOI: 10.1080/07391102.2023.2204362] [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: 12/19/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
Enterotoxaemia (ET) is a severe disease that affects domestic ruminants, including sheep and goats, and is caused by Clostridium perfringens type B and D strains. The disease is characterized by the production of Epsilon toxin (ETX), which has a significant impact on the farming industry due to its high lethality. The binding of ETX to the host cell receptor is crucial, but still poorly understood. Therefore, the structural features of goat Myelin and lymphocytic (MAL) protein were investigated and defined in this study. We induced the mutations in aromatic amino acid residues of ETX and substituted them with aliphatic residues at domains I and II. Subsequently, protein-protein interactions (PPI) were performed between ETX (wild)-MAL and ETX (mutated)-MAL protein predicting the domain sites of ETX structure. Further, molecular dynamics (MD) simulation studies were performed for both complexes to investigate the dynamic behavior of the proteins. The binding efficiency between 'ETX (wild)-MAL protein' and 'ETX (mutated)-MAL protein complex' interactions were compared and showed that the former had stronger interactions and binding efficiency due to the higher stability of the complex. The MD analysis showed destabilization and higher fluctuations in the PPI of the mutated heterodimeric ETX-MAL complex which is otherwise essential for its functional conformation. Such kind of interactions with mutated functional domains of ligands provided much-needed clarity in understanding the pre-pore complex formation of epsilon toxin with the MAL protein receptor of goats. The findings from this study would provide an impetus for designing a novel vaccine for Enterotoxaemia in goats.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sunil Kumar
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Kumaresan Gururaj
- ICAR-Central Institute for Research on Goats, Makhdoom, Mathura, India
| | | | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratna Prabha
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - U B Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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2
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Liu Z, Zhang C, Zhang Q, Zhang Y, Yu DJ. TM-search: An Efficient and Effective Tool for Protein Structure Database Search. J Chem Inf Model 2024; 64:1043-1049. [PMID: 38270339 DOI: 10.1021/acs.jcim.3c01455] [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: 01/26/2024]
Abstract
The quickly increasing size of the Protein Data Bank is challenging biologists to develop a more scalable protein structure alignment tool for fast structure database search. Although many protein structure search algorithms and programs have been designed and implemented for this purpose, most require a large amount of computational time. We propose a novel protein structure search approach, TM-search, which is based on the pairwise structure alignment program TM-align and a new iterative clustering algorithm. Benchmark tests demonstrate that TM-search is 27 times faster than a TM-align full database search while still being able to identify ∼90% of all high TM-score hits, which is 2-10 times more than other existing programs such as Foldseek, Dali, and PSI-BLAST.
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Affiliation(s)
- Zi Liu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
- Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States
| | - Qidi Zhang
- Computer Department, Jingdezhen Ceramic University, Jingdezhen 333403, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw, Ann Arbor, Michigan 48109-2218, United States
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei, Nanjing 210094, China
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3
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Whitchurch JB, Schneider S, Hilger AC, Köllges R, Stegmann JD, Waffenschmidt L, Dyer L, Thiele H, Dhabhai B, Dakal TC, Müller A, Norris DP, Reutter HM. PKD1L1 Is Involved in Congenital Chylothorax. Cells 2024; 13:149. [PMID: 38247840 PMCID: PMC10814685 DOI: 10.3390/cells13020149] [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: 11/07/2023] [Revised: 12/29/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Besides visceral heterotaxia, Pkd1l1 null mouse embryos exhibit general edema and perinatal lethality. In humans, congenital chylothorax (CCT) is a frequent cause of fetal hydrops. In 2021, Correa and colleagues reported ultrarare compound heterozygous variants in PKD1L1 exhibiting in two consecutive fetuses with severe hydrops, implicating a direct role of PKD1L1 in fetal hydrops formation. Here, we performed an exome survey and identified ultrarare compound heterozygous variants in PKD1L1 in two of the five case-parent trios with CCT. In one family, the affected carried the ultrarare missense variants c.1543G>A(p.Gly515Arg) and c.3845T>A(p.Val1282Glu). In the other family, the affected carried the ultrarare loss-of-function variant (LoF) c.863delA(p.Asn288Thrfs*3) and the ultrarare missense variant c.6549G>T(p.Gln2183His). Investigation of the variants' impact on PKD1L1 protein localization suggests the missense variants cause protein dysfunction and the LoF variant causes protein mislocalization. Further analysis of Pkd1l1 mutant mouse embryos revealed about 20% of Pkd1l1-/- embryos display general edema and pleural effusion at 14.5 dpc. Immunofluorescence staining at 14.5 dpc in Pkd1l1-/- embryos displayed both normal and massively altered lymphatic vessel morphologies. Together, our studies suggest the implication of PKD1L1 in congenital lymphatic anomalies, including CCTs.
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Affiliation(s)
- Jonathan B. Whitchurch
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (J.B.W.); (L.D.); (D.P.N.)
| | - Sophia Schneider
- Department of Neonatology and Paediatric Intensive Care, University Hospital Bonn Center of Paediatrics, 53127 Bonn, Germany; (S.S.); (R.K.); (J.D.S.); (A.M.)
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany;
| | - Alina C. Hilger
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany;
| | - Ricarda Köllges
- Department of Neonatology and Paediatric Intensive Care, University Hospital Bonn Center of Paediatrics, 53127 Bonn, Germany; (S.S.); (R.K.); (J.D.S.); (A.M.)
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany;
| | - Jil D. Stegmann
- Department of Neonatology and Paediatric Intensive Care, University Hospital Bonn Center of Paediatrics, 53127 Bonn, Germany; (S.S.); (R.K.); (J.D.S.); (A.M.)
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany;
| | - Lea Waffenschmidt
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany;
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Laura Dyer
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (J.B.W.); (L.D.); (D.P.N.)
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany;
| | - Bhanupriya Dhabhai
- Genome & Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur 313001, India; (B.D.); (T.C.D.)
| | - Tikam Chand Dakal
- Genome & Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur 313001, India; (B.D.); (T.C.D.)
| | - Andreas Müller
- Department of Neonatology and Paediatric Intensive Care, University Hospital Bonn Center of Paediatrics, 53127 Bonn, Germany; (S.S.); (R.K.); (J.D.S.); (A.M.)
| | - Dominic P. Norris
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (J.B.W.); (L.D.); (D.P.N.)
| | - Heiko M. Reutter
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany;
- Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, 91054 Erlangen, Germany
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Mahasongkram K, Glab-ampai K, Kaewchim K, Saenlom T, Chulanetra M, Sookrung N, Nathalang O, Chaicumpa W. Agonistic Bivalent Human scFvs-Fcγ Fusion Antibodies to OX40 Ectodomain Enhance T Cell Activities against Cancer. Vaccines (Basel) 2023; 11:1826. [PMID: 38140230 PMCID: PMC10747724 DOI: 10.3390/vaccines11121826] [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: 11/01/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
(1) Background: Understanding how advanced cancers evade host innate and adaptive immune opponents has led to cancer immunotherapy. Among several immunotherapeutic strategies, the reversal of immunosuppression mediated by regulatory T cells in the tumor microenvironment (TME) using blockers of immune-checkpoint signaling in effector T cells is the most successful treatment measure. Furthermore, agonists of T cell costimulatory molecules (CD40, 4-1BB, OX40) play an additional anti-cancer role to that of checkpoint blocking in combined therapy and serve also as adjuvant/neoadjuvant/induction therapy to conventional cancer treatments, such as tumor resection and radio- and chemo- therapies. (2) Methods and Results: In this study, novel agonistic antibodies to the OX40/CD134 ectodomain (EcOX40), i.e., fully human bivalent single-chain variable fragments (HuscFvs) linked to IgG Fc (bivalent HuscFv-Fcγ fusion antibodies) were generated by using phage-display technology and genetic engineering. The HuscFvs in the fusion antibodies bound to the cysteine-rich domain-2 of the EcOX40, which is known to be involved in OX40-OX40L signaling for NF-κB activation in T cells. The fusion antibodies caused proliferation, and increased the survival and cytokine production of CD3-CD28-activated human T cells. They showed enhancement trends for other effector T cell activities like granzyme B production and lysis of ovarian cancer cells when added to the activated T cells. (3) Conclusions: The novel OX40 agonistic fusion antibodies should be further tested step-by-step toward their safe use as an adjunctive non-immunogenic cancer immunotherapeutic agent.
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Affiliation(s)
- Kodchakorn Mahasongkram
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
| | - Kantaphon Glab-ampai
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
| | - Kanasap Kaewchim
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thanatsaran Saenlom
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
| | - Monrat Chulanetra
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
| | - Nitat Sookrung
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
- Biomedical Research Incubator Unit, Department of Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Oytip Nathalang
- Graduate Program in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, Rangsit Campus, Pathum Thani 12120, Thailand;
| | - Wanpen Chaicumpa
- Center of Research Excellence in Therapeutic Proteins and Antibody Engineering, Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (K.M.); (K.G.-a.); (K.K.); (T.S.); (M.C.); (N.S.)
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5
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Zhi Y, Wu X, Chen Y, Chen X, Chen X, Luo H, Yi X, Lin X, Ma L, Chen Y, Cao Y, Li F, Zhou P. A novel TWIK2 channel inhibitor binds at the bottom of the selectivity filter and protects against LPS-induced experimental endotoxemia in vivo. Biochem Pharmacol 2023; 218:115894. [PMID: 37898389 DOI: 10.1016/j.bcp.2023.115894] [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: 08/26/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
TWIK2 channel plays a critical role in NLRP3 inflammasome activation and mice deficient in TWIK2 channel are protected from sepsis and inflammatory lung injury. However, inhibitors of TWIK2 channel are currently in an early stage of development, and the molecular determinants underlying the chemical modulation of TWIK2 channel remain unexplored. In this study, we identified NPBA and the synthesized derivative NPBA-4 potently and selectively inhibited TWIK2 channel by using whole-cell patch clamp techniques. Furthermore, the mutation of the last residues of the selectivity filter in both P1 and P2 (i.e., T106A, T214A) of TWIK2 channel substantially abolished the effect of NPBA on TWIK2 channel. Our data suggest that NPBA blocked TWIK2 channel through binding at the bottom of the selectivity filter, which was also supported by molecular docking prediction. Moreover, we found that NPBA significantly suppressed NLRP3 inflammasome activation in macrophages and alleviated LPS-induced endotoxemia and organ injury in vivo. Notably, the protective effects of NPBA against LPS-induced endotoxemia were abolished in Kcnk6-/- mice. In summary, our study has uncovered a series of novel inhibitors of TWIK2 channel and revealed their distinct molecular determinants interacting TWIK2 channel. These findings provide new insights into the mechanisms of pharmacological action on TWIK2 channel and opportunities for the development of selective TWIK2 channel modulators to treat related inflammatory diseases.
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Affiliation(s)
- Yuanxing Zhi
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Anesthesiology, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Xiaoyan Wu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yanshan Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xingyuan Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiangyu Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hui Luo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xin Yi
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiuling Lin
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Liang Ma
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yao Chen
- Department of Anesthesiology, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Ying Cao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Fengxian Li
- Department of Anesthesiology, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China
| | - Pingzheng Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Anesthesiology, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, China.
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6
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Lee JW, Won JH, Jeon S, Choo Y, Yeon Y, Oh JS, Kim M, Kim S, Joung I, Jang C, Lee SJ, Kim TH, Jin KH, Song G, Kim ES, Yoo J, Paek E, Noh YK, Joo K. DeepFold: enhancing protein structure prediction through optimized loss functions, improved template features, and re-optimized energy function. Bioinformatics 2023; 39:btad712. [PMID: 37995286 PMCID: PMC10699847 DOI: 10.1093/bioinformatics/btad712] [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: 06/14/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
MOTIVATION Predicting protein structures with high accuracy is a critical challenge for the broad community of life sciences and industry. Despite progress made by deep neural networks like AlphaFold2, there is a need for further improvements in the quality of detailed structures, such as side-chains, along with protein backbone structures. RESULTS Building upon the successes of AlphaFold2, the modifications we made include changing the losses of side-chain torsion angles and frame aligned point error, adding loss functions for side chain confidence and secondary structure prediction, and replacing template feature generation with a new alignment method based on conditional random fields. We also performed re-optimization by conformational space annealing using a molecular mechanics energy function which integrates the potential energies obtained from distogram and side-chain prediction. In the CASP15 blind test for single protein and domain modeling (109 domains), DeepFold ranked fourth among 132 groups with improvements in the details of the structure in terms of backbone, side-chain, and Molprobity. In terms of protein backbone accuracy, DeepFold achieved a median GDT-TS score of 88.64 compared with 85.88 of AlphaFold2. For TBM-easy/hard targets, DeepFold ranked at the top based on Z-scores for GDT-TS. This shows its practical value to the structural biology community, which demands highly accurate structures. In addition, a thorough analysis of 55 domains from 39 targets with publicly available structures indicates that DeepFold shows superior side-chain accuracy and Molprobity scores among the top-performing groups. AVAILABILITY AND IMPLEMENTATION DeepFold tools are open-source software available at https://github.com/newtonjoo/deepfold.
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Affiliation(s)
- Jae-Won Lee
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Jong-Hyun Won
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Seonggwang Jeon
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Yujin Choo
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
- Department of Artificial intelligence, Hanyang University, Seoul 04763, Korea
| | - Yubin Yeon
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Jin-Seon Oh
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
- Department of Artificial intelligence, Hanyang University, Seoul 04763, Korea
| | - Minsoo Kim
- Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - SeonHwa Kim
- School of Electrical Engineering, Korea University, Seoul 02841, Korea
| | | | - Cheongjae Jang
- Artificial Intelligence Institute, Hanyang University, Seoul 04763, Korea
| | - Sung Jong Lee
- Basic Science Research Institute, Changwon National University, Changwon 51140, Korea
| | - Tae Hyun Kim
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
| | - Kyong Hwan Jin
- School of Electrical Engineering, Korea University, Seoul 02841, Korea
| | - Giltae Song
- School of Computer Science and Engineering, Pusan National University, Busan 46241, Korea
| | - Eun-Sol Kim
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Korea
| | - Eunok Paek
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
| | - Yung-Kyun Noh
- Department of Computer Science, Hanyang University, Seoul 04763, Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Korea
| | - Keehyoung Joo
- Center for Advanced Computation, Korea Institute for Advanced Study, Seoul 02455, Korea
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7
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Zheng W, Wuyun Q, Freddolino PL, Zhang Y. Integrating deep learning, threading alignments, and a multi-MSA strategy for high-quality protein monomer and complex structure prediction in CASP15. Proteins 2023; 91:1684-1703. [PMID: 37650367 PMCID: PMC10840719 DOI: 10.1002/prot.26585] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/04/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
We report the results of the "UM-TBM" and "Zheng" groups in CASP15 for protein monomer and complex structure prediction. These prediction sets were obtained using the D-I-TASSER and DMFold-Multimer algorithms, respectively. For monomer structure prediction, D-I-TASSER introduced four new features during CASP15: (i) a multiple sequence alignment (MSA) generation protocol that combines multi-source MSA searching and a structural modeling-based MSA ranker; (ii) attention-network based spatial restraints; (iii) a multi-domain module containing domain partition and arrangement for domain-level templates and spatial restraints; (iv) an optimized I-TASSER-based folding simulation system for full-length model creation guided by a combination of deep learning restraints, threading alignments, and knowledge-based potentials. For 47 free modeling targets in CASP15, the final models predicted by D-I-TASSER showed average TM-score 19% higher than the standard AlphaFold2 program. We thus showed that traditional Monte Carlo-based folding simulations, when appropriately coupled with deep learning algorithms, can generate models with improved accuracy over end-to-end deep learning methods alone. For protein complex structure prediction, DMFold-Multimer generated models by integrating a new MSA generation algorithm (DeepMSA2) with the end-to-end modeling module from AlphaFold2-Multimer. For the 38 complex targets, DMFold-Multimer generated models with an average TM-score of 0.83 and Interface Contact Score of 0.60, both significantly higher than those of competing complex prediction tools. Our analyses on complexes highlighted the critical role played by MSA generating, ranking, and pairing in protein complex structure prediction. We also discuss future room for improvement in the areas of viral protein modeling and complex model ranking.
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Affiliation(s)
- Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Qiqige Wuyun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
- Department of Computer Science, School of Computing, National University of Singapore, 117417 Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117596, Singapore
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8
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Choi S, Prabhakar PK, Chowdhury R, Pendergast TH, Urbanowicz BR, Maranas C, Devos KM. A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5532-5546. [PMID: 37402629 PMCID: PMC10540729 DOI: 10.1093/jxb/erad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023]
Abstract
Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.
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Affiliation(s)
- Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Pradeep K Prabhakar
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ratul Chowdhury
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Thomas H Pendergast
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Costas Maranas
- Chemical Engineering, Penn State University, State College, PA 16801, USA
| | - Katrien M Devos
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602, USA
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA
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9
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Yan Q, Wei J, Song J, Li M, Guan X, Song J. Study on the Properties and Synergistic Antioxidant Effects of Novel Bifunctional Fusion Proteins Expressed Using the UTuT6 System. Antioxidants (Basel) 2023; 12:1766. [PMID: 37760069 PMCID: PMC10526088 DOI: 10.3390/antiox12091766] [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: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Important antioxidant enzymes, glutathione peroxidase (GPx) and superoxide dismutase (SOD), are involved in maintaining redox balance. They can protect each other and result in more efficiently removing excessive reactive oxygen species (ROS), protecting cells against injury, and maintaining the normal metabolism of ROS. In this study, human cytosolic GPx (hGPx1) and human phospholipid hydroperoxide GPx (hGPx4) genes were integrated into the same open reading frame with human extracellular SOD active site (SOD3-72P) genes, respectively, and several novel fusion proteins were obtained by using the UTuT6 expression system for the first time. Among them, Se-hGPx1UAG-L4-SOD3-72P is the bifunctional fusion protein with the highest GPx activity and the best anti-hydrogen peroxide inactivation ability thus far. The Se-hGPx4UAG-L3-SOD3-72P fusion protein exhibits the strongest alkali and high temperature resistance and a greater protective effect against lipoprotein peroxidation damage. Se-hGPx1UAG-L4-SOD3-72P and Se-hGPx4UAG-L3-SOD3-72P fusion proteins both have good synergistic and antioxidant abilities in H2O2-induced RBCs and liver damage models. We believe that this research will help with the development of novel bifunctional fusion proteins and the investigation of the synergistic and catalytic mechanisms of GPx and SOD, which are important in creating novel protein therapeutics.
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Affiliation(s)
- Qi Yan
- College of Pharmaceutical Science, Jilin University, Changchun 130021, China; (Q.Y.)
| | - Jingyan Wei
- College of Pharmaceutical Science, Jilin University, Changchun 130021, China; (Q.Y.)
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130000, China
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Junxia Song
- College of Pharmaceutical Science, Jilin University, Changchun 130021, China; (Q.Y.)
| | - Mengna Li
- College of Pharmaceutical Science, Jilin University, Changchun 130021, China; (Q.Y.)
| | - Xin Guan
- College of Pharmaceutical Science, Jilin University, Changchun 130021, China; (Q.Y.)
| | - Jian Song
- School of Microelectronics, Shanghai University, Shanghai 201800, China
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10
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Muñoz-Muñoz PLA, Mares-Alejandre RE, Meléndez-López SG, Ramos-Ibarra MA. Structural Insights into the Giardia lamblia Target of Rapamycin Homolog: A Bioinformatics Approach. Int J Mol Sci 2023; 24:11992. [PMID: 37569368 PMCID: PMC10418948 DOI: 10.3390/ijms241511992] [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: 06/02/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
TOR proteins, also known as targets of rapamycin, are serine/threonine kinases involved in various signaling pathways that regulate cell growth. The protozoan parasite Giardia lamblia is the causative agent of giardiasis, a neglected infectious disease in humans. In this study, we used a bioinformatics approach to examine the structural features of GTOR, a G. lamblia TOR-like protein, and predict functional associations. Our findings confirmed that it shares significant similarities with functional TOR kinases, including a binding domain for the FKBP-rapamycin complex and a kinase domain resembling that of phosphatidylinositol 3-kinase-related kinases. In addition, it can form multiprotein complexes such as TORC1 and TORC2. These results provide valuable insights into the structure-function relationship of GTOR, highlighting its potential as a molecular target for controlling G. lamblia cell proliferation. Furthermore, our study represents a step toward rational drug design for specific anti-giardiasis therapeutic agents.
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Affiliation(s)
| | - Rosa E. Mares-Alejandre
- Biotechnology and Biosciences Research Group, School of Chemical Sciences and Engineering, Autonomous University of Baja California, Tijuana 22390, Mexico; (P.L.A.M.-M.); (S.G.M.-L.); (M.A.R.-I.)
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11
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Rcheulishvili N, Mao J, Papukashvili D, Feng S, Liu C, Wang X, He Y, Wang PG. Design, evaluation, and immune simulation of potentially universal multi-epitope mpox vaccine candidate: focus on DNA vaccine. Front Microbiol 2023; 14:1203355. [PMID: 37547674 PMCID: PMC10403236 DOI: 10.3389/fmicb.2023.1203355] [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: 04/10/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Monkeypox (mpox) is a zoonotic infectious disease caused by the mpox virus. Mpox symptoms are similar to smallpox with less severity and lower mortality. As yet mpox virus is not characterized by as high transmissibility as some severe acute respiratory syndrome 2 (SARS-CoV-2) variants, still, it is spreading, especially among men who have sex with men (MSM). Thus, taking preventive measures, such as vaccination, is highly recommended. While the smallpox vaccine has demonstrated considerable efficacy against the mpox virus due to the antigenic similarities, the development of a universal anti-mpox vaccine remains a necessary pursuit. Recently, nucleic acid vaccines have garnered special attention owing to their numerous advantages compared to traditional vaccines. Importantly, DNA vaccines have certain advantages over mRNA vaccines. In this study, a potentially universal DNA vaccine candidate against mpox based on conserved epitopes was designed and its efficacy was evaluated via an immunoinformatics approach. The vaccine candidate demonstrated potent humoral and cellular immune responses in silico, indicating the potential efficacy in vivo and the need for further research.
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Affiliation(s)
| | | | | | | | | | | | - Yunjiao He
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Peng George Wang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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12
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Kunamneni A, Montera MA, Durvasula R, Alles SRA, Goyal S, Westlund KN. Rapid Generation and Molecular Docking Analysis of Single-Chain Fragment Variable (scFv) Antibody Selected by Ribosome Display Targeting Cholecystokinin B Receptor (CCK-BR) for Reduction of Chronic Neuropathic Pain. Int J Mol Sci 2023; 24:11035. [PMID: 37446213 DOI: 10.3390/ijms241311035] [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: 05/02/2023] [Revised: 06/06/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
A robust cell-free platform technology, ribosome display in combination with cloning, expression, and purification was utilized to develop single chain Fragment variable (scFv) antibody variants as pain therapy directed at the mouse cholecystokinin B (CCK-B) receptor. Three effective CCK-B peptide-specific scFvs were generated through ribosomal display technology. Soluble expression and ELISA analysis showed that one antibody, scFv77-2 had the highest binding and could be purified from bacterial cells in large quantities. Octet measurements further revealed that the CCK-B scFv77-2 antibody had binding kinetics of KD = 1.794 × 10-8 M. Molecular modeling and docking analyses suggested that the scFv77-2 antibody shaped a proper cavity to embed the whole CCK-B peptide molecule and that a steady-state complex was formed relying on intermolecular forces, including hydrogen bonding, electrostatic force, and hydrophobic interactions. Thus, the scFv antibody can be applied for mechanistic intermolecular interactions and functional in vivo studies of CCK-BR. The high affinity scFv77-2 antibody showed good efficacy with binding to CCK-BR tested in a chronic pain model. In vivo studies validated the efficacy of the CCK-B receptor (CCK-BR) scFv77-2 antibody as a potential therapy for chronic trigeminal nerve injury-induced pain. Mice were given a single dose of the CCK-B receptor (CCK-BR) scFv antibody 3 weeks after induction of a chronic trigeminal neuropathic pain model, during the transition from acute to chronic pain. The long-term effectiveness for the reduction of mechanical hypersensitivity was evident, persisting for months. The anxiety- and depression-related behaviors typically accompanying persisting hypersensitivity subsequently never developed in the mice given CCK-BR scFv. The effectiveness of the antibody is the basis for further development of the lead CCK-BR scFv as a promising non-opioid therapeutic for chronic pain and the long-term reduction of chronic pain- and anxiety-related behaviors.
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Affiliation(s)
- Adinarayana Kunamneni
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL 32224-1865, USA
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153-3328, USA
| | - Marena A Montera
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Ravi Durvasula
- Department of Internal Medicine, Mayo Clinic, Jacksonville, FL 32224-1865, USA
- Department of Medicine, Loyola University Medical Center, Maywood, IL 60153-3328, USA
| | - Sascha R A Alles
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Sachin Goyal
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
| | - Karin N Westlund
- Department of Anesthesiology & Critical Care Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM 87131-0001, USA
- Biomedical Laboratory Research & Development (121F), New Mexico VA Health Care System, Albuquerque, NM 87108-5153, USA
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13
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Rcheulishvili N, Mao J, Papukashvili D, Feng S, Liu C, Yang X, Lin J, He Y, Wang PG. Development of a Multi-Epitope Universal mRNA Vaccine Candidate for Monkeypox, Smallpox, and Vaccinia Viruses: Design and In Silico Analyses. Viruses 2023; 15:1120. [PMID: 37243206 PMCID: PMC10222975 DOI: 10.3390/v15051120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
Notwithstanding the presence of a smallpox vaccine that is effective against monkeypox (mpox), developing a universal vaccine candidate against monkeypox virus (MPXV) is highly required as the mpox multi-country outbreak has increased global concern. MPXV, along with variola virus (VARV) and vaccinia virus (VACV), belongs to the Orthopoxvirus genus. Due to the genetic similarity of antigens in this study, we have designed a potentially universal mRNA vaccine based on conserved epitopes that are specific to these three viruses. In order to design a potentially universal mRNA vaccine, antigens A29, A30, A35, B6, and M1 were selected. The conserved sequences among the three viral species-MPXV, VACV, and VARV-were detected, and B and T cell epitopes containing the conserved elements were used for the design of the multi-epitope mRNA construct. Immunoinformatics analyses demonstrated the stability of the vaccine construct and optimal binding to MHC molecules. Humoral and cellular immune responses were induced by immune simulation analyses. Eventually, based on in silico analysis, the universal mRNA multi-epitope vaccine candidate designed in this study may have a potential protection against MPXV, VARV, and VACV that will contribute to the advancement of prevention strategies for unpredictable pandemics.
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Affiliation(s)
- Nino Rcheulishvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Jiawei Mao
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Dimitri Papukashvili
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Shunping Feng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Cong Liu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Xidan Yang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
- School of Nursing, Southwest Medical University, Luzhou 646000, China
| | - Jihui Lin
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
- School of Nursing, Southwest Medical University, Luzhou 646000, China
| | - Yunjiao He
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
| | - Peng George Wang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen 518000, China; (N.R.); (J.M.); (D.P.); (S.F.); (C.L.); (X.Y.); (J.L.)
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14
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Alberini G, Alexis Paz S, Corradi B, Abrams CF, Benfenati F, Maragliano L. Molecular Dynamics Simulations of Ion Permeation in Human Voltage-Gated Sodium Channels. J Chem Theory Comput 2023; 19:2953-2972. [PMID: 37116214 DOI: 10.1021/acs.jctc.2c00990] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The recent determination of cryo-EM structures of voltage-gated sodium (Nav) channels has revealed many details of these proteins. However, knowledge of ionic permeation through the Nav pore remains limited. In this work, we performed atomistic molecular dynamics (MD) simulations to study the structural features of various neuronal Nav channels based on homology modeling of the cryo-EM structure of the human Nav1.4 channel and, in addition, on the recently resolved configuration for Nav1.2. In particular, single Na+ permeation events during standard MD runs suggest that the ion resides in the inner part of the Nav selectivity filter (SF). On-the-fly free energy parametrization (OTFP) temperature-accelerated molecular dynamics (TAMD) was also used to calculate two-dimensional free energy surfaces (FESs) related to single/double Na+ translocation through the SF of the homology-based Nav1.2 model and the cryo-EM Nav1.2 structure, with different realizations of the DEKA filter domain. These additional simulations revealed distinct mechanisms for single and double Na+ permeation through the wild-type SF, which has a charged lysine in the DEKA ring. Moreover, the configurations of the ions in the SF corresponding to the metastable states of the FESs are specific for each SF motif. Overall, the description of these mechanisms gives us new insights into ion conduction in human Nav cryo-EM-based and cryo-EM configurations that could advance understanding of these systems and how they differ from potassium and bacterial Nav channels.
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Affiliation(s)
- Giulio Alberini
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Sergio Alexis Paz
- Departamento de Química Teórica y Computacional, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Fisicoquímica de Córdoba (INFIQC), X5000HUA Córdoba, Argentina
| | - Beatrice Corradi
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Experimental Medicine, Università degli Studi di Genova, Viale Benedetto XV 3, 16132 Genova, Italy
| | - Cameron F Abrams
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Fabio Benfenati
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe), Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
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15
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Guo B, Zheng H, Jiang H, Li X, Guan N, Zuo Y, Zhang Y, Yang H, Wang X. Enhanced compound-protein binding affinity prediction by representing protein multimodal information via a coevolutionary strategy. Brief Bioinform 2023; 24:6995409. [PMID: 36682005 DOI: 10.1093/bib/bbac628] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/12/2022] [Accepted: 12/25/2022] [Indexed: 01/23/2023] Open
Abstract
Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying machine-learning methods. To overcome this limitation, in a novel end-to-end architecture (named FeatNN), we develop a coevolutionary strategy to jointly represent the structure and sequence features of proteins and ultimately optimize the mathematical models for predicting CPA. Furthermore, from the perspective of data-driven approach, we proposed a rational method that can utilize both high- and low-quality databases to optimize the accuracy and generalization ability of FeatNN in CPA prediction tasks. Notably, we visually interpret the feature interaction process between sequence and structure in the rationally designed architecture. As a result, FeatNN considerably outperforms the state-of-the-art (SOTA) baseline in virtual drug evaluation tasks, indicating the feasibility of this approach for practical use. FeatNN provides an outstanding method for higher CPA prediction accuracy and better generalization ability by efficiently representing multimodal information of proteins via a coevolutionary strategy.
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Affiliation(s)
- Binjie Guo
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Hanyu Zheng
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Haohan Jiang
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Xiaodan Li
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Naiyu Guan
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Yanming Zuo
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Yicheng Zhang
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
| | - Hengfu Yang
- School of Computer Science, Hunan First Normal University, Changsha, 410205 Hunan, China
| | - Xuhua Wang
- Department of Neurobiology and Department of Rehabilitation Medicine, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310058, China
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, 1369 West Wenyi Road, Hangzhou 311121, China
- NHC and CAMS Key Laboratory of Medical Neurobiology, Zhejiang University, Hangzhou 310058, China
- Co-innovation Center of Neuroregeneration, Nantong University, Nantong, 226001 Jiangsu, China
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16
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Li M, Feng X, Reid WR, Tang F, Liu N. Multiple-P450 Gene Co-Up-Regulation in the Development of Permethrin Resistance in the House Fly, Musca domestica. Int J Mol Sci 2023; 24:ijms24043170. [PMID: 36834582 PMCID: PMC9959456 DOI: 10.3390/ijms24043170] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
This paper reports a study conducted at the whole transcriptome level to characterize the P450 genes involved in the development of pyrethroid resistance, utilizing expression profile analyses of 86 cytochrome P450 genes in house fly strains with different levels of resistance to pyrethroids/permethrin. Interactions among the up-regulated P450 genes and possible regulatory factors in different autosomes were examined in house fly lines with different combinations of autosomes from a resistant house fly strain, ALHF. Eleven P450 genes that were significantly up-regulated, with levels > 2-fold those in the resistant ALHF house flies, were in CYP families 4 and 6 and located on autosomes 1, 3 and 5. The expression of these P450 genes was regulated by trans- and/or cis-acting factors, especially on autosomes 1 and 2. An in vivo functional study indicated that the up-regulated P450 genes also conferred permethrin resistance in Drosophila melanogaster transgenic lines. An in vitro functional study confirmed that the up-regulated P450 genes are able to metabolize not only cis- and trans-permethrin, but also two metabolites of permethrin, PBalc and PBald. In silico homology modeling and the molecular docking methodology further support the metabolic capacity of these P450s for permethrin and substrates. Taken together, the findings of this study highlight the important function of multi-up-regulated P450 genes in the development of insecticide resistance in house flies.
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Affiliation(s)
- Ming Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
- Department of Entomology, University of California, San Diego, CA 92093, USA
| | - Xuechun Feng
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518000, China
| | - William R. Reid
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Fang Tang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
- Correspondence: ; Tel.: +1-334-844-5076
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Designing multi-epitope mRNA construct as a universal influenza vaccine candidate for future epidemic/pandemic preparedness. Int J Biol Macromol 2023; 226:885-899. [PMID: 36521707 DOI: 10.1016/j.ijbiomac.2022.12.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Despite the availability of prevention and treatment strategies and advancing immunization approaches, the influenza virus remains a global threat that continues to plague humanity with unpredictable pandemics. Due to the unusual genetic variability and segmented genome, the reassortment between different strains of influenza is facilitated and the viruses continuously evolve and adapt to the host cell's immunity. This underlies the seasonal vaccine mismatches that decrease the vaccine efficacy and increase the risk of outbreaks. Thus, the development of a universal vaccine covering all the influenza A and B strains would reduce the pervasiveness of the influenza virus. In the current study, a potentially universal influenza multi-epitope vaccine was designed based on the experimentally tested conserved T cell and B cell epitopes of hemagglutinin (HA), neuraminidase (NA), nucleoprotein (NP), and matrix-2 proton channel (M2) of the virus. The immune simulation and molecular docking of the vaccine construct with TLR2, TLR3, and TLR4 elicited the favorable immunogenicity of the vaccine and the formation of stable complexes, respectively. Ultimately, based on the immunoinformatics analysis, the universal mRNA multi-epitope vaccine designed in this study might have a protection potential against the various subtypes of influenza A and B.
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18
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Adiyaman R, McGuffin LJ. Using Local Protein Model Quality Estimates to Guide a Molecular Dynamics-Based Refinement Strategy. Methods Mol Biol 2023; 2627:119-140. [PMID: 36959445 DOI: 10.1007/978-1-0716-2974-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The refinement of predicted 3D models aims to bring them closer to the native structure by fixing errors including unusual bonds and torsion angles and irregular hydrogen bonding patterns. Refinement approaches based on molecular dynamics (MD) simulations using different types of restraints have performed well since CASP10. ReFOLD, developed by the McGuffin group, was one of the many MD-based refinement approaches, which were tested in CASP 12. When the performance of the ReFOLD method in CASP12 was evaluated, it was observed that ReFOLD suffered from the absence of a reliable guidance mechanism to reach consistent improvement for the quality of predicted 3D models, particularly in the case of template-based modelling (TBM) targets. Therefore, here we propose to utilize the local quality assessment score produced by ModFOLD6 to guide the MD-based refinement approach to further increase the accuracy of the predicted 3D models. The relative performance of the new local quality assessment guided MD-based refinement protocol and the original MD-based protocol ReFOLD are compared utilizing many different official scoring methods. By using the per-residue accuracy (or local quality) score to guide the refinement process, we are able to prevent the refined models from undesired structural deviations, thereby leading to more consistent improvements. This chapter will include a detailed analysis of the performance of the local quality assessment guided MD-based protocol versus that deployed in the original ReFOLD method.
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Affiliation(s)
- Recep Adiyaman
- School of Biological Sciences, University of Reading, Reading, UK
| | - Liam J McGuffin
- School of Biological Sciences, University of Reading, Reading, UK.
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19
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Challa SR, Nalamolu KR, Fornal CA, Mohandass A, Mussman JP, Schaibley C, Kashyap A, Sama V, Wang BC, Klopfenstein JD, Pinson DM, Kunamneni A, Veeravalli KK. The interplay between MMP-12 and t-PA in the brain after ischemic stroke. Neurochem Int 2022; 161:105436. [PMID: 36283468 PMCID: PMC9898869 DOI: 10.1016/j.neuint.2022.105436] [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: 08/26/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
Tissue-type plasminogen activator (t-PA) expression is known to increase following transient focal cerebral ischemia and reperfusion. Previously, we reported downregulation of t-PA upon suppression of matrix metalloproteinase-12 (MMP-12), following transient focal cerebral ischemia and reperfusion. We now present data on the temporal expression of t-PA in the brain after transient ischemia, as well as the interaction between MMP-12 and t-PA, two proteases associated with the breakdown of the blood-brain barrier (BBB) and ischemic brain damage. We hypothesized that there might be reciprocal interactions between MMP-12 and t-PA in the brain after ischemic stroke. This hypothesis was tested using shRNA-mediated gene silencing and computational modeling. Suppression of t-PA following transient ischemia and reperfusion in rats attenuated MMP-12 expression in the brain. The overall effect of t-PA shRNA administration was to attenuate the degradation of BBB tight junction protein claudin-5, diminish BBB disruption, and reduce neuroinflammation by decreasing the expression of the microglia/macrophage pro-inflammatory M1 phenotype (CD68, iNOS, IL-1β, and TNFα). Reduced BBB disruption and subsequent lack of infiltration of macrophages (the main source of MMP-12 in the ischemic brain) could account for the decrease in MMP-12 expression after t-PA suppression. Computational modeling of in silico protein-protein interactions indicated that MMP-12 and t-PA may interact physically. Overall, our findings demonstrate that MMP-12 and t-PA interact directly or indirectly at multiple levels in the brain following an ischemic stroke. The present findings could be useful in the development of new pharmacotherapies for the treatment of stroke.
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Affiliation(s)
- Siva Reddy Challa
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Pharmacology, KVSR Siddhartha College of Pharmaceutical Sciences, Vijayawada, Andhra Pradesh, India
| | - Koteswara Rao Nalamolu
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Casimir A Fornal
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Adithya Mohandass
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Justin P Mussman
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Claire Schaibley
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Aanan Kashyap
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Vinay Sama
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | - Billy C Wang
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Children's Hospital of Illinois, OSF HealthCare Saint Francis Medical Center, Peoria, IL, USA
| | - Jeffrey D Klopfenstein
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Illinois Neurological Institute, OSF HealthCare Saint Francis Medical Center, Peoria, IL, USA
| | - David M Pinson
- Department of Health Sciences Education and Pathology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA
| | | | - Krishna Kumar Veeravalli
- Department of Cancer Biology and Pharmacology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Neurosurgery, University of Illinois College of Medicine at Peoria, Peoria, IL, USA; Department of Neurology, University of Illinois College of Medicine at Peoria, Peoria, IL, USA.
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20
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Zhang J, Li H, Zhao X, Wu Q, Huang SY. Holo Protein Conformation Generation from Apo Structures by Ligand Binding Site Refinement. J Chem Inf Model 2022; 62:5806-5820. [PMID: 36342197 DOI: 10.1021/acs.jcim.2c00895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An important part in structure-based drug design is the selection of an appropriate protein structure. It has been revealed that a holo protein structure that contains a well-defined binding site is a much better choice than an apo structure in structure-based drug discovery. Therefore, it is valuable to obtain a holo-like protein conformation from apo structures in the case where no holo structure is available. Meeting the need, we present a robust approach to generate reliable holo-like structures from apo structures by ligand binding site refinement with restraints derived from holo templates with low homology. Our method was tested on a test set of 32 proteins from the DUD-E data set and compared with other approaches. It was shown that our method successfully refined the apo structures toward the corresponding holo conformations for 23 of 32 proteins, reducing the average all-heavy-atom RMSD of binding site residues by 0.48 Å. In addition, when evaluated against all the holo structures in the protein data bank, our method can improve the binding site RMSD for 14 of 19 cases that experience significant conformational changes. Furthermore, our refined structures also demonstrate their advantages over the apo structures in ligand binding mode predictions by both rigid docking and flexible docking and in virtual screening on the database of active and decoy ligands from the DUD-E. These results indicate that our method is effective in recovering holo-like conformations and will be valuable in structure-based drug discovery.
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Affiliation(s)
- Jinze Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Hao Li
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Xuejun Zhao
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Qilong Wu
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan430074, Hubei, P. R. China
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21
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Cai H, Yu J, Qiao Y, Ma Y, Zheng J, Lin M, Yan Q, Huang L. Effect of the Type VI Secretion System Secreted Protein Hcp on the Virulence of Aeromonas salmonicida. Microorganisms 2022; 10:microorganisms10122307. [PMID: 36557560 PMCID: PMC9784854 DOI: 10.3390/microorganisms10122307] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/23/2022] Open
Abstract
Aeromonas salmonicida, a psychrophilic bacterial pathogen, is widely distributed in marine freshwater, causing serious economic losses to major salmon farming areas in the world. At present, it is still one of the most important pathogens threatening salmon farming. Hcp (haemolysin-coregulated protein) is an effector protein in the type-VI secretion system (T6SS), which is secreted by T6SS and functions as its structural component. The results of our previous genomic sequencing showed that hcp existed in the mesophilic A. salmonicida SRW-OG1 isolated from naturally infected Epinephelus coioides. To further explore the role of Hcp in A. salmonicida SRW-OG1, we constructed an hcp-RNAi strain and verified its effect on the virulence of A. salmonicida. The results showed that compared with the wild strain, the hcp-RNAi strain suffered from different degrees of decreased adhesion, growth, biofilm formation, extracellular product secretion, and virulence. It was suggested that hcp may be an important virulence gene of A. salmonicida SRW-OG1.
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Affiliation(s)
- Hongyan Cai
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Jiaying Yu
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Ying Qiao
- Fourth Institute of Oceanography, Ministry of Natural Resources, No. 26, New Century Avenue, Beihai 536000, China
| | - Ying Ma
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Jiang Zheng
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Mao Lin
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
| | - Qingpi Yan
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
- Correspondence: (Q.Y.); (L.H.)
| | - Lixing Huang
- Key Laboratory of Healthy Mariculture for the East China Sea, Fisheries College, Ministry of Agriculture, Jimei University, Xiamen 361021, China
- Correspondence: (Q.Y.); (L.H.)
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22
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Structure-based virtual screening and molecular dynamics of potential inhibitors targeting sodium-bile acid co-transporter of carcinogenic liver fluke Clonorchis sinensis. PLoS Negl Trop Dis 2022; 16:e0010909. [DOI: 10.1371/journal.pntd.0010909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
Background
Clonorchis sinensis requires bile acid transporters as this fluke inhabits bile juice-filled biliary ducts, which provide an extreme environment. Clonorchis sinensis sodium-bile acid co-transporter (CsSBAT) is indispensable for the fluke’s survival in the final host, as it circulates taurocholate and prevents bile toxicity in the fluke; hence, it is recognized as a useful drug target.
Methodology and principal findings
In the present study, using structure-based virtual screening approach, we presented inhibitor candidates targeting a bile acid-binding pocket of CsSBAT. CsSBAT models were built using tertiary structure modeling based on a bile acid transporter template (PDB ID: 3zuy and 4n7x) and were applied into AutoDock Vina for competitive docking simulation. First, potential compounds were identified from PubChem (holding more than 100,000 compounds) by applying three criteria: i) interacting more favorably with CsSBAT than with a human homolog, ii) intimate interaction to the inward- and outward-facing conformational states, iii) binding with CsSBAT preferably to natural bile acids. Second, two compounds were identified following the Lipinski’s rule of five. Third, other two compounds of molecular weight higher than 500 Da (Mr > 500 Da) were presumed to efficiently block the transporter via a feasible rational screening strategy. Of these candidates, compound 9806452 exhibited the least hepatotoxicity that may enhance drug-likeness properties.
Conclusions
It is proposed that compound 9806452 act as a potential inhibitor toward CsSBAT and further studies are warranted for drug development process against clonorchiasis.
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23
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Papukashvili D, Rcheulishvili N, Liu C, Wang X, He Y, Wang PG. Strategy of developing nucleic acid-based universal monkeypox vaccine candidates. Front Immunol 2022; 13:1050309. [PMID: 36389680 PMCID: PMC9646902 DOI: 10.3389/fimmu.2022.1050309] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/12/2022] [Indexed: 08/08/2023] Open
Abstract
Until May 2022, zoonotic infectious disease monkeypox (MPX) caused by the monkeypox virus (MPXV) was one of the forgotten viruses considered to be geographically limited in African countries even though few cases outside of Africa were identified. Central and West African countries are known to be endemic for MPXV. However, since the number of human MPX cases has rapidly increased outside of Africa the global interest in this virus has markedly grown. The majority of infected people with MPXV have never been vaccinated against smallpox virus. Noteworthily, the MPXV spreads fast in men who have sex with men (MSM). Preventive measures against MPXV are essential to be taken, indeed, vaccination is the key. Due to the antigenic similarities, the smallpox vaccine is efficient against MPXV. Nevertheless, there is no specific MPXV vaccine until now. Nucleic acid vaccines deserve special attention since the emergency approval of two messenger RNA (mRNA)-based coronavirus disease 2019 (COVID-19) vaccines in 2020. This milestone in vaccinology has opened a new platform for developing more mRNA- or DNA-based vaccines. Certainly, this type of vaccine has a number of advantages including time- and cost-effectiveness over conventional vaccines. The platform of nucleic acid-based vaccines gives humankind a huge opportunity. Ultimately, there is a strong need for developing a universal vaccine against MPXV. This review will shed the light on the strategies for developing nucleic acid vaccines against MPXV in a timely manner. Consequently, developing nucleic acid-based vaccines may alleviate the global threat against MPXV.
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Affiliation(s)
| | | | | | | | - Yunjiao He
- *Correspondence: Yunjiao He, ; Peng George Wang,
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24
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Rcheulishvili N, Papukashvili D, Liu C, Ji Y, He Y, Wang PG. Promising strategy for developing mRNA-based universal influenza virus vaccine for human population, poultry, and pigs- focus on the bigger picture. Front Immunol 2022; 13:1025884. [PMID: 36325349 PMCID: PMC9618703 DOI: 10.3389/fimmu.2022.1025884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/03/2022] [Indexed: 08/08/2023] Open
Abstract
Since the first outbreak in the 19th century influenza virus has remained emergent owing to the huge pandemic potential. Only the pandemic of 1918 caused more deaths than any war in world history. Although two types of influenza- A (IAV) and B (IBV) cause epidemics annually, influenza A deserves more attention as its nature is much wilier. IAVs have a large animal reservoir and cause the infection manifestation not only in the human population but in poultry and domestic pigs as well. This many-sided characteristic of IAV along with the segmented genome gives rise to the antigenic drift and shift that allows evolving the new strains and new subtypes, respectively. As a result, the immune system of the body is unable to recognize them. Importantly, several highly pathogenic avian IAVs have already caused sporadic human infections with a high fatality rate (~60%). The current review discusses the promising strategy of using a potentially universal IAV mRNA vaccine based on conserved elements for humans, poultry, and pigs. This will better aid in averting the outbreaks in different susceptible species, thus, reduce the adverse impact on agriculture, and economics, and ultimately, prevent deadly pandemics in the human population.
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Affiliation(s)
| | | | | | | | - Yunjiao He
- *Correspondence: Yunjiao He, ; Peng George Wang,
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25
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Characterization of Treponema denticola Major Surface Protein (Msp) by Deletion Analysis and Advanced Molecular Modeling. J Bacteriol 2022; 204:e0022822. [PMID: 35913147 PMCID: PMC9487533 DOI: 10.1128/jb.00228-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Treponema denticola, a keystone pathogen in periodontitis, is a model organism for studying Treponema physiology and host-microbe interactions. Its major surface protein Msp forms an oligomeric outer membrane complex that binds fibronectin, has cytotoxic pore-forming activity, and disrupts several intracellular processes in host cells. T. denticola msp is an ortholog of the Treponema pallidum tprA to -K gene family that includes tprK, whose remarkable in vivo hypervariability is proposed to contribute to T. pallidum immune evasion. We recently identified the primary Msp surface-exposed epitope and proposed a model of the Msp protein as a β-barrel protein similar to Gram-negative bacterial porins. Here, we report fine-scale Msp mutagenesis demonstrating that both the N and C termini as well as the centrally located Msp surface epitope are required for native Msp oligomer expression. Removal of as few as three C-terminal amino acids abrogated Msp detection on the T. denticola cell surface, and deletion of four residues resulted in complete loss of detectable Msp. Substitution of a FLAG tag for either residues 6 to 13 of mature Msp or an 8-residue portion of the central Msp surface epitope resulted in expression of full-length Msp but absence of the oligomer, suggesting roles for both domains in oligomer formation. Consistent with previously reported Msp N-glycosylation, proteinase K treatment of intact cells released a 25 kDa polypeptide containing the Msp surface epitope into culture supernatants. Molecular modeling of Msp using novel metagenome-derived multiple sequence alignment (MSA) algorithms supports the hypothesis that Msp is a large-diameter, trimeric outer membrane porin-like protein whose potential transport substrate remains to be identified. IMPORTANCE The Treponema denticola gene encoding its major surface protein (Msp) is an ortholog of the T. pallidum tprA to -K gene family that includes tprK, whose remarkable in vivo hypervariability is proposed to contribute to T. pallidum immune evasion. Using a combined strategy of fine-scale mutagenesis and advanced predictive molecular modeling, we characterized the Msp protein and present a high-confidence model of its structure as an oligomer embedded in the outer membrane. This work adds to knowledge of Msp-like proteins in oral treponemes and may contribute to understanding the evolutionary and potential functional relationships between T. denticola Msp and the orthologous T. pallidum Tpr proteins.
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26
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Zhang H, Shang R, Kim K, Zheng W, Johnson CJ, Sun L, Niu X, Liu L, Zhou J, Liu L, Zhang Z, Uyeno TA, Pei J, Fissette SD, Green SA, Samudra SP, Wen J, Zhang J, Eggenschwiler JT, Menke DB, Bronner ME, Grishin NV, Li W, Ye K, Zhang Y, Stolfi A, Bi P. Evolution of a chordate-specific mechanism for myoblast fusion. SCIENCE ADVANCES 2022; 8:eadd2696. [PMID: 36054355 PMCID: PMC10848958 DOI: 10.1126/sciadv.add2696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Vertebrate myoblast fusion allows for multinucleated muscle fibers to compound the size and strength of mononucleated cells, but the evolution of this important process is unknown. We investigated the evolutionary origins and function of membrane-coalescing agents Myomaker and Myomixer in various groups of chordates. Here, we report that Myomaker likely arose through gene duplication in the last common ancestor of tunicates and vertebrates, while Myomixer appears to have evolved de novo in early vertebrates. Functional tests revealed a complex evolutionary history of myoblast fusion. A prevertebrate phase of muscle multinucleation driven by Myomaker was followed by the later emergence of Myomixer that enables the highly efficient fusion system of vertebrates. Evolutionary comparisons between vertebrate and nonvertebrate Myomaker revealed key structural and mechanistic insights into myoblast fusion. Thus, our findings suggest an evolutionary model of chordate fusogens and illustrate how new genes shape the emergence of novel morphogenetic traits and mechanisms.
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Affiliation(s)
- Haifeng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Renjie Shang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Kwantae Kim
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | | | - Lei Sun
- The Fifth People’s Hospital of Shanghai, and Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiang Niu
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, USA
| | - Liang Liu
- Department of Statistics, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jingqi Zhou
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Lingshu Liu
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Zheng Zhang
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | | | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Skye D. Fissette
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Stephen A. Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Junfei Wen
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
| | - Jianli Zhang
- College of Engineering, University of Georgia, Athens, GA, USA
| | | | | | - Marianne E. Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nick V. Grishin
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
| | - Kaixiong Ye
- Department of Genetics, University of Georgia, Athens, GA, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pengpeng Bi
- Center for Molecular Medicine, University of Georgia, Athens, GA, USA
- Department of Genetics, University of Georgia, Athens, GA, USA
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27
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I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction. Nat Protoc 2022; 17:2326-2353. [PMID: 35931779 DOI: 10.1038/s41596-022-00728-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/24/2022] [Indexed: 01/17/2023]
Abstract
Most proteins in cells are composed of multiple folding units (or domains) to perform complex functions in a cooperative manner. Relative to the rapid progress in single-domain structure prediction, there are few effective tools available for multi-domain protein structure assembly, mainly due to the complexity of modeling multi-domain proteins, which involves higher degrees of freedom in domain-orientation space and various levels of continuous and discontinuous domain assembly and linker refinement. To meet the challenge and the high demand of the community, we developed I-TASSER-MTD to model the structures and functions of multi-domain proteins through a progressive protocol that combines sequence-based domain parsing, single-domain structure folding, inter-domain structure assembly and structure-based function annotation in a fully automated pipeline. Advanced deep-learning models have been incorporated into each of the steps to enhance both the domain modeling and inter-domain assembly accuracy. The protocol allows for the incorporation of experimental cross-linking data and cryo-electron microscopy density maps to guide the multi-domain structure assembly simulations. I-TASSER-MTD is built on I-TASSER but substantially extends its ability and accuracy in modeling large multi-domain protein structures and provides meaningful functional insights for the targets at both the domain- and full-chain levels from the amino acid sequence alone.
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28
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Proteome Exploration of
Legionella pneumophila
To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach. Microbiol Spectr 2022; 10:e0037322. [PMID: 35863001 PMCID: PMC9430848 DOI: 10.1128/spectrum.00373-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Legionella pneumophila
is a human pathogen distributed worldwide, causing Legionnaires’ disease (LD), a severe form of pneumonia and respiratory tract infection.
L. pneumophila
is emerging as an antibiotic-resistant strain, and controlling LD is now difficult. Hence, developing novel drugs and vaccines against
L. pneumophila
is a major research priority.
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29
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Zhou X, Peng C, Zheng W, Li Y, Zhang G, Zhang Y. DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction. Nucleic Acids Res 2022; 50:W235-W245. [PMID: 35536281 PMCID: PMC9252800 DOI: 10.1093/nar/gkac340] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 01/19/2023] Open
Abstract
Most proteins in nature contain multiple folding units (or domains). The revolutionary success of AlphaFold2 in single-domain structure prediction showed potential to extend deep-learning techniques for multi-domain structure modeling. This work presents a significantly improved method, DEMO2, which integrates analogous template structural alignments with deep-learning techniques for high-accuracy domain structure assembly. Starting from individual domain models, inter-domain spatial restraints are first predicted with deep residual convolutional networks, where full-length structure models are assembled using L-BFGS simulations under the guidance of a hybrid energy function combining deep-learning restraints and analogous multi-domain template alignments searched from the PDB. The output of DEMO2 contains deep-learning inter-domain restraints, top-ranked multi-domain structure templates, and up to five full-length structure models. DEMO2 was tested on a large-scale benchmark and the blind CASP14 experiment, where DEMO2 was shown to significantly outperform its predecessor and the state-of-the-art protein structure prediction methods. By integrating with new deep-learning techniques, DEMO2 should help fill the rapidly increasing gap between the improved ability of tertiary structure determination and the high demand for the high-quality multi-domain protein structures. The DEMO2 server is available at https://zhanggroup.org/DEMO/.
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Affiliation(s)
- Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chunxiang Peng
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou 310023, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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30
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Kvetkina A, Pislyagin E, Menchinskaya E, Yurchenko E, Kalina R, Kozlovskiy S, Kaluzhskiy L, Menshov A, Kim N, Peigneur S, Tytgat J, Ivanov A, Ayvazyan N, Leychenko E, Aminin D. Kunitz-Type Peptides from Sea Anemones Protect Neuronal Cells against Parkinson's Disease Inductors via Inhibition of ROS Production and ATP-Induced P2X7 Receptor Activation. Int J Mol Sci 2022; 23:ijms23095115. [PMID: 35563513 PMCID: PMC9103184 DOI: 10.3390/ijms23095115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) is a socially significant disease, during the development of which oxidative stress and inflammation play a significant role. Here, we studied the neuroprotective effects of four Kunitz-type peptides from Heteractis crispa and Heteractis magnifica sea anemones against PD inductors. The peptide HCIQ1c9, which was obtained for the first time, inhibited trypsin less than other peptides due to unfavorable interactions of Arg17 with Lys43 in the enzyme. Its activity was reduced by up to 70% over the temperature range of 60–100 °C, while HCIQ2c1, HCIQ4c7, and HMIQ3c1 retained their conformation and stayed active up to 90–100 °C. All studied peptides inhibited paraquat- and rotenone-induced intracellular ROS formation, in particular NO, and scavenged free radicals outside the cells. The peptides did not modulate the TRPV1 channels but they affected the P2X7R, both of which are considered therapeutic targets in Parkinson’s disease. HMIQ3c1 and HCIQ4c7 almost completely inhibited the ATP-induced uptake of YO-PRO-1 dye in Neuro-2a cells through P2X7 ion channels and significantly reduced the stable calcium response in these cells. The complex formation of the peptides with the P2X7R extracellular domain was determined via SPR analysis. Thus, these peptides may be considered promising compounds to protect neuronal cells against PD inductors, which act as ROS production inhibitors and partially act as ATP-induced P2X7R activation inhibitors.
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Affiliation(s)
- Aleksandra Kvetkina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Evgeny Pislyagin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Ekaterina Menchinskaya
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Ekaterina Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Rimma Kalina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Sergei Kozlovskiy
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Leonid Kaluzhskiy
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia; (L.K.); (A.I.)
| | - Alexander Menshov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Natalia Kim
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Steve Peigneur
- Toxicology and Pharmacology, Campus Gasthuisberg O&N2, University of Leuven (KU Leuven), Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium; (S.P.); (J.T.)
| | - Jan Tytgat
- Toxicology and Pharmacology, Campus Gasthuisberg O&N2, University of Leuven (KU Leuven), Herestraat 49, P.O. Box 922, B-3000 Leuven, Belgium; (S.P.); (J.T.)
| | - Alexis Ivanov
- V.N. Orekhovich Institute of Biomedical Chemistry, 10, Pogodinskaya St., 119121 Moscow, Russia; (L.K.); (A.I.)
| | - Naira Ayvazyan
- L.A. Orbeli Institute of Physiology, National Academy of Sciences of Armenia, Yerevan 0028, Armenia;
| | - Elena Leychenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
| | - Dmitry Aminin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia; (A.K.); (E.P.); (E.M.); (E.Y.); (R.K.); (S.K.); (A.M.); (N.K.); (E.L.)
- Correspondence:
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31
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Zheng W, Wuyun Q, Zhou X, Li Y, Freddolino PL, Zhang Y. LOMETS3: integrating deep learning and profile alignment for advanced protein template recognition and function annotation. Nucleic Acids Res 2022; 50:W454-W464. [PMID: 35420129 PMCID: PMC9252734 DOI: 10.1093/nar/gkac248] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022] Open
Abstract
Deep learning techniques have significantly advanced the field of protein structure prediction. LOMETS3 (https://zhanglab.ccmb.med.umich.edu/LOMETS/) is a new generation meta-server approach to template-based protein structure prediction and function annotation, which integrates newly developed deep learning threading methods. For the first time, we have extended LOMETS3 to handle multi-domain proteins and to construct full-length models with gradient-based optimizations. Starting from a FASTA-formatted sequence, LOMETS3 performs four steps of domain boundary prediction, domain-level template identification, full-length template/model assembly and structure-based function prediction. The output of LOMETS3 contains (i) top-ranked templates from LOMETS3 and its component threading programs, (ii) up to 5 full-length structure models constructed by L-BFGS (limited-memory Broyden–Fletcher–Goldfarb–Shanno algorithm) optimization, (iii) the 10 closest Protein Data Bank (PDB) structures to the target, (iv) structure-based functional predictions, (v) domain partition and assembly results, and (vi) the domain-level threading results, including items (i)–(iii) for each identified domain. LOMETS3 was tested in large-scale benchmarks and the blind CASP14 (14th Critical Assessment of Structure Prediction) experiment, where the overall template recognition and function prediction accuracy is significantly beyond its predecessors and other state-of-the-art threading approaches, especially for hard targets without homologous templates in the PDB. Based on the improved developments, LOMETS3 should help significantly advance the capability of broader biomedical community for template-based protein structure and function modelling.
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Affiliation(s)
- Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qiqige Wuyun
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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32
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Zhou X, Li Y, Zhang C, Zheng W, Zhang G, Zhang Y. Progressive assembly of multi-domain protein structures from cryo-EM density maps. NATURE COMPUTATIONAL SCIENCE 2022; 2:265-275. [PMID: 35844960 PMCID: PMC9281201 DOI: 10.1038/s43588-022-00232-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 03/21/2022] [Indexed: 05/20/2023]
Abstract
Progress in cryo-electron microscopy has provided the potential for large-size protein structure determination. However, the success rate for solving multi-domain proteins remains low because of the difficulty in modelling inter-domain orientations. Here we developed domain enhanced modeling using cryo-electron microscopy (DEMO-EM), an automatic method to assemble multi-domain structures from cryo-electron microscopy maps through a progressive structural refinement procedure combining rigid-body domain fitting and flexible assembly simulations with deep-neural-network inter-domain distance profiles. The method was tested on a large-scale benchmark set of proteins containing up to 12 continuous and discontinuous domains with medium- to low-resolution density maps, where DEMO-EM produced models with correct inter-domain orientations (template modeling score (TM-score) >0.5) for 97% of cases and outperformed state-of-the-art methods. DEMO-EM was applied to the severe acute respiratory syndrome coronavirus 2 genome and generated models with average TM-score and root-mean-square deviation of 0.97 and 1.3 Å, respectively, with respect to the deposited structures. These results demonstrate an efficient pipeline that enables automated and reliable large-scale multi-domain protein structure modelling from cryo-electron microscopy maps.
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Affiliation(s)
- Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
- Correspondence and requests for materials should be addressed to Yang Zhang.
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Repurposing Lansoprazole and Posaconazole to treat leishmaniasis: Integration of in vitro testing, pharmacological corroboration, and mechanisms of action. J Food Drug Anal 2022; 30:128-149. [PMID: 35647721 PMCID: PMC9931003 DOI: 10.38212/2224-6614.3394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
Leishmaniasis remains a serious public health problem in many tropical regions of the world. Among neglected tropical diseases, the mortality rate of leishmaniasis is second only to malaria. All currently approved therapeutics have toxic side effects and face rapidly increasing resistance. To identify existing drugs with antileishmanial activity and predict the mechanism of action, we designed a drug-discovery pipeline utilizing both in-silico and in-vitro methods. First, we screened compounds from the Selleckchem Bio-Active Compound Library containing ~1622 FDA-approved drugs and narrowed these down to 96 candidates based on data mining for possible anti-parasitic properties. Next, we completed preliminary in-vitro testing of compounds against Leishmania amastigotes and selected the most promising active compounds, Lansoprazole and Posaconazole. We identified possible Leishmania drug targets of Lansoprazole and Posaconazole using several available servers. Our in-silico screen identified likely Lansoprazole targets as the closely related calcium-transporting ATPases (LdBPK_352080.1, LdBPK_040010.1, and LdBPK_170660.1), and the Posaconazole target as lanosterol 14-alpha-demethylase (LdBPK_111100.1). Further validation showed LdBPK_352080.1 to be the most plausible target based on induced-fit docking followed by long (100ns) MD simulations to confirm the stability of the docked complexes. We present a likely ion channel-based mechanism of action of Lansoprazole against Leishmania calcium-transporting ATPases, which are essential for parasite metabolism and infectivity. The LdBPK_111100.1 interaction with Posaconazole is very similar to the known fungal orthologue. Herein, we present two novel anti-leishmanial agents, Posaconazole and Lansoprazole, already approved by the FDA for different indications and propose plausible mechanisms of action for their antileishmanial activity.
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34
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Gupta Y, Maciorowski D, Medernach B, Becker DP, Durvasula R, Libertin CR, Kempaiah P. Iron dysregulation in COVID-19 and reciprocal evolution of SARS-CoV-2: Natura nihil frustra facit. J Cell Biochem 2022; 123:601-619. [PMID: 34997606 PMCID: PMC9015563 DOI: 10.1002/jcb.30207] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022]
Abstract
After more than a year of the COVID-19 pandemic, SARS-CoV-2 infection rates with newer variants continue to devastate much of the world. Global healthcare systems are overwhelmed with high positive patient numbers. Silent hypoxia accompanied by rapid deterioration and some cases with septic shock is responsible for COVID-19 mortality in many hospitalized patients. There is an urgent need to further understand the relationships and interplay with human host components during pathogenesis and immune evasion strategies. Currently, acquired immunity through vaccination or prior infection usually provides sufficient protection against the emerging variants of SARS-CoV-2 except Omicron variant requiring recent booster. New strains have shown higher viral loads and greater transmissibility with more severe disease presentations. Notably, COVID-19 has a peculiar prognosis in severe patients with iron dysregulation and hypoxia which is still poorly understood. Studies have shown abnormally low serum iron levels in severe infection but a high iron overload in lung fibrotic tissue. Data from our in-silico structural analysis of the spike protein sequence along with host proteolysis processing suggests that the viral spike protein fragment mimics Hepcidin and is resistant to the major human proteases. This functional spike-derived peptide dubbed "Covidin" thus may be intricately involved with host ferroportin binding and internalization leading to dysregulated host iron metabolism. Here, we propose the possible role of this potentially allogenic mimetic hormone corresponding to severe COVID-19 immunopathology and illustrate that this molecular mimicry is responsible for a major pathway associated with severe disease status. Furthermore, through 3D molecular modeling and docking followed by MD simulation validation, we have unraveled the likely role of Covidin in iron dysregulation in COVID-19 patients. Our meta-analysis suggests the Hepcidin mimetic mechanism is highly conserved among its host range as well as among all new variants to date including Omicron. Extensive analysis of current mutations revealed that new variants are becoming alarmingly more resistant to selective human proteases associated with host defense.
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Affiliation(s)
- Yash Gupta
- Infectious DiseasesMayo ClinicJacksonvilleFloridaUSA
| | - Dawid Maciorowski
- School of Medicine and Public HealthUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | - Brian Medernach
- Department of MedicineLoyola University Medical CenterChicagoIllinoisUSA
| | - Daniel P. Becker
- Department of Chemistry and BiochemistryLoyola University ChicagoChicagoIllinoisUSA
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35
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CR-I-TASSER: assemble protein structures from cryo-EM density maps using deep convolutional neural networks. Nat Methods 2022; 19:195-204. [PMID: 35132244 PMCID: PMC8852347 DOI: 10.1038/s41592-021-01389-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 12/17/2021] [Indexed: 11/19/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has become a leading approach for protein structure determination, but it remains challenging to accurately model atomic structures with cryo-EM density maps. We propose a hybrid method, CR-I-TASSER, which integrates deep neural-network learning with I-TASSER assembly simulations for automated cryo-EM structure determination. The method is benchmarked on 778 proteins with simulated and experimental density maps, where CR-I-TASSER constructs models with a correct fold (TM-score>0.5) for 643 targets that is 64% higher than the best of other de novo and refinement-based approaches on high-resolution data samples. Detailed data analyses showed that the major advantage of CR-I-TASSER lies in the deep-learning based Cα position prediction, which significantly improves the threading template quality and therefore boosts the accuracy of final models through optimized fragment assembly simulations. These results demonstrate a new avenue to determine cryo-EM protein structures with high accuracy and robustness covering various target types and density-map resolutions.
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36
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Docking-guided rational engineering of a macrolide glycosyltransferase glycodiversifies epothilone B. Commun Biol 2022; 5:100. [PMID: 35087210 PMCID: PMC8795383 DOI: 10.1038/s42003-022-03047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/06/2022] [Indexed: 11/09/2022] Open
Abstract
Glycosyltransferases typically display acceptor substrate flexibility but more stringent donor specificity. BsGT-1 is a highly effective glycosyltransferase to glycosylate macrolides, including epothilones, promising antitumor compounds. Here, we show that BsGT-1 has three major regions significantly influencing the glycodiversification of epothilone B based on structural molecular docking, "hot spots" alanine scanning, and site saturation mutagenesis. Mutations in the PSPG-like motif region and the C2 loop region are more likely to expand donor preference; mutations of the flexible N3 loop region located at the mouth of the substrate-binding cavity produce novel epothilone oligosaccharides. These "hot spots" also functioned in homologues of BsGT-1. The glycosides showed significantly enhanced water solubility and decreased cytotoxicity, although the glycosyl appendages of epothilone B also reduced drug permeability and attenuated antitumor efficacy. This study laid a foundation for the rational engineering of other GTs to synthesize valuable small molecules.
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37
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Uddin MB, Alam MN, Hasan M, Hossain SMB, Debnath M, Begum R, Samad MA, Hoque SF, Chowdhury MSR, Rahman MM, Hossain MM, Hassan MM, Lundkvist Å, Järhult JD, El Zowalaty ME, Ahmed SSU. Molecular Detection of Colistin Resistance mcr-1 Gene in Multidrug-Resistant Escherichia coli Isolated from Chicken. Antibiotics (Basel) 2022; 11:antibiotics11010097. [PMID: 35052973 PMCID: PMC8772701 DOI: 10.3390/antibiotics11010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 08/12/2021] [Accepted: 08/27/2021] [Indexed: 11/29/2022] Open
Abstract
Zoonotic and antimicrobial-resistant Escherichia coli (hereafter, E. coli) is a global public health threat which can lead to detrimental effects on human health. Here, we aim to investigate the antimicrobial resistance and the presence of mcr-1 gene in E. coli isolated from chicken feces. Ninety-four E. coli isolates were obtained from samples collected from different locations in Bangladesh, and the isolates were identified using conventional microbiological tests. Phenotypic disk diffusion tests using 20 antimicrobial agents were performed according to CLSI-EUCAST guidelines, and minimum inhibitory concentrations (MICs) were determined for a subset of samples. E. coli isolates showed high resistance to colistin (88.30%), ciprofloxacin (77.66%), trimethoprim/sulfamethoxazole (76.60%), tigecycline (75.53%), and enrofloxacin (71.28%). Additionally, the pathotype eaeA gene was confirmed in ten randomly selected E. coli isolates using primer-specific polymerase chain reaction (PCR). The presence of mcr-1 gene was confirmed using PCR and sequencing analysis in six out of ten E. coli isolates. Furthermore, sequencing and phylogenetic analyses revealed a similarity between the catalytic domain of Neisseria meningitidis lipooligosaccharide phosphoethanolamine transferase A (LptA) and MCR proteins, indicating that the six tested isolates were colistin resistant. Finally, the findings of the present study showed that E. coli isolated from chicken harbored mcr-1 gene, and multidrug and colistin resistance. These findings accentuate the need to implement strict measures to limit the imprudent use of antibiotics, particularly colistin, in agriculture and poultry farms.
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Affiliation(s)
- Md Bashir Uddin
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Mohammad Nurul Alam
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - S. M. Bayejed Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mita Debnath
- Kazi Farms Poultry Laboratory, Gazipur 1700, Bangladesh;
| | - Ruhena Begum
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Mohammed A. Samad
- Bangladesh Livestock Research Institute (BLRI), Savar 1341, Bangladesh; (R.B.); (M.A.S.)
| | - Syeda Farjana Hoque
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.H.); (S.F.H.)
| | - Md. Shahidur Rahman Chowdhury
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mahfujur Rahman
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Md. Mukter Hossain
- Department of Medicine, Sylhet Agricultural University, Sylhet 3100, Bangladesh; (M.N.A.); (S.M.B.H.); (M.S.R.C.); (M.M.R.); (M.M.H.)
| | - Mohammad Mahmudul Hassan
- Department of Physiology, Biochemistry and Pharmacology, Chattogram Veterinary and Animal Sciences University, Chattogram 4225, Bangladesh;
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Josef D. Järhult
- Department of Medical Sciences, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
| | - Mohamed E. El Zowalaty
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, SE 75 123 Uppsala, Sweden;
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet 3100, Bangladesh
- Correspondence: (M.B.U.); (M.E.E.Z.); (S.S.U.A.)
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Engel H, Guischard F, Krause F, Nandy J, Kaas P, Höfflin N, Köhn M, Kilb N, Voigt K, Wolf S, Aslan T, Baezner F, Hahne S, Ruckes C, Weygant J, Zinina A, Akmeriç EB, Antwi EB, Dombrovskij D, Franke P, Lesch KL, Vesper N, Weis D, Gensch N, Di Ventura B, Öztürk MA. finDr: A web server for in silico D-peptide ligand identification. Synth Syst Biotechnol 2021; 6:402-413. [PMID: 34901479 PMCID: PMC8632724 DOI: 10.1016/j.synbio.2021.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/20/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
In the rapidly expanding field of peptide therapeutics, the short in vivo half-life of peptides represents a considerable limitation for drug action. D-peptides, consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids (AAs), do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation, resulting in a favourable pharmacokinetic profile. To experimentally identify D-peptide binders to interesting therapeutic targets, so-called mirror-image phage display is typically performed, whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display. This technique is extremely powerful, but it requires the synthesis of the target in D-form, which is challenging for large proteins. Here we present finDr, a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure (https://findr.biologie.uni-freiburg.de/). finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank (PDB) for their ability to bind to the target. In a separate, heuristic approach to search the chemical space of 12-mer peptides, finDr executes a customizable evolutionary algorithm (EA) for the de novo identification or optimization of D-peptide ligands. As a proof of principle, we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3 (PSMα3), a toxin of methicillin-resistant Staphylococcus aureus (MRSA). We validate the predictions using in vitro binding assays, supporting the success of this approach. Compared to conventional methods, finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation. We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.
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Key Words
- D-AA, dextrorotatory amino acid
- D-peptide
- EA, evolutionary algorithm
- Evolutionary algorithm
- L-AA, levorotatory amino acid
- MD, molecular dynamics
- MIEA, mirror-image evolutionary algorithm
- MIPD, mirror-image phage display
- MIVS, mirror-image virtual screening
- MRSA, methicillin-resistant Staphylococcus aureus
- Mirror-image phage display
- Molecular docking
- NCL, native chemical ligation
- PD-1, receptor programmed death 1
- PPI, protein-protein interaction
- PSMα3, phenol soluble modulin alpha 3
- Peptide design
- SPPS, solid phase peptide synthesis
- Web server
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Affiliation(s)
- Helena Engel
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Felix Guischard
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Krause
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Janina Nandy
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Paulina Kaas
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nico Höfflin
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Normann Kilb
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- AG Roth-Lab for MicroarrayCopying, ZBSA–Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104, Freiburg, Germany
| | - Karsten Voigt
- Institute of Biology III, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Hermann-Herder-Strasse 3a, 79104, Freiburg, Germany
| | - Tahira Aslan
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Fabian Baezner
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Salomé Hahne
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Carolin Ruckes
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Joshua Weygant
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Alisa Zinina
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Emir Bora Akmeriç
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Enoch B. Antwi
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Dennis Dombrovskij
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Philipp Franke
- Institute for Biochemistry, University of Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Klara L. Lesch
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19A, 79104, Freiburg, Germany
- Internal Medicine IV, Department of Medicine, Medical Center, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - Niklas Vesper
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Daniel Weis
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
| | - Nicole Gensch
- Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Corresponding author. Core Facility Signalling Factory, Centre for Biological Signaling Studies (BIOSS), University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Barbara Di Ventura
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
| | - Mehmet Ali Öztürk
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany
- Institute of Biology II, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany
- Corresponding author. Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104, Freiburg, Germany.
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Decoding the link of microbiome niches with homologous sequences enables accurately targeted protein structure prediction. Proc Natl Acad Sci U S A 2021; 118:2110828118. [PMID: 34873061 DOI: 10.1073/pnas.2110828118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 12/26/2022] Open
Abstract
Information derived from metagenome sequences through deep-learning techniques has significantly improved the accuracy of template free protein structure modeling. However, most of the deep learning-based modeling studies are based on blind sequence database searches and suffer from low efficiency in computational resource utilization and model construction, especially when the sequence library becomes prohibitively large. We proposed a MetaSource model built on 4.25 billion microbiome sequences from four major biomes (Gut, Lake, Soil, and Fermentor) to decode the inherent linkage of microbial niches with protein homologous families. Large-scale protein family folding experiments on 8,700 unknown Pfam families showed that a microbiome targeted approach with multiple sequence alignment constructed from individual MetaSource biomes requires more than threefold less computer memory and CPU (central processing unit) time but generates contact-map and three-dimensional structure models with a significantly higher accuracy, compared with that using combined metagenome datasets. These results demonstrate an avenue to bridge the gap between the rapidly increasing metagenome databases and the limited computing resources for efficient genome-wide database mining, which provides a useful bluebook to guide future microbiome sequence database and modeling development for high-accuracy protein structure and function prediction.
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Soto-Ospina A, Araque Marín P, Bedoya GDJ, Villegas Lanau A. Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. Biochem Res Int 2021; 2021:9542038. [PMID: 34881055 PMCID: PMC8648483 DOI: 10.1155/2021/9542038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022] Open
Abstract
Alzheimer's disease manifests itself in brain tissue by neuronal death, due to aggregation of β-amyloid, produced by senile plaques, and hyperphosphorylation of the tau protein, which produces neurofibrillary tangles. One of the genetic markers of the disease is the gene that translates the presenilin-2 protein, which has mutations that favor the appearance of the disease and has no reported crystallographic structure. In view of this, protein modeling is performed using prediction and structural refinement tools followed by an energetic and stereochemical characterization for its validation. For the simulation, four reported mutations are chosen, which are Met239Ile, Met239Val, Ser130Leu, and Thr122Arg, all associated with various functional responses. From a theoretical analysis, a preliminary bioinformatic study is made to find the phosphorylation patterns in the protein and the hydropathic index according to the polarity and chemical environment. Molecular visualization was carried out with the Chimera 1.14 software, and the theoretical calculation with the hybrid quantum mechanics/molecular mechanics system from the semi-empirical method, with Spartan18 software and an AustinModel1 basis. These relationships allow for studying the system from a structural approach with the determination of small distance changes, potential surfaces, electrostatic maps, and angle changes, which favor the comparison between wild-type and mutant systems. With the results obtained, it is expected to complement experimental data reported in the literature from models that would allow us to understand the effects of the selected mutations.
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Affiliation(s)
- Alejandro Soto-Ospina
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
| | - Pedronel Araque Marín
- EIA University, School of Life Sciences, Research and Innovation in Chemistry Formulations Group, Envigado, Colombia
| | | | - Andrés Villegas Lanau
- University of Antioquia, Faculty of Medicine, Group Molecular Genetics, Medellín, Colombia
- University of Antioquia, Faculty of Medicine, Group Neuroscience of Antioquia, Medellín, Colombia
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Engineered Fully Human Single-Chain Monoclonal Antibodies to PIM2 Kinase. Molecules 2021; 26:molecules26216436. [PMID: 34770845 PMCID: PMC8588357 DOI: 10.3390/molecules26216436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/24/2021] [Indexed: 11/17/2022] Open
Abstract
Proviral integration site of Moloney virus-2 (PIM2) is overexpressed in multiple human cancer cells and high level is related to poor prognosis; thus, PIM2 kinase is a rational target of anti-cancer therapeutics. Several chemical inhibitors targeting PIMs/PIM2 or their downstream signaling molecules have been developed for treatment of different cancers. However, their off-target toxicity is common in clinical trials, so they could not be advanced to official approval for clinical application. Here, we produced human single-chain antibody fragments (HuscFvs) to PIM2 by using phage display library, which was constructed in a way that a portion of phages in the library carried HuscFvs against human own proteins on their surface with the respective antibody genes in the phage genome. Bacterial derived-recombinant PIM2 (rPIM2) was used as an antigenic bait to fish out the rPIM2-bound phages from the library. Three E. coli clones transfected with the HuscFv genes derived from the rPIM2-bound phages expressed HuscFvs that bound also to native PIM2 from cancer cells. The HuscFvs presumptively interact with the PIM2 at the ATP binding pocket and kinase active loop. They were as effective as small chemical drug inhibitor (AZD1208, which is an ATP competitive inhibitor of all PIM isoforms for ex vivo use) in inhibiting PIM kinase activity. The HuscFvs should be engineered into a cell-penetrating format and tested further towards clinical application as a novel and safe pan-anti-cancer therapeutics.
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Mortuza SM, Zheng W, Zhang C, Li Y, Pearce R, Zhang Y. Improving fragment-based ab initio protein structure assembly using low-accuracy contact-map predictions. Nat Commun 2021; 12:5011. [PMID: 34408149 PMCID: PMC8373938 DOI: 10.1038/s41467-021-25316-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/04/2021] [Indexed: 11/28/2022] Open
Abstract
Sequence-based contact prediction has shown considerable promise in assisting non-homologous structure modeling, but it often requires many homologous sequences and a sufficient number of correct contacts to achieve correct folds. Here, we developed a method, C-QUARK, that integrates multiple deep-learning and coevolution-based contact-maps to guide the replica-exchange Monte Carlo fragment assembly simulations. The method was tested on 247 non-redundant proteins, where C-QUARK could fold 75% of the cases with TM-scores (template-modeling scores) ≥0.5, which was 2.6 times more than that achieved by QUARK. For the 59 cases that had either low contact accuracy or few homologous sequences, C-QUARK correctly folded 6 times more proteins than other contact-based folding methods. C-QUARK was also tested on 64 free-modeling targets from the 13th CASP (critical assessment of protein structure prediction) experiment and had an average GDT_TS (global distance test) score that was 5% higher than the best CASP predictors. These data demonstrate, in a robust manner, the progress in modeling non-homologous protein structures using low-accuracy and sparse contact-map predictions.
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Affiliation(s)
- S M Mortuza
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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43
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Human Transbodies to Reverse Transcriptase Connection Subdomain of HIV-1 Gag-Pol Polyprotein Reduce Infectiousness of the Virus Progeny. Vaccines (Basel) 2021; 9:vaccines9080893. [PMID: 34452018 PMCID: PMC8402387 DOI: 10.3390/vaccines9080893] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022] Open
Abstract
HIV-1 progeny are released from infected cells as immature particles that are unable to infect new cells. Gag-Pol polyprotein dimerization via the reverse transcriptase connection domain (RTCDs) is pivotal for proper activation of the virus protease (PR protein) in an early event of the progeny virus maturation process. Thus, the RTCD is a potential therapeutic target for a broadly effective anti-HIV agent through impediment of virus maturation. In this study, human single-chain antibodies (HuscFvs) that bound to HIV-1 RTCD were generated using phage display technology. Computerized simulation guided the selection of the transformed Escherichia coli-derived HuscFvs that bound to the RTCD dimer interface. The selected HuscFvs were linked molecularly to human-derived-cell-penetrating peptide (CPP) to make them cell-penetrable (i.e., become transbodies). The CPP-HuscFvs/transbodies produced by a selected transformed E. coli clone were tested for anti-HIV-1 activity. CPP-HuscFvs of transformed E. coli clone 11 (CPP-HuscFv11) that presumptively bound at the RTCD dimer interface effectively reduced reverse transcriptase activity in the newly released virus progeny. Infectiousness of the progeny viruses obtained from CPP-HuscFv11-treated cells were reduced by a similar magnitude to those obtained from protease/reverse transcriptase inhibitor-treated cells, indicating anti-HIV-1 activity of the transbodies. The CPP-HuscFv11/transbodies to HIV-1 RTCD could be an alternative, anti-retroviral agent for long-term HIV-1 treatment.
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Zheng W, Li Y, Zhang C, Zhou X, Pearce R, Bell EW, Huang X, Zhang Y. Protein structure prediction using deep learning distance and hydrogen-bonding restraints in CASP14. Proteins 2021; 89:1734-1751. [PMID: 34331351 DOI: 10.1002/prot.26193] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/06/2021] [Accepted: 07/22/2021] [Indexed: 11/10/2022]
Abstract
In this article, we report 3D structure prediction results by two of our best server groups ("Zhang-Server" and "QUARK") in CASP14. These two servers were built based on the D-I-TASSER and D-QUARK algorithms, which integrated four newly developed components into the classical protein folding pipelines, I-TASSER and QUARK, respectively. The new components include: (a) a new multiple sequence alignment (MSA) collection tool, DeepMSA2, which is extended from the DeepMSA program; (b) a contact-based domain boundary prediction algorithm, FUpred, to detect protein domain boundaries; (c) a residual convolutional neural network-based method, DeepPotential, to predict multiple spatial restraints by co-evolutionary features derived from the MSA; and (d) optimized spatial restraint energy potentials to guide the structure assembly simulations. For 37 FM targets, the average TM-scores of the first models produced by D-I-TASSER and D-QUARK were 96% and 112% higher than those constructed by I-TASSER and QUARK, respectively. The data analysis indicates noticeable improvements produced by each of the four new components, especially for the newly added spatial restraints from DeepPotential and the well-tuned force field that combines spatial restraints, threading templates, and generic knowledge-based potentials. However, challenges still exist in the current pipelines. These include difficulties in modeling multi-domain proteins due to low accuracy in inter-domain distance prediction and modeling protein domains from oligomer complexes, as the co-evolutionary analysis cannot distinguish inter-chain and intra-chain distances. Specifically tuning the deep learning-based predictors for multi-domain targets and protein complexes may be helpful to address these issues.
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Affiliation(s)
- Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaogen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Eric W Bell
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
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Muñoz-Muñoz PLA, Mares-Alejandre RE, Meléndez-López SG, Ramos-Ibarra MA. Bioinformatic Analysis of Two TOR (Target of Rapamycin)-Like Proteins Encoded by Entamoeba histolytica Revealed Structural Similarities with Functional Homologs. Genes (Basel) 2021; 12:genes12081139. [PMID: 34440318 PMCID: PMC8391992 DOI: 10.3390/genes12081139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 01/04/2023] Open
Abstract
The target of rapamycin (TOR), also known as FKBP-rapamycin associated protein (FRAP), is a protein kinase belonging to the PIKK (phosphatidylinositol 3-kinase (PI3K)-related kinases) family. TOR kinases are involved in several signaling pathways that control cell growth and proliferation. Entamoeba histolytica, the protozoan parasite that causes human amoebiasis, contains two genes encoding TOR-like proteins: EhFRAP and EhTOR2. To assess their potential as drug targets to control the cell proliferation of E. histolytica, we studied the structural features of EhFRAP and EhTOR2 using a biocomputational approach. The overall results confirmed that both TOR amoebic homologs share structural similarities with functional TOR kinases, and show inherent abilities to form TORC complexes and participate in protein-protein interaction networks. To our knowledge, this study represents the first in silico characterization of the structure-function relationships of EhFRAP and EhTOR2.
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Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. CELL REPORTS METHODS 2021; 1:100014. [PMID: 34355210 PMCID: PMC8336924 DOI: 10.1016/j.crmeth.2021.100014] [Citation(s) in RCA: 227] [Impact Index Per Article: 75.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 05/03/2021] [Indexed: 12/23/2022]
Abstract
Structure prediction for proteins lacking homologous templates in the Protein Data Bank (PDB) remains a significant unsolved problem. We developed a protocol, C-I-TASSER, to integrate interresidue contact maps from deep neural-network learning with the cutting-edge I-TASSER fragment assembly simulations. Large-scale benchmark tests showed that C-I-TASSER can fold more than twice the number of non-homologous proteins than the I-TASSER, which does not use contacts. When applied to a folding experiment on 8,266 unsolved Pfam families, C-I-TASSER successfully folded 4,162 domain families, including 504 folds that are not found in the PDB. Furthermore, it created correct folds for 85% of proteins in the SARS-CoV-2 genome, despite the quick mutation rate of the virus and sparse sequence profiles. The results demonstrated the critical importance of coupling whole-genome and metagenome-based evolutionary information with optimal structure assembly simulations for solving the problem of non-homologous protein structure prediction.
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Affiliation(s)
- Wei Zheng
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eric W. Bell
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Balic Z, Misra S, Willard B, Reinhardt DP, Apte SS, Hubmacher D. Alternative splicing of the metalloprotease ADAMTS17 spacer regulates secretion and modulates autoproteolytic activity. FASEB J 2021; 35:e21310. [PMID: 33484187 DOI: 10.1096/fj.202001120rr] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/16/2022]
Abstract
ADAMTS proteases mediate biosynthesis and breakdown of secreted extracellular matrix (ECM) molecules in numerous physiological and disease processes. In addition to their catalytic domains, ADAMTS proteases contain ancillary domains, which mediate substrate recognition and ECM binding and confer distinctive properties and roles to individual ADAMTS proteases. Although alternative splicing can greatly expand the structural and functional diversity of ADAMTS proteases, it has been infrequently reported and functional consequences have been rarely investigated. Here, we characterize the structural and functional impact of alternative splicing of ADAMTS17, mutations in which cause Weill-Marchesani syndrome 4. Two novel ADAMTS17 splice variants, ADAMTS17A and ADAMTS17B, were investigated by structural modeling, mass spectrometry, and biochemical approaches. Our results identify a novel disulfide-bridged insertion in the ADAMTS17A spacer that originates from inclusion of a novel exon. This insertion results in differential autoproteolysis of ADAMTS17, and thus, predicts altered proteolytic activity against other substrates. The second variant, ADAMTS17B, results from an in-frame exon deletion and prevents ADAMTS17B secretion. Thus, alternative splicing of the ADAMTS spacer significantly regulates the physiologically relevant proteolytic activity of ADAMTS17, either by altering proteolytic specificity (ADAMTS17A) or by altering cellular localization (ADAMTS17B).
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Affiliation(s)
- Zerina Balic
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Belinda Willard
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | | | - Suneel S Apte
- Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Dirk Hubmacher
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Ding Y, Tang X, Du Y, Chen H, Yu D, Zhu B, Yuan B. Co-existence of Alport syndrome and C3 glomerulonephritis in a proband with family history. Eur J Med Res 2021; 26:71. [PMID: 34238373 PMCID: PMC8265006 DOI: 10.1186/s40001-021-00543-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 06/28/2021] [Indexed: 01/07/2023] Open
Abstract
Background Alport syndrome and C3 glomerulonephritis (C3GN) are rare kidney diseases, frequently responsible for familial haematuria, proteinuria, and renal impairment. With the rapid development of molecular genetic testing, Alport syndrome causes have been restricted mostly to variants in the COL4A5 or COL4A3/COL4A4 genes. Moreover, a broad range of genetic contributors in the complement and complement-regulating proteins are definitely implicated in the pathogenesis of C3GN. Methods We sought a family with persistent microscopic haematuria associated with renal failure. Clinicopathologic and follow-up data were obtained, and molecular genetic testing was used to screen for pathogenic variants. Results We describe a three-generation family with Alport syndrome showing a dominant maternal inheritance. Notably, renal biopsy showed the concurrent histological evidence of C3GN in the proband harbouring an uncommon heterozygous variation in CFHR5, c.508G > A. The alteration leads to replacement of a highly conserved residue at position 170 of the β-strand subunit of CFHR5 (p.Val170Met). In silico analysis showed that the variation was predicted to deregulate complement activation by altering the structural properties and enhancing C3b binding capacity to compete with Complement Factor H (CFH), which was in line with experimental data previously published. Conclusions The comorbidity findings between Alport syndrome and C3GN indicate an underlying overlap and require further study. Supplementary Information The online version contains supplementary material available at 10.1186/s40001-021-00543-5.
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Affiliation(s)
- Yin Ding
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Xuanli Tang
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Yuanyuan Du
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Hongyu Chen
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Dongrong Yu
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Bin Zhu
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China
| | - Bohan Yuan
- Department of Nephrology (Key Laboratory of Management of Kidney Disease in Zhejiang Province), Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Tiyuchang Road 453, Hangzhou, 310007, People's Republic of China.
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Pearce R, Zhang Y. Toward the solution of the protein structure prediction problem. J Biol Chem 2021; 297:100870. [PMID: 34119522 PMCID: PMC8254035 DOI: 10.1016/j.jbc.2021.100870] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/20/2022] Open
Abstract
Since Anfinsen demonstrated that the information encoded in a protein's amino acid sequence determines its structure in 1973, solving the protein structure prediction problem has been the Holy Grail of structural biology. The goal of protein structure prediction approaches is to utilize computational modeling to determine the spatial location of every atom in a protein molecule starting from only its amino acid sequence. Depending on whether homologous structures can be found in the Protein Data Bank (PDB), structure prediction methods have been historically categorized as template-based modeling (TBM) or template-free modeling (FM) approaches. Until recently, TBM has been the most reliable approach to predicting protein structures, and in the absence of reliable templates, the modeling accuracy sharply declines. Nevertheless, the results of the most recent community-wide assessment of protein structure prediction experiment (CASP14) have demonstrated that the protein structure prediction problem can be largely solved through the use of end-to-end deep machine learning techniques, where correct folds could be built for nearly all single-domain proteins without using the PDB templates. Critically, the model quality exhibited little correlation with the quality of available template structures, as well as the number of sequence homologs detected for a given target protein. Thus, the implementation of deep-learning techniques has essentially broken through the 50-year-old modeling border between TBM and FM approaches and has made the success of high-resolution structure prediction significantly less dependent on template availability in the PDB library.
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Affiliation(s)
- Robin Pearce
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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Liu Y, Zhu F, Shen Z, Moural TW, Liu L, Li Z, Liu X, Xu H. Glutaredoxins and thioredoxin peroxidase involved in defense of emamectin benzoate induced oxidative stress in Grapholita molesta. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 176:104881. [PMID: 34119223 DOI: 10.1016/j.pestbp.2021.104881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/08/2021] [Accepted: 05/19/2021] [Indexed: 06/12/2023]
Abstract
Glutaredoxins (Grxs) and thioredoxin peroxidases (Tpxs) are major antioxidant enzyme families involved in regulating cellular redox homeostasis and in defense of enhanced oxidative stress through scavenging reactive oxygen species (ROS). However, the functions of these enzymes have not been reported in the oriental fruit moth, Grapholita molesta (Busck), a worldwide pest of stone and pome fruits. Here, we identified four new antioxidant genes, GmGrx, GmGrx3, GmGrx5, and GmTpx which were induced by exposure with emamectin benzoate, a commonly used biopesticide for G. molesta control. Other environmental factors (low and high temperatures, Escherichia coli and Metarhizium anisopliae) also significantly induced the expression of these genes. After GmGrx or GmTpx silenced by RNA interference (RNAi), the percentage of larval survival to emamectin benzoate were significantly decreased, demonstrating that GmGrx and GmTpx are involved in protecting G. molesta from stresses induced by emamectin benzoate. Furthermore, silenced GmGrx, GmGrx3, GmGrx5, or GmTpx significantly enhanced the enzymatic activities of superoxide dismutase (SOD) (except GmTpx) and peroxidase (POD), as well as the contents of hydrogen peroxide and metabolites ascorbate. Taken together, our results suggest that GmGrx, GmGrx3, GmGrx5, and GmTpx may play critical roles in antioxidant defense. Specially, GmGrx and GmTpx contribute to the defense of oxidative damage induced by exposure to emamectin benzoate through scavenging excessive ROS in G. molesta. Our findings provided a theoretical basis for understanding functions of insect glutaredoxin and peroxidase systems.
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Affiliation(s)
- Yanjun Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China; Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Fang Zhu
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Zhongjian Shen
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Timothy W Moural
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Lining Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhen Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaoxia Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Huanli Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China.
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