101
|
Carabias A, Camara-Wilpert S, Mestre MR, Lopéz-Méndez B, Hendriks IA, Zhao R, Pape T, Fuglsang A, Luk SHC, Nielsen ML, Pinilla-Redondo R, Montoya G. Retron-Eco1 assembles NAD +-hydrolyzing filaments that provide immunity against bacteriophages. Mol Cell 2024; 84:2185-2202.e12. [PMID: 38788717 DOI: 10.1016/j.molcel.2024.05.001] [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: 09/26/2023] [Revised: 03/15/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD+ during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD+ hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.
Collapse
Affiliation(s)
- Arturo Carabias
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| | - Sarah Camara-Wilpert
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mario Rodríguez Mestre
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Blanca Lopéz-Méndez
- Protein Purification and Characterization Facility, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ruiliang Zhao
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Sean Hoi-Ching Luk
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Michael L Nielsen
- Proteomics Department, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Rafael Pinilla-Redondo
- Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| |
Collapse
|
102
|
Shrestha S, Taujale R, Katiyar S, Kannan N. Multi-omics reveals new links between Fructosamine-3-Kinase (FN3K) and core metabolic pathways. NPJ Syst Biol Appl 2024; 10:64. [PMID: 38830903 PMCID: PMC11148063 DOI: 10.1038/s41540-024-00390-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024] Open
Abstract
Fructosamine-3-kinases (FN3Ks) are a conserved family of repair enzymes that phosphorylate reactive sugars attached to lysine residues in peptides and proteins. Although FN3Ks are present across the Tree of Life and share detectable sequence similarity to eukaryotic protein kinases, the biological processes regulated by these kinases are largely unknown. To address this knowledge gap, we leveraged the FN3K CRISPR Knock-Out (KO) HepG2 cell line alongside an integrative multi-omics study combining transcriptomics, metabolomics, and interactomics to place these enzymes in a pathway context. The integrative analyses revealed the enrichment of pathways related to oxidative stress response, lipid biosynthesis (cholesterol and fatty acids), and carbon and co-factor metabolism. Moreover, enrichment of nicotinamide adenine dinucleotide (NAD) binding proteins and localization of human FN3K (HsFN3K) to mitochondria suggests potential links between FN3K and NAD-mediated energy metabolism and redox balance. We report specific binding of HsFN3K to NAD compounds in a metal and concentration-dependent manner and provide insight into their binding mode using modeling and experimental site-directed mutagenesis. Our studies provide a framework for targeting these understudied kinases in diabetic complications and metabolic disorders where redox balance and NAD-dependent metabolic processes are altered.
Collapse
Affiliation(s)
- Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Samiksha Katiyar
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
| |
Collapse
|
103
|
Schmitz M, Ballestin JB, Liang J, Tomas F, Freist L, Voigt K, Di Ventura B, Öztürk MA. Int&in: A machine learning-based web server for active split site identification in inteins. Protein Sci 2024; 33:e4985. [PMID: 38717278 PMCID: PMC11078102 DOI: 10.1002/pro.4985] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/06/2024] [Accepted: 03/24/2024] [Indexed: 05/12/2024]
Abstract
Inteins are proteins that excise themselves out of host proteins and ligate the flanking polypeptides in an auto-catalytic process called protein splicing. In nature, inteins are either contiguous or split. In the case of split inteins, the two fragments must first form a complex for the splicing to occur. Contiguous inteins have previously been artificially split in two fragments because split inteins allow for distinct applications than contiguous ones. Even naturally split inteins have been split at unnatural split sites to obtain fragments with reduced affinity for one another, which are useful to create conditional inteins or to study protein-protein interactions. So far, split sites in inteins have been heuristically identified. We developed Int&in, a web server freely available for academic research (https://intein.biologie.uni-freiburg.de) that runs a machine learning model using logistic regression to predict active and inactive split sites in inteins with high accuracy. The model was trained on a dataset of 126 split sites generated using the gp41-1, Npu DnaE and CL inteins and validated using 97 split sites extracted from the literature. Despite the limited data size, the model, which uses various protein structural features, as well as sequence conservation information, achieves an accuracy of 0.79 and 0.78 for the training and testing sets, respectively. We envision Int&in will facilitate the engineering of novel split inteins for applications in synthetic and cell biology.
Collapse
Affiliation(s)
- Mirko Schmitz
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- 4HF Biotec GmbHFreiburgGermany
| | - Jara Ballestin Ballestin
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Bioprocess Innovation Unit, ViraTherapeutics GmbHRumAustria
| | - Junsheng Liang
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Franziska Tomas
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
- Department of Molecular Life SciencesUniversity of ZurichZurichSwitzerland
| | - Leon Freist
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Karsten Voigt
- Institute of Biology III, University of FreiburgFreiburgGermany
| | - Barbara Di Ventura
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| | - Mehmet Ali Öztürk
- BIOSS and CIBSS Research Signalling Centers, University of FreiburgFreiburgGermany
- Institute of Biology II, University of FreiburgFreiburgGermany
| |
Collapse
|
104
|
Javid M, Shahverdi AR, Ghasemi A, Moosavi-Movahedi AA, Ebrahim-Habibi A, Sepehrizadeh Z. Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics. Protein J 2024; 43:522-543. [PMID: 38662183 DOI: 10.1007/s10930-024-10195-z] [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] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
Collapse
Affiliation(s)
- Mehri Javid
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azadeh Ebrahim-Habibi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
105
|
Shankar SS, Banarjee R, Jathar SM, Rajesh S, Ramasamy S, Kulkarni MJ. De novo structure prediction of meteorin and meteorin-like protein for identification of domains, functional receptor binding regions, and their high-risk missense variants. J Biomol Struct Dyn 2024; 42:4522-4536. [PMID: 37288801 DOI: 10.1080/07391102.2023.2220804] [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: 03/07/2023] [Accepted: 05/29/2023] [Indexed: 06/09/2023]
Abstract
Meteorin (Metrn) and Meteorin-like (Metrnl) are homologous secreted proteins involved in neural development and metabolic regulation. In this study, we have performed de novo structure prediction and analysis of both Metrn and Metrnl using Alphafold2 (AF2) and RoseTTAfold (RF). Based on the domain and structural homology analysis of the predicted structures, we have identified that these proteins are composed of two functional domains, a CUB domain and an NTR domain, connected by a hinge/loop region. We have identified the receptor binding regions of Metrn and Metrnl using the machine-learning tools ScanNet and Masif. These were further validated by docking Metrnl with its reported KIT receptor, thus establishing the role of each domain in the receptor interaction. Also, we have studied the effect of non-synonymous SNPs on the structure and function of these proteins using an array of bioinformatics tools and selected 16 missense variants in Metrn and 10 in Metrnl that can affect the protein stability. This is the first study to comprehensively characterize the functional domains of Metrn and Metrnl at their structural level and identify the functional domains, and protein binding regions. This study also highlights the interaction mechanism of the KIT receptor and Metrnl. The predicted deleterious SNPs will allow further understanding of the role of these variants in modulating the plasma levels of these proteins in disease conditions such as diabetes.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- S Shiva Shankar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Reema Banarjee
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Swaraj M Jathar
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - S Rajesh
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Sureshkumar Ramasamy
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
| | - Mahesh J Kulkarni
- Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
106
|
Boesch DJ, Singla A, Han Y, Kramer DA, Liu Q, Suzuki K, Juneja P, Zhao X, Long X, Medlyn MJ, Billadeau DD, Chen Z, Chen B, Burstein E. Structural organization of the retriever-CCC endosomal recycling complex. Nat Struct Mol Biol 2024; 31:910-924. [PMID: 38062209 PMCID: PMC11260360 DOI: 10.1038/s41594-023-01184-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/17/2023] [Indexed: 12/19/2023]
Abstract
The recycling of membrane proteins from endosomes to the cell surface is vital for cell signaling and survival. Retriever, a trimeric complex of vacuolar protein-sorting-associated protein (VPS)35L, VPS26C and VPS29, together with the CCC complex comprising coiled-coil domain-containing (CCDC)22, CCDC93 and copper metabolism domain-containing (COMMD) proteins, plays a crucial role in this process. The precise mechanisms underlying retriever assembly and its interaction with CCC have remained elusive. Here, we present a high-resolution structure of retriever in humans determined using cryogenic electron microscopy. The structure reveals a unique assembly mechanism, distinguishing it from its remotely related paralog retromer. By combining AlphaFold predictions and biochemical, cellular and proteomic analyses, we further elucidate the structural organization of the entire retriever-CCC complex across evolution and uncover how cancer-associated mutations in humans disrupt complex formation and impair membrane protein homeostasis. These findings provide a fundamental framework for understanding the biological and pathological implications associated with retriever-CCC-mediated endosomal recycling.
Collapse
Affiliation(s)
- Daniel J Boesch
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Amika Singla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yan Han
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel A Kramer
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Qi Liu
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Puneet Juneja
- Cryo-EM Facility, Office of Biotechnology, Iowa State University, Ames, IA, USA
| | - Xuefeng Zhao
- Information Technology Services, Iowa State University, Ames, IA, USA
| | - Xin Long
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael J Medlyn
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Daniel D Billadeau
- Division of Oncology Research, College of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhe Chen
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Baoyu Chen
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| | - Ezra Burstein
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| |
Collapse
|
107
|
Weeramange C, Menjivar C, O'Neil PT, El Qaidi S, Harrison KS, Meinhardt S, Bird CL, Sreenivasan S, Hardwidge PR, Fenton AW, Hefty PS, Bose JL, Swint-Kruse L. Fructose-1-kinase has pleiotropic roles in Escherichia coli. J Biol Chem 2024; 300:107352. [PMID: 38723750 PMCID: PMC11157272 DOI: 10.1016/j.jbc.2024.107352] [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: 01/23/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/21/2024] Open
Abstract
In Escherichia coli, the master transcription regulator catabolite repressor activator (Cra) regulates >100 genes in central metabolism. Cra binding to DNA is allosterically regulated by binding to fructose-1-phosphate (F-1-P), but the only documented source of F-1-P is from the concurrent import and phosphorylation of exogenous fructose. Thus, many have proposed that fructose-1,6-bisphosphate (F-1,6-BP) is also a physiological regulatory ligand. However, the role of F-1,6-BP has been widely debated. Here, we report that the E. coli enzyme fructose-1-kinase (FruK) can carry out its "reverse" reaction under physiological substrate concentrations to generate F-1-P from F-1,6-BP. We further show that FruK directly binds Cra with nanomolar affinity and forms higher order, heterocomplexes. Growth assays with a ΔfruK strain and fruK complementation show that FruK has a broader role in metabolism than fructose catabolism. Since fruK itself is repressed by Cra, these newly-reported events add layers to the dynamic regulation of E. coli's central metabolism that occur in response to changing nutrients. These findings might have wide-spread relevance to other γ-proteobacteria, which conserve both Cra and FruK.
Collapse
Affiliation(s)
- Chamitha Weeramange
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cindy Menjivar
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Pierce T O'Neil
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Kelly S Harrison
- The Department of Molecular Biosciences, The University of Kansas - Lawrence, Lawrence, Kansas, USA
| | - Sarah Meinhardt
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Cole L Bird
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Shwetha Sreenivasan
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Aron W Fenton
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - P Scott Hefty
- College of Veterinary Medicine, Kansas State University, Manhattan, Kansas, USA
| | - Jeffrey L Bose
- The Department of Microbiology, Molecular Genetics and Immunology, The University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Liskin Swint-Kruse
- The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas, USA.
| |
Collapse
|
108
|
Mozibullah M, Eslampanah Seyedi H, Khatun M, Solayman M. Identification and analysis of oncogenic non-synonymous single nucleotide polymorphisms in the human NRAS gene: An exclusive in silico study. J Genet Eng Biotechnol 2024; 22:100378. [PMID: 38797553 PMCID: PMC11087716 DOI: 10.1016/j.jgeb.2024.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND N-ras protein is encoded by the NRAS gene and operates as GDP-GTP-controlled on/off switching. N-ras interacts with cellular signaling networks that regulate various cellular activities including cell proliferation and survival. The nonsynonymous single nucleotide polymorphism (nsSNPs)-mediated alteration can substantially disrupt the structure and activity of the corresponding protein. N-ras has been reported to be associated with numerous diseases including cancers due to the nsSNPs. A comprehensive study on the NRAS gene to unveil the potentially damaging and oncogenic nsSNPs is yet to be accomplished. Hence, this extensive in silico study is intended to identify the disease-associated, specifically oncogenic nsSNPs of the NRAS gene. RESULTS Out of 140 missense variants, 7 nsSNPs (I55R, G60E, G60R, Y64D, L79F, D119G, and V152F) were identified to be damaging utilizing 10 computational tools that works based on different algorithms with high accuracy. Among those, G60E, G60R, and D119G variants were further filtered considering their location in the highly conserved region and later identified as oncogenic variants. Interestingly, G60E and G60R variants were revealed to be particularly associated with lung adenocarcinoma, rhabdomyosarcoma, and prostate adenocarcinoma. Therefore, D119G could be subjected to detailed investigation for identifying its association with specific cancer. CONCLUSION This in silico study identified the deleterious and oncogenic missense variants of the human NRAS gene that could be utilized for designing further experimental investigation. The outcomes of this study would be worthwhile in future research for developing personalized medicine.
Collapse
Affiliation(s)
- Md Mozibullah
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | | | - Marina Khatun
- Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh
| | - Md Solayman
- Department of Biochemistry and Molecular Biology, Primeasia University, Bangladesh.
| |
Collapse
|
109
|
Aktaş E, Özdemir Özgentürk N. A comprehensive examination of ACE2 receptor and prediction of spike glycoprotein and ACE2 interaction based on in silico analysis of ACE2 receptor. J Biomol Struct Dyn 2024; 42:4412-4428. [PMID: 37349943 DOI: 10.1080/07391102.2023.2220814] [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: 02/12/2023] [Accepted: 05/28/2023] [Indexed: 06/24/2023]
Abstract
The ACE2 receptor plays a vital role not only in the SARS-CoV-induced epidemic but also in various other diseases, including cardiovascular diseases and ARDS. While studies have explored the interactions between ACE2 and SARS-CoV proteins, comprehensive research utilizing bioinformatic tools on the ACE2 protein has been lacking. The one aim of present study was to extensively analyze the regions of the ACE2 protein. After utilizing all bioinformatics tools especially G104 and L108 regions on ACE2 were come forward. The results of our analysis revealed that possible mutations or deletions in the G104 and L108 regions play a critical role in both the biological functioning and the determination of the chemical-physical properties of ACE2. Additionally, these regions were found to be more susceptible to mutations or deletions compared to other regions of the ACE2 protein. Notably, the randomly selected peptide, LQQNGSSVLS (100-109), which includes G104 and L108, exhibited a crucial role in binding the RBD of the spike protein, as supported by docking scores. Furthermore, both MDs and iMODs results provided evidence that G104 and L108 influence the dynamics of ACE2-spike complexes. This study is expected to offer a new perspective on the ACE2-SARS-CoV interaction and other research areas where ACE2 plays a significant role, such as biotechnology (protein engineering, enzyme optimization), medicine (RAS, pulmonary and cardiac diseases), and basic research (structural motifs, stabilizing protein folds, or facilitating important inter molecular contacts, protein's proper structure and function).Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Emre Aktaş
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| | - Nehir Özdemir Özgentürk
- Faculty of Art and Science, Molecular Biology and Genetics, Yıldız Technical University, Istanbul, Turkey
| |
Collapse
|
110
|
Jayaraman M, Kumar R, Panchalingam S, Jeyaraman J. Mechanistic insights into the conformational changes and alterations in residual communications due to the mutations in the pncA Gene of Mycobacterium tuberculosis: A computational perspective for effective therapeutic solutions. Comput Biol Chem 2024; 110:108065. [PMID: 38615420 DOI: 10.1016/j.compbiolchem.2024.108065] [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: 12/04/2023] [Revised: 03/11/2024] [Accepted: 04/01/2024] [Indexed: 04/16/2024]
Abstract
Due to its emerging resistance to first-line anti-TB medications, tuberculosis (TB) is one of the most contagious illness in the world. According to reports, the effectiveness of treating TB is severely impacted by drug resistance, notably resistance caused by mutations in the pncA gene-encoded pyrazinamidase (PZase) to the front-line drug pyrazinamide (PZA). The present study focused on investigating the resistance mechanism caused by the mutations D12N, T47A, and H137R to better understand the structural and molecular events responsible for the resistance acquired by the pncA gene of Mycobacterium tuberculosis (MTB) at the structural level. Bioinformatics analysis predicted that all three mutations were deleterious and located near the active centre of the pncA, affecting its functional activity. Furthermore, molecular dynamics simulation (MDS) results established that mutations significantly reduced the structural stability and caused the rearrangement of FE2+ in the active centre of pncA. Moreover, essential dynamics analysis, including principal component analysis (PCA) and free energy landscape (FEL), concluded variations in the protein motion and decreased conformational space in the mutants. Additionally, the mutations potentially impacted the network topologies and altered the residual communications in the network. The complex simulation study results established the significant movement of the flap region from the active centre of mutant complexes, further supporting the flap region's significance in developing resistance to the PZA drug. This study advances our knowledge of the primary cause of the mechanism of PZA resistance and the structural dynamics of pncA mutants, which will help us to design new and potent chemical scaffolds to treat drug-resistant TB (DR-TB).
Collapse
Affiliation(s)
- Manikandan Jayaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India
| | - Rajalakshmi Kumar
- Mahatma Gandhi Medical Advanced Research Institute, Sri Balaji Vidyapeeth (Deemed to be University), Pillayarkuppam, Puducherry 607402, India
| | - Santhiya Panchalingam
- Centre for Ocean Research, Sathyabama Institute of Science and Technology (Deemed to be University), Chennai, Tamil Nadu 600119, India
| | - Jeyakanthan Jeyaraman
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu 630004, India.
| |
Collapse
|
111
|
Zakharova K, Liu M, Greenwald JR, Caldwell BC, Qi Z, Wysocki VH, Bell CE. Structural Basis for the Interaction of Redβ Single-Strand Annealing Protein with Escherichia coli Single-Stranded DNA-Binding Protein. J Mol Biol 2024; 436:168590. [PMID: 38663547 DOI: 10.1016/j.jmb.2024.168590] [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: 02/22/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024]
Abstract
Redβ is a protein from bacteriophage λ that binds to single-stranded DNA (ssDNA) to promote the annealing of complementary strands. Together with λ-exonuclease (λ-exo), Redβ is part of a two-component DNA recombination system involved in multiple aspects of genome maintenance. The proteins have been exploited in powerful methods for bacterial genome engineering in which Redβ can anneal an electroporated oligonucleotide to a complementary target site at the lagging strand of a replication fork. Successful annealing in vivo requires the interaction of Redβ with E. coli single-stranded DNA-binding protein (SSB), which coats the ssDNA at the lagging strand to coordinate access of numerous replication proteins. Previous mutational analysis revealed that the interaction between Redβ and SSB involves the C-terminal domain (CTD) of Redβ and the C-terminal tail of SSB (SSB-Ct), the site for binding of numerous host proteins. Here, we have determined the x-ray crystal structure of Redβ CTD in complex with a peptide corresponding to the last nine residues of SSB (MDFDDDIPF). Formation of the complex is predominantly mediated by hydrophobic interactions between two phenylalanine side chains of SSB (Phe-171 and Phe-177) and an apolar groove on the CTD, combined with electrostatic interactions between the C-terminal carboxylate of SSB and Lys-214 of the CTD. Mutation of any of these residues to alanine significantly disrupts the interaction of full-length Redβ and SSB proteins. Structural knowledge of this interaction will help to expand the utility of Redβ-mediated recombination to a wider range of bacterial hosts for applications in synthetic biology.
Collapse
Affiliation(s)
- Katerina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Mengqi Liu
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Jacelyn R Greenwald
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Brian C Caldwell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA
| | - Zihao Qi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Vicki H Wysocki
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Charles E Bell
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, USA; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
112
|
Banerjee A, Mathew S, Naqvi MM, Yilmaz SZ, Zacharopoulou M, Doruker P, Kumita JR, Yang SH, Gur M, Itzhaki LS, Gordon R, Bahar I. Influence of point mutations on PR65 conformational adaptability: Insights from molecular simulations and nanoaperture optical tweezers. SCIENCE ADVANCES 2024; 10:eadn2208. [PMID: 38820156 PMCID: PMC11141623 DOI: 10.1126/sciadv.adn2208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 04/29/2024] [Indexed: 06/02/2024]
Abstract
PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A) and an archetypal tandem repeat protein. Its conformational mechanics plays a crucial role in PP2A function by opening/closing substrate binding/catalysis interface. Using in silico saturation mutagenesis, we identified PR65 "hinge" residues whose substitutions could alter its conformational adaptability and thereby PP2A function, and selected six mutations that were verified to be expressed and soluble. Molecular simulations and nanoaperture optical tweezers revealed consistent results on the specific effects of the mutations on the structure and dynamics of PR65. Two mutants observed in simulations to stabilize extended/open conformations exhibited higher corner frequencies and lower translational scattering in experiments, indicating a shift toward extended conformations, whereas another displayed the opposite features, confirmed by both simulations and experiments. The study highlights the power of single-molecule nanoaperture-based tweezers integrated with in silico approaches for exploring the effect of mutations on protein structure and dynamics.
Collapse
Affiliation(s)
- Anupam Banerjee
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Samuel Mathew
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Mohsin M. Naqvi
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Sema Z. Yilmaz
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
| | - Maria Zacharopoulou
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Janet R. Kumita
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Mert Gur
- Department of Mechanical Engineering, Istanbul Technical University, 34437 Istanbul, Turkey
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Laura S. Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria V8P 5C2, Canada
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| |
Collapse
|
113
|
De Oliveira DH, Gowda V, Sparrman T, Gustafsson L, Sanches Pires R, Riekel C, Barth A, Lendel C, Hedhammar M. Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers. Nat Commun 2024; 15:4670. [PMID: 38821983 PMCID: PMC11143275 DOI: 10.1038/s41467-024-49111-5] [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: 10/26/2023] [Accepted: 05/24/2024] [Indexed: 06/02/2024] Open
Abstract
The major ampullate Spidroin 1 (MaSp1) is the main protein of the dragline spider silk. The C-terminal (CT) domain of MaSp1 is crucial for the self-assembly into fibers but the details of how it contributes to the fiber formation remain unsolved. Here we exploit the fact that the CT domain can form silk-like fibers by itself to gain knowledge about this transition. Structural investigations of fibers from recombinantly produced CT domain from E. australis MaSp1 reveal an α-helix to β-sheet transition upon fiber formation and highlight the helix No4 segment as most likely to initiate the structural conversion. This prediction is corroborated by the finding that a peptide corresponding to helix No4 has the ability of pH-induced conversion into β-sheets and self-assembly into nanofibrils. Our results provide structural information about the CT domain in fiber form and clues about its role in triggering the structural conversion of spidroins during fiber assembly.
Collapse
Affiliation(s)
- Danilo Hirabae De Oliveira
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Vasantha Gowda
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Linnea Gustafsson
- Spiber Technologies AB, Roslagstullsbacken 15, 114 21, Stockholm, Sweden
| | | | - Christian Riekel
- European Synchrotron Radiation Facility, B.P. 220, F-38043, Grenoble Cedex, France
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christofer Lendel
- Department of Chemistry, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - My Hedhammar
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden.
| |
Collapse
|
114
|
Mogire RM, Miruka SA, Juma DW, McNamara CW, Andagalu B, Burrows JN, Chenu E, Duffy J, Ogutu BR, Akala HM. Protein target similarity is positive predictor of in vitro antipathogenic activity: a drug repurposing strategy for Plasmodium falciparum. J Cheminform 2024; 16:63. [PMID: 38831351 PMCID: PMC11145868 DOI: 10.1186/s13321-024-00856-7] [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: 11/26/2023] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Drug discovery is an intricate and costly process. Repurposing existing drugs and active compounds offers a viable pathway to develop new therapies for various diseases. By leveraging publicly available biomedical information, it is possible to predict compounds' activity and identify their potential targets across diverse organisms. In this study, we aimed to assess the antiplasmodial activity of compounds from the Repurposing, Focused Rescue, and Accelerated Medchem (ReFRAME) library using in vitro and bioinformatics approaches. We assessed the in vitro antiplasmodial activity of the compounds using blood-stage and liver-stage drug susceptibility assays. We used protein sequences of known targets of the ReFRAME compounds with high antiplasmodial activity (EC50 < 10 uM) to conduct a protein-pairwise search to identify similar Plasmodium falciparum 3D7 proteins (from PlasmoDB) using NCBI protein BLAST. We further assessed the association between the compounds' in vitro antiplasmodial activity and level of similarity between their known and predicted P. falciparum target proteins using simple linear regression analyses. BLAST analyses revealed 735 P. falciparum proteins that were similar to the 226 known protein targets associated with the ReFRAME compounds. Antiplasmodial activity of the compounds was positively associated with the degree of similarity between the compounds' known targets and predicted P. falciparum protein targets (percentage identity, E value, and bit score), the number of the predicted P. falciparum targets, and their respective mutagenesis index and fitness scores (R2 between 0.066 and 0.92, P < 0.05). Compounds predicted to target essential P. falciparum proteins or those with a druggability index of 1 showed the highest antiplasmodial activity.
Collapse
Affiliation(s)
- Reagan M Mogire
- Center for Research On Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
| | - Silviane A Miruka
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Dennis W Juma
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya
| | - Case W McNamara
- Calibr-Skaggs Institute for Innovative Medicine, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Ben Andagalu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
| | | | - Elodie Chenu
- Medicines for Malaria Venture, Geneva, Switzerland
| | - James Duffy
- Medicines for Malaria Venture, Geneva, Switzerland
| | - Bernhards R Ogutu
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya
| | - Hoseah M Akala
- Center for Clinical Research, Kenya Medical Research Institute (KEMRI), P. O. Box 54, Kisumu, 40100, Kenya.
- Center for Research in Therapeutic Sciences, Strathmore University, P.O. Box 59857-00200, Nairobi, Kenya.
- Department of Emerging Infections Diseases (DEID), Walter Reed Army Institute of Research - Africa, Kisumu, Kenya.
| |
Collapse
|
115
|
Vetriselvan Y, Manoharan A, Murugan M, Jayakumar S, Govindasamy C, Ravikumar S. In Silico Characterization of Pathogenic Homeodomain Missense Mutations in the PITX2 Gene. Biochem Genet 2024:10.1007/s10528-024-10836-z. [PMID: 38802693 DOI: 10.1007/s10528-024-10836-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Paired homologous domain transcription factor 2 (PITX2) is critically involved in ocular and cardiac development. Mutations in PITX2 are consistently reported in association with Axenfeld-Rieger syndrome, an autosomal dominant genetic disorder and atrial fibrillation, a common cardiac arrhythmia. In this study, we have mined missense mutations in PITX2 gene from NCBI-dbSNP and Ensembl databases, evaluated the pathogenicity of the missense variants in the homeodomain and C-terminal region using five in silico prediction tools SIFT, PolyPhen2, GERP, Mutation Assessor and CADD. Fifteen homeodomain mutations G42V, G42R, R45W, S49Y, R53W, E53D, E55V, R62H, P65S, R69H, G75R, R84G, R86K, R87W, R91P were found to be highly pathogenic by both SIFT, PolyPhen2 were further functionally characterized using I-Mutant 2.0, Consurf, MutPred and Project Hope. The findings of the study can be used for prioritizing mutations in the context of genetic studies.
Collapse
Affiliation(s)
- Yogesh Vetriselvan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Aarthi Manoharan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Manoranjani Murugan
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Swetha Jayakumar
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India
| | - Chandramohan Govindasamy
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, P.O. Box 10219, 11433, Riyadh, Saudi Arabia
| | - Sambandam Ravikumar
- Department of Medical Biotechnology, Aarupadai Veedu Medical College and Hospital, Vinayaka Mission's Research Foundation (DU), Kirumampakkam, Puducherry, 607403, India.
| |
Collapse
|
116
|
Da Conceição LMA, Cabral LM, Pereira GRC, De Mesquita JF. An In Silico Analysis of Genetic Variants and Structural Modeling of the Human Frataxin Protein in Friedreich's Ataxia. Int J Mol Sci 2024; 25:5796. [PMID: 38891993 PMCID: PMC11172458 DOI: 10.3390/ijms25115796] [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: 04/17/2024] [Revised: 05/15/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
Friedreich's Ataxia (FRDA) stands out as the most prevalent form of hereditary ataxias, marked by progressive movement ataxia, loss of vibratory sensitivity, and skeletal deformities, severely affecting daily functioning. To date, the only medication available for treating FRDA is Omaveloxolone (Skyclarys®), recently approved by the FDA. Missense mutations within the human frataxin (FXN) gene, responsible for intracellular iron homeostasis regulation, are linked to FRDA development. These mutations induce FXN dysfunction, fostering mitochondrial iron accumulation and heightened oxidative stress, ultimately triggering neuronal cell death pathways. This study amalgamated 226 FXN genetic variants from the literature and database searches, with only 18 previously characterized. Predictive analyses revealed a notable prevalence of detrimental and destabilizing predictions for FXN mutations, predominantly impacting conserved residues crucial for protein function. Additionally, an accurate, comprehensive three-dimensional model of human FXN was constructed, serving as the basis for generating genetic variants I154F and W155R. These variants, selected for their severe clinical implications, underwent molecular dynamics (MD) simulations, unveiling flexibility and essential dynamic alterations in their N-terminal segments, encompassing FXN42, FXN56, and FXN78 domains pivotal for protein maturation. Thus, our findings indicate potential interaction profile disturbances in the FXN42, FXN56, and FXN78 domains induced by I154F and W155R mutations, aligning with the existing literature.
Collapse
Affiliation(s)
- Loiane Mendonça Abrantes Da Conceição
- Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Avenida Pasteur, 296, Urca, Rio de Janeiro 22290-250, Brazil (J.F.D.M.)
| | - Lucio Mendes Cabral
- Pharmaceutical Industrial Technology Laboratory, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
| | - Gabriel Rodrigues Coutinho Pereira
- Pharmaceutical Industrial Technology Laboratory, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
- Laboratory of Molecular Modeling & QSAR, Federal University of Rio de Janeiro (UFRJ), Avenida Carlos Chagas Filho, 373, Cidade Universitária, Rio de Janeiro 21941-590, Brazil
| | - Joelma Freire De Mesquita
- Laboratory of Bioinformatics and Computational Biology, Federal University of the State of Rio de Janeiro (UNIRIO), Avenida Pasteur, 296, Urca, Rio de Janeiro 22290-250, Brazil (J.F.D.M.)
| |
Collapse
|
117
|
Hameleers L, Pijning T, Gray BB, Fauré R, Jurak E. Novel β-galactosidase activity and first crystal structure of Glycoside Hydrolase family 154. N Biotechnol 2024; 80:1-11. [PMID: 38163476 DOI: 10.1016/j.nbt.2023.12.011] [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: 07/31/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-β-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-β-Gal showed exo-β-galactosidase activity with regiopreference for hydrolyzing β-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides. In addition, we determined the high resolution crystal structure of BD-β-Gal, thus providing the first structural characterization of a GH154 enzyme. Surprisingly, this revealed an (α/α)6 topology, which has not been observed before for β-galactosidases. BD-β-Gal displayed low structural homology with characterized CAZymes, but conservation analysis suggested that the active site was located in a central cavity, with conserved E73, R252, and D253 as putative catalytic residues. Interestingly, BD-β-Gal has a tetrameric structure and a flexible loop from a neighboring protomer may contribute to its reaction specificity. Finally, we showed that the founding member of GH154, BT3677 from Bacteroides thetaiotaomicron, described as β-glucuronidase, displayed exo-β-galactosidase activity like BD-β-Gal but lacked a tetrameric structure.
Collapse
Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Tjaard Pijning
- Department of Biomolecular X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, the Netherlands
| | - Brandon B Gray
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Edita Jurak
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands.
| |
Collapse
|
118
|
Woodard AM, Peccati F, Navo CD, Jiménez-Osés G, Mitchell DA. Darobactin Substrate Engineering and Computation Show Radical Stability Governs Ether versus C-C Bond Formation. J Am Chem Soc 2024; 146:14328-14340. [PMID: 38728535 PMCID: PMC11225102 DOI: 10.1021/jacs.4c03994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
The Gram-negative selective antibiotic darobactin A has attracted interest owing to its intriguing fused bicyclic structure and unique targeting of the outer membrane protein BamA. Darobactin, a ribosomally synthesized and post-translationally modified peptide (RiPP), is produced by a radical S-adenosyl methionine (rSAM)-dependent enzyme (DarE) and contains one ether and one C-C cross-link. Herein, we analyze the substrate tolerance of DarE and describe an underlying catalytic principle of the enzyme. These efforts produced 51 enzymatically modified darobactin variants, revealing that DarE can install the ether and C-C cross-links independently and in different locations on the substrate. Notable variants with fused bicyclic structures were characterized, including darobactin W3Y, with a non-Trp residue at the twice-modified central position, and darobactin K5F, which displays a fused diether ring pattern. While lacking antibiotic activity, quantum mechanical modeling of darobactins W3Y and K5F aided in the elucidation of the requisite features for high-affinity BamA engagement. We also provide experimental evidence for β-oxo modification, which adds support for a proposed DarE mechanism. Based on these results, ether and C-C cross-link formation was investigated computationally, and it was determined that more stable and longer-lived aromatic Cβ radicals correlated with ether formation. Further, molecular docking and transition state structures based on high-level quantum mechanical calculations support the different indole connectivity observed for ether (Trp-C7) and C-C (Trp-C6) cross-links. Finally, mutational analysis and protein structural predictions identified substrate residues that govern engagement to DarE. Our work informs on darobactin scaffold engineering and further unveils the underlying principles of rSAM catalysis.
Collapse
Affiliation(s)
- Austin M Woodard
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Francesca Peccati
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Douglas A Mitchell
- Department of Chemistry, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
- Department of Microbiology, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
119
|
Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [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: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
Collapse
Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| |
Collapse
|
120
|
Adams MC, Schiltz C, Sun J, Hosford C, Johnson V, Pan H, Borbat P, Freed J, Thomason L, Court C, Court D, Chappie J. The crystal structure of bacteriophage λ RexA provides novel insights into the DNA binding properties of Rex-like phage exclusion proteins. Nucleic Acids Res 2024; 52:4659-4675. [PMID: 38554102 PMCID: PMC11077077 DOI: 10.1093/nar/gkae212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 03/07/2024] [Accepted: 03/12/2024] [Indexed: 04/01/2024] Open
Abstract
RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.
Collapse
Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Jing Sun
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Virginia M Johnson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hao Pan
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Peter P Borbat
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
- National Biomedical Resource for Advanced Electron Spin Resonance Spectroscopy, Cornell University, Ithaca, NY 14853, USA
| | - Lynn C Thomason
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Carolyn Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Donald L Court
- Center for Cancer Research, National Cancer Institute, Frederick, MD21702, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
121
|
Mei Y, Chang L, Ji Y, Yang B, Zhao J, Chen H, Chen W. Biomolecular investigations into BBI reveal an enzymatic mechanism for PUFA isomerisation in bifidobacterium CFA bioconversion strains. Int J Biol Macromol 2024; 268:131836. [PMID: 38692553 DOI: 10.1016/j.ijbiomac.2024.131836] [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: 01/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Multiple species of Bifidobacterium exhibit the ability to bioconvert conjugated fatty acids (CFAs), which is considered an important pathway for these strains to promote host health. However, there has been limited progress in understanding the enzymatic mechanism of CFA bioconversion by bifidobacteria, despite the increasing number of studies identifying CFA-producing strains. The protein responsible for polyunsaturated fatty acid (PUFA) isomerization in B. breve CCFM683 has recently been discovered and named BBI, providing a starting point for exploring Bifidobacterium isomerases (BIs). This study presents the sequence classification of membrane-bound isomerases from four common Bifidobacterium species that produce CFA. Heterologous expression, purification, and enzymatic studies of the typical sequences revealed that all possess a single c9, t11 isomer as the product and share common features in terms of enzymatic properties and catalytic kinetics. Using molecular docking and alanine scanning, Lys84, Tyr198, Asn202, and Leu245 located in the binding pocket were identified as critical to the catalytic activity, a finding further confirmed by site-directed mutagenesis-based screening assays. Overall, these findings provide insightful knowledge concerning the molecular mechanisms of BIs. This will open up additional opportunities for the use of bifidobacteria and CFAs in probiotic foods and precision nutrition.
Collapse
Affiliation(s)
- Yongchao Mei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Lulu Chang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Yibin Ji
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bo Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Haiqin Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China.
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, PR China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| |
Collapse
|
122
|
Shiv R, Rakeswari, Farjana N, Subbiah U, Ajith A, Balaji A, Mohanasatheesh S. Characterization of missense nonsynonymous single-nucleotide polymorphism of runt-related transcription factor-2 gene - An in silico approach. Indian J Pharmacol 2024; 56:198-205. [PMID: 39078184 PMCID: PMC11286098 DOI: 10.4103/ijp.ijp_533_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 02/23/2024] [Accepted: 06/04/2024] [Indexed: 07/31/2024] Open
Abstract
OBJECTIVES Single-nucleotide polymorphism (SNP) codes for multiple amino acids, impacting protein functions and disease prognosis. Runt-related transcription factor-2 (RUNX2), a transcription factor linked to osteoblast differentiation, regulates cell proliferation in endothelium and osteoblastic cells. Understanding Runx2's role in nonosseous tissues is rapidly advancing. This study aims to identify harmful SNPs of the RUNX2 gene that may alter disease susceptibility using computational techniques. METHODS The study uses various in silico methods to identify nonsynonymous SNPs (nsSNPs) of the RUNX2 gene, which could potentially alter protein structure and functions, with further analyses by I-Mutant, ConSurf, Netsurf 3.0, GeneMANIA, and Have (y)Our Protein Explained. RESULTS Six missense nsSNPs were identified as potentially harmful, disease-causing, and damaging. Four were found to be unstable, while five were conserved. All six nsSNPs had a coiled secondary structure. Five nsSNPs were found to be destabilized. CONCLUSION The RUNX2 gene's deleterious missense nsSNPs were identified by this study, and they may be exploited in future experimental studies. These high-risk nsSNPs might be considered target molecules in therapeutic and diagnostic therapies in teeth and bone development.
Collapse
Affiliation(s)
- Ragul Shiv
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Rakeswari
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Nilofer Farjana
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Usha Subbiah
- Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Athira Ajith
- Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Anitha Balaji
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - S. Mohanasatheesh
- Department of Periodontics, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| |
Collapse
|
123
|
Gogishvili D, Illes-Toth E, Harris MJ, Hopley C, Teunissen CE, Abeln S. Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP). Proteins 2024; 92:649-664. [PMID: 38149328 DOI: 10.1002/prot.26656] [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: 10/04/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/28/2023]
Abstract
Glial fibrillary acidic protein (GFAP) is a promising biomarker for brain and spinal cord disorders. Recent studies have highlighted the differences in the reliability of GFAP measurements in different biological matrices. The reason for these discrepancies is poorly understood as our knowledge of the protein's 3-dimensional conformation, proteoforms, and aggregation remains limited. Here, we investigate the structural properties of GFAP under different conditions. For this, we characterized recombinant GFAP proteins from various suppliers and applied hydrogen-deuterium exchange mass spectrometry (HDX-MS) to provide a snapshot of the conformational dynamics of GFAP in artificial cerebrospinal fluid (aCSF) compared to the phosphate buffer. Our findings indicate that recombinant GFAP exists in various conformational species. Furthermore, we show that GFAP dimers remained intact under denaturing conditions. HDX-MS experiments show an overall decrease in H-bonding and an increase in solvent accessibility of GFAP in aCSF compared to the phosphate buffer, with clear indications of mixed EX2 and EX1 kinetics. To understand possible structural interface regions and the evolutionary conservation profiles, we combined HDX-MS results with the predicted GFAP-dimer structure by AlphaFold-Multimer. We found that deprotected regions with high structural flexibility in aCSF overlap with predicted conserved dimeric 1B and 2B domain interfaces. Structural property predictions combined with the HDX data show an overall deprotection and signatures of aggregation in aCSF. We anticipate that the outcomes of this research will contribute to a deeper understanding of the structural flexibility of GFAP and ultimately shed light on its behavior in different biological matrices.
Collapse
Affiliation(s)
- Dea Gogishvili
- Bioinformatics, Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Eva Illes-Toth
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Matthew J Harris
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Christopher Hopley
- National Measurement Laboratory at Laboratory of the Government Chemist (LGC), Teddington, UK
| | - Charlotte E Teunissen
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Neurochemistry Laboratory, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Sanne Abeln
- Bioinformatics, Computer Science Department, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- AI Technology for Life, Department of Computing and Information Sciences, Department of Biology, Utrecht University, Utrecht, The Netherlands
| |
Collapse
|
124
|
Khuman A, Yadav V, Chaudhary B. Evolutionary dynamics of the cytoskeletal profilin gene family in Brassica juncea L. reveal its roles in silique development and stress resilience. Int J Biol Macromol 2024; 266:131247. [PMID: 38565371 DOI: 10.1016/j.ijbiomac.2024.131247] [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: 02/16/2024] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/04/2024]
Abstract
Essential to plant adaptation, cell wall (CW) integrity is maintained by CW-biosynthesis genes. Cytoskeletal actin-(de)polymerizing, phospholipid-binding profilin (PRF) proteins play important roles in maintaining cellular homeostasis across kingdoms. However, evolutionary selection of PRF genes and their systematic characterization in family Brassicaceae, especially in Brassica juncea remain unexplored. Here, a comprehensive analysis of genome-wide identification of BjPRFs, their phylogenetic association, genomic localization, gene structure, and transcriptional profiling were performed in an evolutionary framework. Identification of 23 BjPRFs in B. juncea indicated an evolutionary conservation within Brassicaceae. The BjPRFs evolved through paralogous and orthologous gene formation in Brassica genomes. Evolutionary divergence of BjPRFs indicated purifying selection, with nonsynonymous (dN)/synonymous (dS) value of 0.090 for orthologous gene-pairs. Hybrid homology-modeling identified evolutionary distinct and conserved domains in BjPRFs which suggested that these proteins evolved following the divergence of monocot and eudicot plants. RNA-seq profiles of BjPRFs revealed their functional evolution in spatiotemporal manner during plant-development and stress-conditions in diploid/amphidiploid Brassica species. Real-Time PCR experiments in seedling, vegetative, floral and silique tissues of B. juncea suggested their essential roles in systematic plant development. These observations underscore the expansion of BjPRFs in B. juncea, and offer valuable evolutionary insights for exploring cellular mechanisms, and stress resilience.
Collapse
Affiliation(s)
| | - Vandana Yadav
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P., India
| | | |
Collapse
|
125
|
Siva Sankari G, James R, Payva F, Sivaramakrishnan V, Vineeth Kumar TV, Kanchi S, Santhy KS. Computational analysis of sodium-dependent phosphate transporter SLC20A1/PiT1 gene identifies missense variations C573F, and T58A as high-risk deleterious SNPs. J Biomol Struct Dyn 2024; 42:4072-4086. [PMID: 37286379 DOI: 10.1080/07391102.2023.2218939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/21/2023] [Indexed: 06/09/2023]
Abstract
SLC20A1/PiT1 is a sodium-dependent inorganic phosphate transporter, initially recognized as the retroviral receptor for Gibbon Ape Leukemia Virus in humans. SNPs in SLC20A1 is associated with Combined Pituitary Hormone Deficiency and Sodium Lithium Counter transport. Using in silico techniques, we have screened the nsSNPs for their deleterious effect on the structure and function of SLC20A1. Screening with sequence and structure-based tools on 430 nsSNPs, filtered 17 nsSNPs which are deleterious. To evaluate the role of these SNPs, protein modeling and MD simulations were performed. A comparative analysis of model generated with SWISS-MODEL and AlphaFold shows that many residues are in the disallowed region of Ramachandran plot. Since SWISS-MODEL structure has a 25-residue deletion, the AlphaFold structure was used to perform MD simulation for equilibration and structure refinement. Further, to understand perturbation of energetics, we performed in silico mutagenesis and ΔΔG calculation using FoldX on MD refined structures, which yielded SNPs that are neutral (3), destabilizing (12) and stabilizing (2) on protein structure. Furthermore, to elucidate the impact of SNPs on structure, we performed MD simulations to discern the changes in RMSD, Rg, RMSF and LigPlot of interacting residues. RMSF profiles of representative SNPs revealed that A114V (neutral) and T58A (positive) were more flexible & C573F (negative) was more rigid compared to wild type, which is also reflected in the changes in number of local interacting residues in LigPlot and ΔΔG. Taken together, our results show that SNPs can lead to structural perturbations and impact the function of SLC20A1 with potential implications for disease.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- G Siva Sankari
- Centre for Wildlife Studies, Kerala Veterinary and Animal Sciences University, Wayanad, Kerala, India
| | - Remya James
- St. Joseph's College for Women, Alappuzha, Kerala, India
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
| | - Febby Payva
- St. Joseph's College for Women, Alappuzha, Kerala, India
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
| | - Venketesh Sivaramakrishnan
- Disease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | | | - Subbarao Kanchi
- Department of Physics, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, India
| | - K S Santhy
- Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, Tamil Nadu, India
| |
Collapse
|
126
|
Çıldır ÖŞ, Özmen Ö, Kul S, Rişvanlı A, Özalp G, Sabuncu A, Kul O. Genetic analysis of PALB2 gene WD40 domain in canine mammary tumour patients. Vet Med Sci 2024; 10:e1366. [PMID: 38527110 PMCID: PMC10962921 DOI: 10.1002/vms3.1366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 11/30/2023] [Accepted: 01/07/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND DNA repair mechanisms are essential for tumorigenesis and disruption of HR mechanism is an important predisposing factor of human breast cancers (BC). PALB2 is an important part of the HR. There are similarities between canine mammary tumours (CMT) and BCs. As its human counterpart, PALB2 mutations could be a predisposing factor of CMT. OBJECTIVES In this study, we aimed to investigate the impacts of PALB2 variants on tumorigenesis and canine mammary tumor (CMT) malignancy. METHODS We performed Sanger sequencing to detect germline mutations in the WD40 domain of the canine PALB2 gene in CMT patients. We conducted in silico analysis to investigate the variants, and compared the germline PALB2 mutations in humans that cause breast cancer (BC) with the variants detected in dogs with CMT. RESULTS We identified an intronic (c.3096+8C>G) variant, two exonic (p.A1050V and p.R1354R) variants, and a 3' UTR variant (c.4071T>C). Of these, p.R1354R and c.4071T>C novel variants were identified for the first time in this study. We found that the p.A1050V mutation had a significant effect. However, we could not determine sufficient similarity due to the differences in nucleotide/amino acid sequences between two species. Nonetheless, possible variants of human sequences in the exact location as their dog counterparts are associated with several cancer types, implying that the variants could be crucial for tumorigenesis in dogs. Our results did not show any effect of the variants on tumor malignancy. CONCLUSIONS The current project is the first study investigating the relationship between the PALB2 gene WD40 domain and CMTs. Our findings will contribute to a better understanding of the pathogenic mechanism of the PALB2 gene in CMTs. In humans, variant positions in canines have been linked to cancer-related phenotypes such as familial BC, endometrial tumor, and hereditary cancer predisposition syndrome. The results of bioinformatics analyses should be investigated through functional tests or case-control studies.
Collapse
Affiliation(s)
- Özge Şebnem Çıldır
- Department of GeneticsFaculty of Veterinary MedicineKafkas UniversityKarsTürkiye
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Özge Özmen
- Department of GeneticsFaculty of Veterinary MedicineAnkara UniversityAnkaraTürkiye
| | - Selim Kul
- Department of Animal BreedingFaculty of Veterinary MedicineYozgat Bozok UniversityYozgatTürkiye
| | - Ali Rişvanlı
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineFırat UniversityElazığTürkiye
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineKyrgyz‐Turkish Manas UniversityBishkekKyrgyzstan
| | - Gözde Özalp
- Department of Obstetrics and GynecologyFaculty of Veterinary MedicineBursa Uludağ UniversityBursaTürkiye
| | - Ahmet Sabuncu
- Department of Obstetrics and GynecologyFaculty of Veterinary Medicineİstanbul UniversityİstanbulTürkiye
| | - Oğuz Kul
- Department of PathologyFaculty of Veterinary MedicineKırıkkale UniversityKırıkkaleTürkiye
| |
Collapse
|
127
|
Sahu M, Rani N, Kumar P. Simulation and Computational Study of RING Domain Mutants of BRCA1 and Ube2k in AD/PD Pathophysiology. Mol Biotechnol 2024; 66:1095-1115. [PMID: 38172369 DOI: 10.1007/s12033-023-01006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Lysine-based post-translational modification (PTM) such as acylation, acetylation, deamination, methylation, SUMOylation, and ubiquitination has proven to be a major regulator of gene expression, chromatin structure, protein stability, protein-protein interaction, protein degradation, and cellular localization. However, besides all the PTMs, ubiquitination stands as the second most common PTM after phosphorylation that is involved in the etiology of neurodegenerative diseases (NDDs) namely, Alzheimer's disease (AD) and Parkinson's disease (PD). NDDs are characterized by the accumulation of misfolded protein aggregates in the brain that lead to disease-related gene mutation and irregular protein homeostasis. The ubiquitin-proteasome system (UPS) is in charge of degrading these misfolded proteins, which involve an interplay of E1, E2, E3, and deubiquitinase enzymes. Impaired UPS has been commonly observed in NDDs and E3 ligases are the key members of the UPS, thus, dysfunction of the same can accelerate the neurodegeneration process. Therefore, the aim of this study is firstly, to find E3 ligases that are common in both AD and PD through data mining. Secondly, to study the impact of mutation on its structure and function. The study deciphered 74 E3 ligases that were common in both AD and PD. Later, 10 hub genes were calculated of which protein-protein interaction, pathway enrichment, lysine site prediction, domain, and motif analysis were performed. The results predicted BRCA1, PML, and TRIM33 as the top three putative lysine-modified E3 ligases involved in AD and PD pathogenesis. However, based on structural characterization, BRCA1 was taken further to study RING domain mutation that inferred K32Y, K32L, K32C, K45V, K45Y, and K45G as potential mutants that alter the structural and functional ability of BRCA1 to interact with Ube2k, E2-conjugating enzyme. The most probable mutant observed after molecular dynamics simulation of 50 ns is K32L. Therefore, our study concludes BRCA1, a potential E3 ligase common in AD and PD, and RING domain mutation at sites K32 and K45 possibly disturbs its interaction with its E2, Ube2k.
Collapse
Affiliation(s)
- Mehar Sahu
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Neetu Rani
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
| |
Collapse
|
128
|
Kannan P, A HB, N MP, D TK, Ramanathan G, Eswaramoorthy R, Ramasamy M. Unravelling the Relacatib activity against the CTSK proteins causing pycnodysostosis: a molecular docking and dynamics approach. J Biomol Struct Dyn 2024; 42:4121-4132. [PMID: 37255004 DOI: 10.1080/07391102.2023.2218927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
Pycnodysostosis is an atypical autosomal recessive condition of Lysosomal storage disorder that originated due to the deficit of the enzyme Cathepsin K which is vital for normal osteoclast action in bone resorption. Abnormal degradation of type 1 collagen and accumulation of toxic undigested collagen fibers in lysosomes of the osteoclast cells resulting in high bone density, brittle bones, and a short stature is caused in CTSK protein-carrying individuals. The broad aim of this study is to identify the most significant variant through various computational pipelines. This study was initiated by retrieving a total number of thirty-six variants from NCBI, HGMD, and UniProt databases, and the Y283C variant was found to be more significant by various standard computational tools. A structural investigation was performed to understand and gain a better knowledge about the interaction profile for the native (1BY8) and variant (Y283C) with Relacatib (a small-molecule drug that blocks the function of Cathepsin K, an enzyme that has been linked to osteoporosis, osteoarthritis, and other bone-degrading diseases). The interaction profile was analyzed using molecular docking. Relacatib (ligand) had an average binding affinity for both native (-7.16 kcal/mol) and Y283C (-6.76 kcal/mol). Finally, Molecular dynamics simulations were done in duplicates to recognize the variant (Y283C) activity of the protein structure against Relacatib for 100 ns. This study assists in comprehending the most pathogenic amino-acid variant, the ligand interaction with the protein structure, and paves the way for understanding the steadiness of the ligand with the native and selected significant amino-acid variant.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Priyanka Kannan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Hadeefa Begum A
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Madhana Priya N
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Thirumal Kumar D
- Faculty of Allied Health Science, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Gnansambandan Ramanathan
- Department of Biomedical Science, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| |
Collapse
|
129
|
Saheb Sharif-Askari N, Hafezi S, Saheb Sharif-Askari F, Ali Hussain Alsayed H, B. M. Ahmed S, Alsafar HS, Halwani R. Multiple inborn errors of type I IFN immunity in a 33-year-old male with a fatal case of COVID-19. Heliyon 2024; 10:e29338. [PMID: 38665565 PMCID: PMC11043952 DOI: 10.1016/j.heliyon.2024.e29338] [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: 11/03/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
The host genetic inborn errors of immunity (IEIs) have been shown to contribute to susceptibility to life-threatening coronavirus disease 2019 (COVID-19), as it had been associated previously with other viral infections. Most genetic association studies have described IEIs as a monogenic defect, while there have been no reports of patients with multiple inherited immune deficiencies. This is a complex case of IEIs predisposing to severe viral infections in an unvaccinated 33-year-old male patient. The patient was admitted with no respiratory symptoms, showed a SARS-CoV-2 PCR positive test on the second day of admission, started developing progressive lung consolidation within three days of hospitalization, and was moved from non-invasive to mechanical ventilation within 12 days of hospitalization. Impaired production of type I IFN was detected in patient PBMCs treated with poly(I:C), at both mRNA and protein levels. Whole exome sequencing revealed three mutations across type I IFN production pathway, which were predicted to be loss-of-function (pLOF). The three mutations were predicted to predispose to severe viral infections: monoallelic R488X TLR3, monoallelic His684Arg TLR3, and biallelic Val363Met IRF3. Functional analysis confirmed that all these mutations dysregulated the type I IFN pathway. Evaluation of TLR3 and IRF3 IFN-β1 luciferase reporter activity showed a hypomorphic suppression of function. TOPO TA cloning was used to ascertain the positioning of both TLR3 variants, indicating that both variants were on the same allele. We have described a unique complex IEI patient with multiple mutations, particularly along type I IFN production pathway.
Collapse
Affiliation(s)
- Narjes Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Shirin Hafezi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Fatemeh Saheb Sharif-Askari
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of pharmacy practice and pharmacotherapeutics, College of pharmacy, University of Sharjah, Sharjah, United Arab Emirates
| | - Hawra Ali Hussain Alsayed
- Department of Pharmacy, Rashid Hospital, Dubai Academic Health Corporation, Dubai, United Arab Emirates
| | - Samrein B. M. Ahmed
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield, S1 1WB, UK
| | - Habiba S. Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, College of Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Genetics and Molecular Biology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Rabih Halwani
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
- Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Prince Abdullah Ben Khaled Celiac Disease Research Chair, department of pediatrics, Faculty of Medicine, King Saud University, Saudi Arabia
| |
Collapse
|
130
|
Godoy AS, Mesquita NCMR, Noske GD, Gawriljuk VO, Lithgo RM, Balcomb BH, Aschenbrenner JC, Tomlinson CWE, Winokan M, Scheen J, Marples PG, Chandran AV, Ni X, Thompson W, Fairhead M, Fearon D, Koekemoer L, Xavier MAE, Walsh M, Oliva G, von Delft F. High-throughput crystallographic fragment screening of Zika virus NS3 Helicase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591279. [PMID: 38746241 PMCID: PMC11092484 DOI: 10.1101/2024.04.27.591279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The Zika virus (ZIKV), discovered in Africa in 1947, swiftly spread across continents, causing significant concern due to its recent association with microcephaly in newborns and Guillain-Barré syndrome in adults. Despite a decrease in prevalence, the potential for a resurgence remains, necessitating urgent therapeutic interventions. Like other flaviviruses, ZIKV presents promising drug targets within its replication machinery, notably the NS3 helicase (NS3Hel) protein, which plays critical roles in viral replication. However, a lack of structural information impedes the development of specific inhibitors targeting NS3Hel. Here we applied high-throughput crystallographic fragment screening on ZIKV NS3Hel, which yielded structures that reveal 3D binding poses of 46 fragments at multiple sites of the protein, including 11 unique fragments in the RNA-cleft site. These fragment structures provide templates for direct design of hit compounds and should thus assist the development of novel direct-acting antivirals against ZIKV and related flaviviruses, thus opening a promising avenue for combating future outbreaks.
Collapse
Affiliation(s)
- Andre S Godoy
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
- ASAP Discovery Consortium: asapdiscovery.org
| | - Nathalya C M R Mesquita
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Gabriela Dias Noske
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Victor Oliveira Gawriljuk
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Ryan M Lithgo
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Blake H Balcomb
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jasmin Cara Aschenbrenner
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Charles W E Tomlinson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Max Winokan
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Jenke Scheen
- Open Molecular Sciences Foundation, Davis, CA 95618, USA
- ASAP Discovery Consortium: asapdiscovery.org
| | - Peter George Marples
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Anu V Chandran
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Xiaomin Ni
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Warren Thompson
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Michael Fairhead
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Daren Fearon
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Lizbé Koekemoer
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Mary-Ann Elvina Xavier
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Martin Walsh
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- ASAP Discovery Consortium: asapdiscovery.org
| | - Glaucius Oliva
- São Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100 - Jardim Santa Angelina, São Carlos, 13563-120, Brazil
| | - Frank von Delft
- Diamond Light Source, Harwell Science and Innovation Campus, Fermi Ave, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Fermi Ave, Didcot, OX11 0FA, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine Research Building, Old Road Campus, Headington, Oxford, OX3 7FZ, UK
- ASAP Discovery Consortium: asapdiscovery.org
| |
Collapse
|
131
|
Yuan M, Wilson IA. The D Gene in CDR H3 Determines a Public Class of Human Antibodies to SARS-CoV-2. Vaccines (Basel) 2024; 12:467. [PMID: 38793718 PMCID: PMC11126049 DOI: 10.3390/vaccines12050467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/24/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Public antibody responses have been found against many infectious agents. Structural convergence of public antibodies is usually determined by immunoglobulin V genes. Recently, a human antibody public class against SARS-CoV-2 was reported, where the D gene (IGHD3-22) encodes a common YYDxxG motif in heavy-chain complementarity-determining region 3 (CDR H3), which determines specificity for the receptor-binding domain (RBD). In this review, we discuss the isolation, structural characterization, and genetic analyses of this class of antibodies, which have been isolated from various cohorts of COVID-19 convalescents and vaccinees. All eleven YYDxxG antibodies with available structures target the SARS-CoV-2 RBD in a similar binding mode, where the CDR H3 dominates the interaction with antigen. The antibodies target a conserved site on the RBD that does not overlap with the receptor-binding site, but their particular angle of approach results in direct steric hindrance to receptor binding, which enables both neutralization potency and breadth. We also review the properties of CDR H3-dominant antibodies that target other human viruses. Overall, unlike most public antibodies, which are identified by their V gene usage, this newly discovered public class of YYDxxG antibodies is dominated by a D-gene-encoded motif and uncovers further opportunities for germline-targeting vaccine design.
Collapse
Affiliation(s)
- Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA;
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| |
Collapse
|
132
|
Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. Nat Commun 2024; 15:3574. [PMID: 38678027 PMCID: PMC11055893 DOI: 10.1038/s41467-024-48030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
Collapse
Affiliation(s)
- Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
133
|
Ma C, Luo Y, Zhang C, Cheng C, Hua N, Liu X, Wu J, Qin L, Yu P, Luo J, Yang F, Jiang LH, Zhang G, Yang W. Evolutionary trajectory of TRPM2 channel activation by adenosine diphosphate ribose and calcium. Sci Bull (Beijing) 2024:S2095-9273(24)00301-3. [PMID: 38734586 DOI: 10.1016/j.scib.2024.04.052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 02/07/2024] [Accepted: 04/19/2024] [Indexed: 05/13/2024]
Abstract
Ion channel activation upon ligand gating triggers a myriad of biological events and, therefore, evolution of ligand gating mechanism is of fundamental importance. TRPM2, a typical ancient ion channel, is activated by adenosine diphosphate ribose (ADPR) and calcium and its activation has evolved from a simple mode in invertebrates to a more complex one in vertebrates, but the evolutionary process is still unknown. Molecular evolutionary analysis of TRPM2s from more than 280 different animal species has revealed that, the C-terminal NUDT9-H domain has evolved from an enzyme to a ligand binding site for activation, while the N-terminal MHR domain maintains a conserved ligand binding site. Calcium gating pattern has also evolved, from one Ca2+-binding site as in sea anemones to three sites as in human. Importantly, we identified a new group represented by olTRPM2, which has a novel gating mode and fills the missing link of the channel gating evolution. We conclude that the TRPM2 ligand binding or activation mode evolved through at least three identifiable stages in the past billion years from simple to complicated and coordinated. Such findings benefit the evolutionary investigations of other channels and proteins.
Collapse
Affiliation(s)
- Cheng Ma
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Protein Facility, Core Facilities, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yanping Luo
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Congyi Zhang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Cheng Cheng
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Ning Hua
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xiaocao Liu
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jianan Wu
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Luying Qin
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peilin Yu
- Department of Toxicology, and Department of Medical Oncology of The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jianhong Luo
- Department of Neurobiology, Affiliated Mental Health Center, College of Brain Science and Brain Medicine, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Fan Yang
- Department of Biophysics, and Kidney Disease Center of The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lin-Hua Jiang
- Sino-UK Joint Laboratory of Brain Function and Injury of Henan Province, and Department of Physiology and Pathophysiology, Xinxiang Medical University, Xinxiang 453004, China; Henan Collaborative Innovation Center of Prevention and Treatment of Mental Disorder, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang 453004, China
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Wei Yang
- Department of Biophysics and Department of Neurosurgery, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; GuiZhou University Medical College, Guiyang 550025, China.
| |
Collapse
|
134
|
Frank HM, Walujkar S, Walsh RM, Laursen WJ, Theobald DL, Garrity PA, Gaudet R. Structural basis of ligand specificity and channel activation in an insect gustatory receptor. Cell Rep 2024; 43:114035. [PMID: 38573859 PMCID: PMC11100771 DOI: 10.1016/j.celrep.2024.114035] [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: 12/10/2023] [Revised: 02/26/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024] Open
Abstract
Gustatory receptors (GRs) are critical for insect chemosensation and are potential targets for controlling pests and disease vectors, making their structural investigation a vital step toward such applications. We present structures of Bombyx mori Gr9 (BmGr9), a fructose-gated cation channel, in agonist-free and fructose-bound states. BmGr9 forms a tetramer similar to distantly related insect odorant receptors (ORs). Upon fructose binding, BmGr9's channel gate opens through helix S7b movements. In contrast to ORs, BmGr9's ligand-binding pocket, shaped by a kinked helix S4 and a shorter extracellular S3-S4 loop, is larger and solvent accessible in both agonist-free and fructose-bound states. Also, unlike ORs, fructose binding by BmGr9 involves helix S5 and a pocket lined with aromatic and polar residues. Structure-based sequence alignments reveal distinct patterns of ligand-binding pocket residue conservation in GR subfamilies associated with different ligand classes. These data provide insight into the molecular basis of GR ligand specificity and function.
Collapse
Affiliation(s)
- Heather M Frank
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Sanket Walujkar
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Richard M Walsh
- The Harvard Cryo-EM Center for Structural Biology, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Willem J Laursen
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA
| | | | - Paul A Garrity
- Department of Biology and Volen Center for Complex Systems, Brandeis University, Waltham, MA 02453, USA.
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
| |
Collapse
|
135
|
Andreas MP, Giessen TW. The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.23.590730. [PMID: 38712110 PMCID: PMC11071394 DOI: 10.1101/2024.04.23.590730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus . Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.
Collapse
|
136
|
Elangeeb ME, Elfaki I, Eleragi AMS, Ahmed EM, Mir R, Alzahrani SM, Bedaiwi RI, Alharbi ZM, Mir MM, Ajmal MR, Tayeb FJ, Barnawi J. Molecular Dynamics Simulation of Kir6.2 Variants Reveals Potential Association with Diabetes Mellitus. Molecules 2024; 29:1904. [PMID: 38675722 PMCID: PMC11054064 DOI: 10.3390/molecules29081904] [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: 03/07/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Diabetes mellitus (DM) represents a problem for the healthcare system worldwide. DM has very serious complications such as blindness, kidney failure, and cardiovascular disease. In addition to the very bad socioeconomic impacts, it influences patients and their families and communities. The global costs of DM and its complications are huge and expected to rise by the year 2030. DM is caused by genetic and environmental risk factors. Genetic testing will aid in early diagnosis and identification of susceptible individuals or populations using ATP-sensitive potassium (KATP) channels present in different tissues such as the pancreas, myocardium, myocytes, and nervous tissues. The channels respond to different concentrations of blood sugar, stimulation by hormones, or ischemic conditions. In pancreatic cells, they regulate the secretion of insulin and glucagon. Mutations in the KCNJ11 gene that encodes the Kir6.2 protein (a major constituent of KATP channels) were reported to be associated with Type 2 DM, neonatal diabetes mellitus (NDM), and maturity-onset diabetes of the young (MODY). Kir6.2 harbors binding sites for ATP and phosphatidylinositol 4,5-diphosphate (PIP2). The ATP inhibits the KATP channel, while the (PIP2) activates it. A Kir6.2 mutation at tyrosine330 (Y330) was demonstrated to reduce ATP inhibition and predisposes to NDM. In this study, we examined the effect of mutations on the Kir6.2 structure using bioinformatics tools and molecular dynamic simulations (SIFT, PolyPhen, SNAP2, PANTHER, PhD&SNP, SNP&Go, I-Mutant, MuPro, MutPred, ConSurf, HOPE, and GROMACS). Our results indicated that M199R, R201H, R206H, and Y330H mutations influence Kir6.2 structure and function and therefore may cause DM. We conclude that MD simulations are useful techniques to predict the effects of mutations on protein structure. In addition, the M199R, R201H, R206H, and Y330H variant in the Kir6.2 protein may be associated with DM. These results require further verification in protein-protein interactions, Kir6.2 function, and case-control studies.
Collapse
Affiliation(s)
- Mohamed E. Elangeeb
- Department of Basic Medical Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ali M. S. Eleragi
- Department of Microbiology, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Elsadig Mohamed Ahmed
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Saudi Arabia;
- Department of Clinical Chemistry, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti 27711, Sudan
| | - Rashid Mir
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Salem M. Alzahrani
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Ruqaiah I. Bedaiwi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Zeyad M. Alharbi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Mohammad Muzaffar Mir
- Department of Clinical Biochemistry, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia;
| | - Mohammad Rehan Ajmal
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia; (S.M.A.); (M.R.A.)
| | - Faris Jamal Tayeb
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| | - Jameel Barnawi
- Department of Medical Laboratory Technology, Prince Fahad Bin Sultan Chair for Biomedical Research, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia; (R.M.); (R.I.B.); (Z.M.A.); (F.J.T.); (J.B.)
| |
Collapse
|
137
|
Kim Y, Kim D, Hieu NM, Byun H, Ahn JH. PySupercharge: a python algorithm for enabling ABC transporter bacterial secretion of all proteins through amino acid mutation. Microb Cell Fact 2024; 23:115. [PMID: 38643109 PMCID: PMC11031901 DOI: 10.1186/s12934-024-02342-z] [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: 11/26/2023] [Accepted: 02/19/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND The process of producing proteins in bacterial systems and secreting them through ATP-binding cassette (ABC) transporters is an area that has been actively researched and used due to its high protein production capacity and efficiency. However, some proteins are unable to pass through the ABC transporter after synthesis, a phenomenon we previously determined to be caused by an excessive positive charge in certain regions of their amino acid sequence. If such an excessive charge is removed, the secretion of any protein through ABC transporters becomes possible. RESULTS In this study, we introduce 'linear charge density' as the criteria for possibility of protein secretion through ABC transporters and confirm that this criterion can be applied to various non-secretable proteins, such as SARS-CoV-2 spike proteins, botulinum toxin light chain, and human growth factors. Additionally, we develop a new algorithm, PySupercharge, that enables the secretion of proteins containing regions with high linear charge density. It selectively converts positively charged amino acids into negatively charged or neutral amino acids after linear charge density analysis to enable protein secretion through ABC transporters. CONCLUSIONS PySupercharge, which also minimizes functional/structural stability loss of the pre-mutation proteins through the use of sequence conservation data, is currently being operated on an accessible web server. We verified the efficacy of PySupercharge-driven protein supercharging by secreting various previously non-secretable proteins commonly used in research, and so suggest this tool for use in future research requiring effective protein production.
Collapse
Affiliation(s)
- Yerin Kim
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Danny Kim
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Nguyen-Mihn Hieu
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea
| | - Hyunjong Byun
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Jung Hoon Ahn
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan, South Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.
| |
Collapse
|
138
|
Fansher D, Besna JN, Fendri A, Pelletier JN. Choose Your Own Adventure: A Comprehensive Database of Reactions Catalyzed by Cytochrome P450 BM3 Variants. ACS Catal 2024; 14:5560-5592. [PMID: 38660610 PMCID: PMC11036407 DOI: 10.1021/acscatal.4c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Cytochrome P450 BM3 monooxygenase is the topic of extensive research as many researchers have evolved this enzyme to generate a variety of products. However, the abundance of information on increasingly diversified variants of P450 BM3 that catalyze a broad array of chemistry is not in a format that enables easy extraction and interpretation. We present a database that categorizes variants by their catalyzed reactions and includes details about substrates to provide reaction context. This database of >1500 P450 BM3 variants is downloadable and machine-readable and includes instructions to maximize ease of gathering information. The database allows rapid identification of commonly reported substitutions, aiding researchers who are unfamiliar with the enzyme in identifying starting points for enzyme engineering. For those actively engaged in engineering P450 BM3, the database, along with this review, provides a powerful and user-friendly platform to understand, predict, and identify the attributes of P450 BM3 variants, encouraging the further engineering of this enzyme.
Collapse
Affiliation(s)
- Douglas
J. Fansher
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Jonathan N. Besna
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| | - Ali Fendri
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
| | - Joelle N. Pelletier
- Chemistry
Department, Université de Montréal, Montreal, QC, Canada H2V 0B3
- PROTEO,
The Québec Network for Research on Protein Function, Engineering,
and Applications, 201
Av. du Président-Kennedy, Montréal, QC, Canada H2X 3Y7
- CGCC,
Center in Green Chemistry and Catalysis, Montreal, QC, Canada H2V 0B3
- Department
of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC, Canada H3T 1J4
| |
Collapse
|
139
|
Lee MS, Tuohy PJ, Kim CY, Yost PP, Lichauco K, Parrish HL, Van Doorslaer K, Kuhns MS. The CD4 transmembrane GGXXG and juxtamembrane (C/F)CV+C motifs mediate pMHCII-specific signaling independently of CD4-LCK interactions. eLife 2024; 12:RP88225. [PMID: 38639990 PMCID: PMC11031086 DOI: 10.7554/elife.88225] [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] [Indexed: 04/20/2024] Open
Abstract
CD4+ T cell activation is driven by five-module receptor complexes. The T cell receptor (TCR) is the receptor module that binds composite surfaces of peptide antigens embedded within MHCII molecules (pMHCII). It associates with three signaling modules (CD3γε, CD3δε, and CD3ζζ) to form TCR-CD3 complexes. CD4 is the coreceptor module. It reciprocally associates with TCR-CD3-pMHCII assemblies on the outside of a CD4+ T cells and with the Src kinase, LCK, on the inside. Previously, we reported that the CD4 transmembrane GGXXG and cytoplasmic juxtamembrane (C/F)CV+C motifs found in eutherian (placental mammal) CD4 have constituent residues that evolved under purifying selection (Lee et al., 2022). Expressing mutants of these motifs together in T cell hybridomas increased CD4-LCK association but reduced CD3ζ, ZAP70, and PLCγ1 phosphorylation levels, as well as IL-2 production, in response to agonist pMHCII. Because these mutants preferentially localized CD4-LCK pairs to non-raft membrane fractions, one explanation for our results was that they impaired proximal signaling by sequestering LCK away from TCR-CD3. An alternative hypothesis is that the mutations directly impacted signaling because the motifs normally play an LCK-independent role in signaling. The goal of this study was to discriminate between these possibilities. Using T cell hybridomas, our results indicate that: intracellular CD4-LCK interactions are not necessary for pMHCII-specific signal initiation; the GGXXG and (C/F)CV+C motifs are key determinants of CD4-mediated pMHCII-specific signal amplification; the GGXXG and (C/F)CV+C motifs exert their functions independently of direct CD4-LCK association. These data provide a mechanistic explanation for why residues within these motifs are under purifying selection in jawed vertebrates. The results are also important to consider for biomimetic engineering of synthetic receptors.
Collapse
Affiliation(s)
- Mark S Lee
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Peter J Tuohy
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Caleb Y Kim
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Philip P Yost
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Katrina Lichauco
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Heather L Parrish
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
| | - Koenraad Van Doorslaer
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
- School of Animal and Comparative Biomedical Sciences, The University of ArizonaTucsonUnited States
- Cancer Biology Graduate Interdisciplinary Program and Genetics Graduate Interdisciplinary Program, The University of ArizonaTucsonUnited States
- The BIO-5 Institute, The University of ArizonaTucsonUnited States
- The University of Arizona Cancer CenterTucsonUnited States
- The Arizona Center on Aging, The University of Arizona College of MedicineTucsonUnited States
| | - Michael S Kuhns
- Department of Immunobiology, The University of Arizona College of MedicineTucsonUnited States
- Cancer Biology Graduate Interdisciplinary Program and Genetics Graduate Interdisciplinary Program, The University of ArizonaTucsonUnited States
- The BIO-5 Institute, The University of ArizonaTucsonUnited States
- The University of Arizona Cancer CenterTucsonUnited States
- The Arizona Center on Aging, The University of Arizona College of MedicineTucsonUnited States
| |
Collapse
|
140
|
Gaussmann S, Peschel R, Ott J, Zak KM, Sastre J, Delhommel F, Popowicz GM, Boekhoven J, Schliebs W, Erdmann R, Sattler M. Modulation of peroxisomal import by the PEX13 SH3 domain and a proximal FxxxF binding motif. Nat Commun 2024; 15:3317. [PMID: 38632234 PMCID: PMC11024197 DOI: 10.1038/s41467-024-47605-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024] Open
Abstract
Import of proteins into peroxisomes depends on PEX5, PEX13 and PEX14. By combining biochemical methods and structural biology, we show that the C-terminal SH3 domain of PEX13 mediates intramolecular interactions with a proximal FxxxF motif. The SH3 domain also binds WxxxF peptide motifs in the import receptor PEX5, demonstrating evolutionary conservation of such interactions from yeast to human. Strikingly, intramolecular interaction of the PEX13 FxxxF motif regulates binding of PEX5 WxxxF/Y motifs to the PEX13 SH3 domain. Crystal structures reveal how FxxxF and WxxxF/Y motifs are recognized by a non-canonical surface on the SH3 domain. The PEX13 FxxxF motif also mediates binding to PEX14. Surprisingly, the potential PxxP binding surface of the SH3 domain does not recognize PEX14 PxxP motifs, distinct from its yeast ortholog. Our data show that the dynamic network of PEX13 interactions with PEX5 and PEX14, mediated by diaromatic peptide motifs, modulates peroxisomal matrix import.
Collapse
Affiliation(s)
- Stefan Gaussmann
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Rebecca Peschel
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Julia Ott
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Krzysztof M Zak
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Judit Sastre
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Florent Delhommel
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Grzegorz M Popowicz
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany
| | - Job Boekhoven
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85747, Garching, Germany
| | - Wolfgang Schliebs
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany
| | - Ralf Erdmann
- Institute of Biochemistry and Pathobiochemistry, Department of Systems Biology, Faculty of Medicine, Ruhr University Bochum, 44780, Bochum, Germany.
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Bavarian NMR Center and Department of Bioscience, Lichtenbergstr. 4, 85747, Garching, Germany.
- Helmholtz Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Ingolstädter Landstr. 1, 85764, Neuherberg, Germany.
| |
Collapse
|
141
|
Singh K, Malik YS. ANN based prediction of ligand binding sites outside deep cavities to facilitate drug designing. Curr Res Struct Biol 2024; 7:100144. [PMID: 38681239 PMCID: PMC11047793 DOI: 10.1016/j.crstbi.2024.100144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 05/01/2024] Open
Abstract
The ever-changing environmental conditions and pollution are the prime reasons for the onset of several emerging and re-merging diseases. This demands the faster designing of new drugs to curb the deadly diseases in less waiting time to cure the animals and humans. Drug molecules interact with only protein surface on specific locations termed as ligand binding sites (LBS). Therefore, the knowledge of LBS is required for rational drug designing. Existing geometrical LBS prediction methods rely on search of cavities based on the fact that 83% of the LBS found in deep cavities, however, these methods usually fail where LBS localize outside deep cavities. To overcome this challenge, the present work provides an artificial neural network (ANN) based method to predict LBS outside deep cavities in animal proteins including human to facilitate drug designing. In the present work a feed-forward backpropagation neural network was trained by utilizing 38 structural, atomic, physiochemical, and evolutionary discriminant features of LBS and non-LBS residues localized in the extracted roughest patch on protein surface. The performance of this ANN based prediction method was found 76% better for those proteins where cavity subspace (extracted by MetaPocket 2.0, a consensus method) failed to predict LBS due to their localization outside the deep cavities. The prediction of LBS outside deep cavities will facilitate in drug designing for the proteins where it is not possible due to lack of LBS information as the geometrical LBS prediction methods rely on extraction of deep cavities.
Collapse
Affiliation(s)
- Kalpana Singh
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, India
| | - Yashpal Singh Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana-141004, India
| |
Collapse
|
142
|
Fijalkowski I, Snauwaert V, Van Damme P. Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression. mBio 2024; 15:e0033324. [PMID: 38511928 PMCID: PMC11005335 DOI: 10.1128/mbio.00333-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
In recent years, it has become evident that the true complexity of bacterial proteomes remains underestimated. Gene annotation tools are known to propagate biases and overlook certain classes of truly expressed proteins, particularly proteoforms-protein isoforms arising from a single gene. Recent (re-)annotation efforts heavily rely on ribosome profiling by providing a direct readout of translation to fully describe bacterial proteomes. In this study, we employ a robust riboproteogenomic pipeline to conduct a systematic census of expressed N-terminal proteoform pairs, representing two isoforms encoded by a single gene raised by annotated and alternative translation initiation, in Salmonella. Intriguingly, conditional-dependent changes in relative utilization of annotated and alternative translation initiation sites (TIS) were observed in several cases. This suggests that TIS selection is subject to regulatory control, adding yet another layer of complexity to our understanding of bacterial proteomes. IMPORTANCE With the emerging theme of genes within genes comprising the existence of alternative open reading frames (ORFs) generated by translation initiation at in-frame start codons, mechanisms that control the relative utilization of annotated and alternative TIS need to be unraveled and our molecular understanding of resulting proteoforms broadened. Utilizing complementary ribosome profiling strategies to map ORF boundaries, we uncovered dual-encoding ORFs generated by in-frame TIS usage in Salmonella. Besides demonstrating that alternative TIS usage may generate proteoforms with different characteristics, such as differential localization and specialized function, quantitative aspects of conditional retapamulin-assisted ribosome profiling (Ribo-RET) translation initiation maps offer unprecedented insights into the relative utilization of annotated and alternative TIS, enabling the exploration of gene regulatory mechanisms that control TIS usage and, consequently, the translation of N-terminal proteoform pairs.
Collapse
Affiliation(s)
- Igor Fijalkowski
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Valdes Snauwaert
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
143
|
Karagöl A, Karagöl T, Smorodina E, Zhang S. Structural bioinformatics studies of glutamate transporters and their AlphaFold2 predicted water-soluble QTY variants and uncovering the natural mutations of L->Q, I->T, F->Y and Q->L, T->I and Y->F. PLoS One 2024; 19:e0289644. [PMID: 38598436 PMCID: PMC11006163 DOI: 10.1371/journal.pone.0289644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/22/2023] [Indexed: 04/12/2024] Open
Abstract
Glutamate transporters play key roles in nervous physiology by modulating excitatory neurotransmitter levels, when malfunctioning, involving in a wide range of neurological and physiological disorders. However, integral transmembrane proteins including the glutamate transporters remain notoriously difficult to study, due to their localization within the cell membrane. Here we present the structural bioinformatics studies of glutamate transporters and their water-soluble variants generated through QTY-code, a protein design strategy based on systematic amino acid substitutions. These include 2 structures determined by X-ray crystallography, cryo-EM, and 6 predicted by AlphaFold2, and their predicted water-soluble QTY variants. In the native structures of glutamate transporters, transmembrane helices contain hydrophobic amino acids such as leucine (L), isoleucine (I), and phenylalanine (F). To design water-soluble variants, these hydrophobic amino acids are systematically replaced by hydrophilic amino acids, namely glutamine (Q), threonine (T) and tyrosine (Y). The QTY variants exhibited water-solubility, with four having identical isoelectric focusing points (pI) and the other four having very similar pI. We present the superposed structures of the native glutamate transporters and their water-soluble QTY variants. The superposed structures displayed remarkable similarity with RMSD 0.528Å-2.456Å, despite significant protein transmembrane sequence differences (41.1%->53.8%). Additionally, we examined the differences of hydrophobicity patches between the native glutamate transporters and their QTY variants. Upon closer inspection, we discovered multiple natural variations of L->Q, I->T, F->Y and Q->L, T->I, Y->F in these transporters. Some of these natural variations were benign and the remaining were reported in specific neurological disorders. We further investigated the characteristics of hydrophobic to hydrophilic substitutions in glutamate transporters, utilizing variant analysis and evolutionary profiling. Our structural bioinformatics studies not only provided insight into the differences between the hydrophobic helices and hydrophilic helices in the glutamate transporters, but they are also expected to stimulate further study of other water-soluble transmembrane proteins.
Collapse
Affiliation(s)
- Alper Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Taner Karagöl
- Istanbul University Istanbul Medical Faculty, Istanbul, Turkey
| | - Eva Smorodina
- Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| |
Collapse
|
144
|
Balasundaram A, C Doss GP. Deciphering the Impact of Rare Missense Variants in EGFR-TKI-Resistant Non-Small-Cell Lung Cancer through Whole Exome Sequencing: A Computational Approach. ACS OMEGA 2024; 9:16288-16302. [PMID: 38617633 PMCID: PMC11007825 DOI: 10.1021/acsomega.3c10229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 04/16/2024]
Abstract
Targeted therapy revolutionizes the treatment of non-small-cell lung cancer (NSCLC), harboring molecular change. Epidermal growth factor receptor(EGFR) mutations play a crucial role in the development of NSCLC, serving as a pivotal factor in its pathogenesis. We elucidated the mechanisms of resistance and potential therapeutic strategies in NSCLC resistant to the EGFR-tyrosine kinase inhibitor (EGFR-TKI). This is achieved by identifying rare missense variants through whole exome sequencing (WES). The goal is to enhance our understanding, identify biomarkers, and lay the groundwork for targeted interventions, thereby offering hope for an improved NSCLC treatment landscape. We conducted WES analysis on 16 NSCLC samples with EGFR-TKI-resistant NSCLC obtained from SRA-NCBI (PRJEB50602) to reveal genomic profiles within the EGFR-TKI. Our findings showed that 48% of the variants were missense, and after filtering with the Ensembl variant effect predictor, 53 rare missense variants in 23 genes were identified as highly deleterious. Further examination using pathogenic tools like PredictSNP revealed 12 deleterious rare missense variants in 7 genes: ZNF717, PSPH, ESRRA, SEMA3G, PTPN7, CAVIN4, and MYBBP1A. Molecular dynamics simulation (MDS) suggested that the L385P variant alters the structural flexibility of ESRRA, potentially leading to unfolding of ERRα proteins. This could impact their function and alter ERRα expression. These insights from MDS enhance our understanding of the structural and dynamic consequences of the L385P ESRRA variant and provide valuable implications for subsequent therapeutic considerations and targeted interventions.
Collapse
Affiliation(s)
- Ambritha Balasundaram
- Laboratory of Integrative
Genomics, Department of Integrative Biology, School of BioSciences
and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Laboratory of Integrative
Genomics, Department of Integrative Biology, School of BioSciences
and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| |
Collapse
|
145
|
Cuevas-Zuviría B, Garcia AK, Rivier AJ, Rucker HR, Carruthers BM, Kaçar B. Emergence of an Orphan Nitrogenase Protein Following Atmospheric Oxygenation. Mol Biol Evol 2024; 41:msae067. [PMID: 38526235 PMCID: PMC11018506 DOI: 10.1093/molbev/msae067] [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: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.
Collapse
Affiliation(s)
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex J Rivier
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Holly R Rucker
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brooke M Carruthers
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| |
Collapse
|
146
|
Amoah AS, Pestov NB, Korneenko TV, Prokhorenko IA, Kurakin GF, Barlev NA. Lipoxygenases at the Intersection of Infection and Carcinogenesis. Int J Mol Sci 2024; 25:3961. [PMID: 38612771 PMCID: PMC11011848 DOI: 10.3390/ijms25073961] [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: 01/31/2024] [Revised: 03/08/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The persisting presence of opportunistic pathogens like Pseudomonas aeruginosa poses a significant threat to many immunocompromised cancer patients with pulmonary infections. This review highlights the complexity of interactions in the host's defensive eicosanoid signaling network and its hijacking by pathogenic bacteria to their own advantage. Human lipoxygenases (ALOXs) and their mouse counterparts are integral elements of the innate immune system, mostly operating in the pro-inflammatory mode. Taking into account the indispensable role of inflammation in carcinogenesis, lipoxygenases have counteracting roles in this process. In addition to describing the structure-function of lipoxygenases in this review, we discuss their roles in such critical processes as cancer cell signaling, metastases, death of cancer and immune cells through ferroptosis, as well as the roles of ALOXs in carcinogenesis promoted by pathogenic infections. Finally, we discuss perspectives of novel oncotherapeutic approaches to harness lipoxygenase signaling in tumors.
Collapse
Affiliation(s)
- Abdul-Saleem Amoah
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (A.-S.A.); (N.A.B.)
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nikolay B. Pestov
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (A.-S.A.); (N.A.B.)
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (T.V.K.); (I.A.P.)
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow 108819, Russia
- Vavilov Institute of General Genetics, Moscow 119991, Russia
| | - Tatyana V. Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (T.V.K.); (I.A.P.)
| | - Igor A. Prokhorenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia; (T.V.K.); (I.A.P.)
| | - Georgy F. Kurakin
- Department of Biochemistry, Pirogov Russian National Research Medical University, Moscow 117513, Russia;
| | - Nickolai A. Barlev
- Institute of Biomedical Chemistry, Moscow 119121, Russia; (A.-S.A.); (N.A.B.)
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Moscow 108819, Russia
| |
Collapse
|
147
|
Zhang C, Lu P, Wei S, Hu C, Miyoshi M, Okamoto K, Itoh H, Okuda S, Suzuki M, Kawakami H, Nagata K. Refolding, Crystallization, and Crystal Structure Analysis of a Scavenger Receptor Cysteine-Rich Domain of Human Salivary Agglutinin Expressed in Escherichia coli. Protein J 2024; 43:283-297. [PMID: 38265733 PMCID: PMC11058800 DOI: 10.1007/s10930-023-10173-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2023] [Indexed: 01/25/2024]
Abstract
Scavenger receptors are a protein superfamily that typically consists of one or more repeats of the scavenger receptor cysteine-rich structural domain (SRCRD), which is an ancient and highly conserved protein module. The expression and purification of eukaryotic proteins containing multiple disulfide bonds has always been challenging. The expression systems that are commonly used to express SRCRD proteins mainly consist of eukaryotic protein expression systems. Herein, we established a high-level expression strategy of a Type B SRCRD unit from human salivary agglutinin using the Escherichia coli expression system, followed by a refolding and purification process. The untagged recombinant SRCRD was expressed in E. coli using the pET-32a vector, which was followed by a refolding process using the GSH/GSSG redox system. The SRCRD expressed in E. coli SHuffle T7 showed better solubility after refolding than that expressed in E. coli BL21(DE3), suggesting the importance of the disulfide bond content prior to refolding. The quality of the refolded protein was finally assessed using crystallization and crystal structure analysis. As proteins refolded from inclusion bodies exhibit a high crystal quality and reproducibility, this method is considered a reliable strategy for SRCRD protein expression and purification. To further confirm the structural integrity of the refolded SRCRD protein, the purified protein was subjected to crystallization using sitting-drop vapor diffusion method. The obtained crystals of SRCRD diffracted X-rays to a resolution of 1.47 Å. The solved crystal structure appeared to be highly conserved, with four disulfide bonds appropriately formed. The surface charge distribution of homologous SRCRD proteins indicates that the negatively charged region at the surface is associated with their calcium-dependent ligand recognition. These results suggest that a high-quality SRCRD protein expressed by E. coli SHuffle T7 can be successfully folded and purified, providing new options for the expression of members of the scavenger receptor superfamily.
Collapse
Affiliation(s)
- Changyu Zhang
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Peng Lu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Sibo Wei
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Chaoyue Hu
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mitsuko Miyoshi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ken Okamoto
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hideaki Itoh
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Suguru Okuda
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroshi Kawakami
- Department of Food Science and Nutrition, Faculty of Home Economics, Kyoritsu Women's University, 2-2-1 Hitotsubashi, Chiyoda-ku, Tokyo, 101-8437, Japan
| | - Koji Nagata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Research Center for Food Safety, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| |
Collapse
|
148
|
Parvathy J, Yazhini A, Srinivasan N, Sowdhamini R. Interfacial residues in protein-protein complexes are in the eyes of the beholder. Proteins 2024; 92:509-528. [PMID: 37982321 DOI: 10.1002/prot.26628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023]
Abstract
Interactions between proteins are vital in almost all biological processes. The characterization of protein-protein interactions helps us understand the mechanistic basis of biological processes, thereby enabling the manipulation of proteins for biotechnological and clinical purposes. The interface residues of a protein-protein complex are assumed to have the following two properties: (a) they always interact with a residue of a partner protein, which forms the basis for distance-based interface residue identification methods, and (b) they are solvent-exposed in the isolated form of the protein and become buried in the complex form, which forms the basis for Accessible Surface Area (ASA)-based methods. The study interrogates this popular assumption by recognizing interface residues in protein-protein complexes through these two methods. The results show that a few residues are identified uniquely by each method, and the extent of conservation, propensities, and their contribution to the stability of protein-protein interaction varies substantially between these residues. The case study analyses showed that interface residues, unique to distance, participate in crucial interactions that hold the proteins together, whereas the interface residues unique to the ASA method have a potential role in the recognition, dynamics, and specificity of the complex and can also be a hotspot. Overall, the study recommends applying both distance and ASA methods so that some interface residues missed by either method but crucial to the stability, recognition, dynamics, and function of protein-protein complexes are identified in a complementary manner.
Collapse
Affiliation(s)
- Jayadevan Parvathy
- Interdisciplinary Mathematical Sciences Initiative (IMI), Indian Institute of Science, Bangalore, India
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
| | | | | | - Ramanathan Sowdhamini
- Molecular Biophysics Unit (MBU), Indian Institute of Science, Bangalore, India
- National Center for Biological Sciences (NCBS), Bangalore, India
| |
Collapse
|
149
|
Lauber F, Deme JC, Liu X, Kjær A, Miller HL, Alcock F, Lea SM, Berks BC. Structural insights into the mechanism of protein transport by the Type 9 Secretion System translocon. Nat Microbiol 2024; 9:1089-1102. [PMID: 38538833 PMCID: PMC10994853 DOI: 10.1038/s41564-024-01644-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/19/2024] [Indexed: 04/06/2024]
Abstract
Secretion systems are protein export machines that enable bacteria to exploit their environment through the release of protein effectors. The Type 9 Secretion System (T9SS) is responsible for protein export across the outer membrane (OM) of bacteria of the phylum Bacteroidota. Here we trap the T9SS of Flavobacterium johnsoniae in the process of substrate transport by disrupting the T9SS motor complex. Cryo-EM analysis of purified substrate-bound T9SS translocons reveals an extended translocon structure in which the previously described translocon core is augmented by a periplasmic structure incorporating the proteins SprE, PorD and a homologue of the canonical periplasmic chaperone Skp. Substrate proteins bind to the extracellular loops of a carrier protein within the translocon pore. As transport intermediates accumulate on the translocon when energetic input is removed, we deduce that release of the substrate-carrier protein complex from the translocon is the energy-requiring step in T9SS transport.
Collapse
Affiliation(s)
- Frédéric Lauber
- Department of Biochemistry, University of Oxford, Oxford, UK
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Justin C Deme
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK
| | - Xiaolong Liu
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Andreas Kjær
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Helen L Miller
- Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
| | - Felicity Alcock
- Department of Biochemistry, University of Oxford, Oxford, UK
- Newcastle University Biosciences Institute, Newcastle University, Newcastle, UK
| | - Susan M Lea
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
- The Central Oxford Structural Molecular Imaging Centre (COSMIC), University of Oxford, Oxford, UK.
| | - Ben C Berks
- Department of Biochemistry, University of Oxford, Oxford, UK.
| |
Collapse
|
150
|
Eerlings R, Gupta P, Lee XY, Nguyen T, El Kharraz S, Handle F, Smeets E, Moris L, Devlies W, Vandewinkel B, Thiry I, Ta DT, Gorkovskiy A, Voordeckers K, Henckaerts E, Pinheiro VB, Claessens F, Verstrepen KJ, Voet A, Helsen C. Rational evolution for altering the ligand preference of estrogen receptor alpha. Protein Sci 2024; 33:e4940. [PMID: 38511482 PMCID: PMC10955623 DOI: 10.1002/pro.4940] [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: 11/02/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 03/22/2024]
Abstract
Estrogen receptor α is commonly used in synthetic biology to control the activity of genome editing tools. The activating ligands, estrogens, however, interfere with various cellular processes, thereby limiting the applicability of this receptor. Altering its ligand preference to chemicals of choice solves this hurdle but requires adaptation of unspecified ligand-interacting residues. Here, we provide a solution by combining rational protein design with multi-site-directed mutagenesis and directed evolution of stably integrated variants in Saccharomyces cerevisiae. This method yielded an estrogen receptor variant, named TERRA, that lost its estrogen responsiveness and became activated by tamoxifen, an anti-estrogenic drug used for breast cancer treatment. This tamoxifen preference of TERRA was maintained in mammalian cells and mice, even when fused to Cre recombinase, expanding the mammalian synthetic biology toolbox. Not only is our platform transferable to engineer ligand preference of any steroid receptor, it can also profile drug-resistance landscapes for steroid receptor-targeted therapies.
Collapse
Affiliation(s)
- Roy Eerlings
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Purvi Gupta
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Xiao Yin Lee
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Tien Nguyen
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Sarah El Kharraz
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Florian Handle
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Elien Smeets
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Lisa Moris
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Department of UrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Wout Devlies
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
- Department of UrologyUniversity Hospitals LeuvenLeuvenBelgium
| | - Bram Vandewinkel
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Irina Thiry
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Duy Tien Ta
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Anton Gorkovskiy
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Karin Voordeckers
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Els Henckaerts
- Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and TransplantationKU LeuvenLeuvenBelgium
| | - Vitor B. Pinheiro
- KU Leuven, Department of Pharmaceutical and Pharmacological SciencesRega Institute for Medical ResearchLeuvenBelgium
| | - Frank Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| | - Kevin J. Verstrepen
- Laboratory of Systems BiologyVIB‐KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory for Genetics and Genomics, Center of Microbial and Plant Genetics, Department M2SKU LeuvenHeverleeBelgium
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of ChemistryKU LeuvenHeverleeBelgium
| | - Christine Helsen
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular MedicineKU LeuvenLeuvenBelgium
| |
Collapse
|