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Tan C, Reilly B, Ma G, Murao A, Jha A, Aziz M, Wang P. Neutrophils disrupt B-1a cell homeostasis by targeting Siglec-G to exacerbate sepsis. Cell Mol Immunol 2024; 21:707-722. [PMID: 38789529 PMCID: PMC11214631 DOI: 10.1038/s41423-024-01165-7] [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: 12/12/2023] [Accepted: 04/11/2024] [Indexed: 05/26/2024] Open
Abstract
B-1a cells, an innate-like cell population, are crucial for pathogen defense and the regulation of inflammation through their release of natural IgM and IL-10. In sepsis, B-1a cell numbers are decreased in the peritoneal cavity as they robustly migrate to the spleen. Within the spleen, migrating B-1a cells differentiate into plasma cells, leading to alterations in their original phenotype and functionality. We discovered a key player, sialic acid-binding immunoglobulin-like lectin-G (Siglec-G), which is expressed predominantly on B-1a cells and negatively regulates B-1a cell migration to maintain homeostasis. Siglec-G interacts with CXCR4/CXCL12 to modulate B-1a cell migration. Neutrophils aid B-1a cell migration via neutrophil elastase (NE)-mediated Siglec-G cleavage. Human studies revealed increased NE expression in septic patients. We identified an NE cleavage sequence in silico, leading to the discovery of a decoy peptide that protects Siglec-G, preserves peritoneal B-1a cells, reduces inflammation, and enhances sepsis survival. The role of Siglec-G in inhibiting B-1a cell migration to maintain their inherent phenotype and function is compromised by NE in sepsis, offering valuable insights into B-1a cell homeostasis. Employing a small decoy peptide to prevent NE-mediated Siglec-G cleavage has emerged as a promising strategy to sustain peritoneal B-1a cell homeostasis, alleviate inflammation, and ultimately improve outcomes in sepsis patients.
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Affiliation(s)
- Chuyi Tan
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA
- Department of Pathophysiology, Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Bridgette Reilly
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Gaifeng Ma
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Atsushi Murao
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Alok Jha
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Monowar Aziz
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA.
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA.
| | - Ping Wang
- Center for Immunology and Inflammation, the Feinstein Institutes for Medical Research, Manhasset, New York, USA.
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, New York, USA.
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2
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Nofi CP, Tan C, Ma G, Kobritz M, Prince JM, Wang H, Aziz M, Wang P. A novel opsonic eCIRP inhibitor for lethal sepsis. J Leukoc Biol 2024; 115:385-400. [PMID: 37774691 PMCID: PMC10799304 DOI: 10.1093/jleuko/qiad119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 10/01/2023] Open
Abstract
Sepsis is a life-threatening inflammatory condition partly orchestrated by the release of various damage-associated molecular patterns such as extracellular cold-inducible RNA-binding protein (eCIRP). Despite advances in understanding the pathogenic role of eCIRP in inflammatory diseases, novel therapeutic strategies to prevent its excessive inflammatory response are lacking. Milk fat globule-epidermal growth factor-VIII (MFG-E8) is critical for the opsonic clearance of apoptotic cells, but its potential involvement in the removal of eCIRP was previously unknown. Here, we report that MFG-E8 can strongly bind eCIRP to facilitate αvβ3-integrin-dependent internalization and lysosome-dependent degradation of MFG-E8/eCIRP complexes, thereby attenuating excessive inflammation. Genetic disruption of MFG-E8 expression exaggerated sepsis-induced systemic accumulation of eCIRP and other cytokines, and consequently exacerbated sepsis-associated acute lung injury. In contrast, MFG-E8-derived oligopeptide recapitulated its eCIRP binding properties, and significantly attenuated eCIRP-induced inflammation to confer protection against sepsis. Our findings suggest a novel therapeutic approach to attenuate eCIRP-induced inflammation to improve outcomes of lethal sepsis.
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Affiliation(s)
- Colleen P Nofi
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Elmezzi Graduate School of Molecular Medicine, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
| | - Chuyi Tan
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
| | - Gaifeng Ma
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
| | - Molly Kobritz
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
| | - Jose M Prince
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
| | - Haichao Wang
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Elmezzi Graduate School of Molecular Medicine, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
| | - Monowar Aziz
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Elmezzi Graduate School of Molecular Medicine, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
| | - Ping Wang
- Center for Immunology and Inflammation, Feinstein Institutes for Medical Research, 350 Community Drive, Manhasset, NY 11030, United States
- Elmezzi Graduate School of Molecular Medicine, 350 Community Drive, Manhasset, NY 11030, United States
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
- Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra Blvd, Hempstead, NY 11549, United States
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3
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Wodak SJ, Vajda S, Lensink MF, Kozakov D, Bates PA. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annu Rev Biophys 2023; 52:183-206. [PMID: 36626764 PMCID: PMC10885158 DOI: 10.1146/annurev-biophys-102622-084607] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dramatic advances were observed for the accurate prediction of single protein chains, driven by a surge of deep learning methodologies entering the prediction field. We review the mainscientific developments that enabled these recent breakthroughs and feature the important role of blind prediction experiments in building up and nurturing the structure prediction field. We discuss how the new wave of artificial intelligence-based methods is impacting the fields of computational and experimental structural biology and highlight areas in which deep learning methods are likely to lead to future developments, provided that major challenges are overcome.
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Affiliation(s)
- Shoshana J Wodak
- VIB-VUB Center for Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium;
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA;
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Marc F Lensink
- Univ. Lille, CNRS, UMR 8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France;
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA;
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, United Kingdom;
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4
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Negahdaripour M, Rahbar MR, Mosalanejad Z, Gholami A. Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9735626. [PMID: 35154362 PMCID: PMC8829439 DOI: 10.1155/2022/9735626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/28/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was characterized as a pandemic by the World Health Organization (WHO) in Dec. 2019. SARS-CoV-2 binds to the cell membrane through spike proteins on its surface and infects the cell. Furin, a host-cell enzyme, possesses a binding site for the spike protein. Thus, molecules that block furin could potentially be a therapeutic solution. Defensins are antimicrobial peptides that can hypothetically inhibit furin because of their arginine-rich structure. Theta-defensins, a subclass of defensins, have attracted attention as drug candidates due to their small size, unique structure, and involvement in several defense mechanisms. Theta-defensins could be a potential treatment for COVID-19 through furin inhibition and an anti-inflammatory mechanism. Note that inflammatory events are a significant and deadly condition that could happen at the later stages of COVID-19 infection. Here, the potential of theta-defensins against SARS-CoV-2 infection was investigated through in silico approaches. Based on docking analysis results, theta-defensins can function as furin inhibitors. Additionally, a novel candidate peptide against COVID-19 with optimal properties regarding antigenicity, stability, electrostatic potential, and binding strength was proposed. Further in vitro/in vivo investigations could verify the efficiency of the designed novel peptide.
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Affiliation(s)
- Manica Negahdaripour
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Mosalanejad
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ahmad Gholami
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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5
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Predicting PY motif-mediated protein-protein interactions in the Nedd4 family of ubiquitin ligases. PLoS One 2021; 16:e0258315. [PMID: 34637467 PMCID: PMC8509885 DOI: 10.1371/journal.pone.0258315] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/23/2021] [Indexed: 01/07/2023] Open
Abstract
The Nedd4 family contains several structurally related but functionally distinct HECT-type ubiquitin ligases. The members of the Nedd4 family are known to recognize substrates through their multiple WW domains, which recognize PY motifs (PPxY, LPxY) or phospho-threonine or phospho-serine residues. To better understand protein interactor recognition mechanisms across the Nedd4 family, we report the development and implementation of a python-based tool, PxYFinder, to identify PY motifs in the primary sequences of previously identified interactors of Nedd4 and related ligases. Using PxYFinder, we find that, on average, half of Nedd4 family interactions are likely PY-motif mediated. Further, we find that PPxY motifs are more prevalent than LPxY motifs and are more likely to occur in proline-rich regions and that PPxY regions are more disordered on average relative to LPxY-containing regions. Informed by consensus sequences for PY motifs across the Nedd4 interactome, we rationally designed a focused peptide library and employed a computational screen, revealing sequence- and biomolecular interaction-dependent determinants of WW-domain/PY-motif interactions. Cumulatively, our efforts provide a new bioinformatic tool and expand our understanding of sequence and structural factors that contribute to PY-motif mediated interactor recognition across the Nedd4 family.
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6
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Abstract
Biological processes are often mediated by complexes formed between proteins and various biomolecules. The 3D structures of such protein-biomolecule complexes provide insights into the molecular mechanism of their action. The structure of these complexes can be predicted by various computational methods. Choosing an appropriate method for modelling depends on the category of biomolecule that a protein interacts with and the availability of structural information about the protein and its interacting partner. We intend for the contents of this chapter to serve as a guide as to what software would be the most appropriate for the type of data at hand and the kind of 3D complex structure required. Particularly, we have dealt with protein-small molecule ligand, protein-peptide, protein-protein, and protein-nucleic acid interactions.Most, if not all, model building protocols perform some sampling and scoring. Typically, several alternate conformations and configurations of the interactors are sampled. Each such sample is then scored for optimization. To boost the confidence in these predicted models, their assessment using other independent scoring schemes besides the inbuilt/default ones would prove to be helpful. This chapter also lists such software and serves as a guide to gauge the fidelity of modelled structures of biomolecular complexes.
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Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill KA, Vajda S, Kozakov D, Schueler-Furman O. Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45. Proteins 2020; 88:1037-1049. [PMID: 31891416 PMCID: PMC7539656 DOI: 10.1002/prot.25871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/17/2019] [Accepted: 12/26/2019] [Indexed: 01/09/2023]
Abstract
Peptide-protein docking is challenging due to the considerable conformational freedom of the peptide. CAPRI rounds 38-45 included two peptide-protein interactions, both characterized by a peptide forming an additional beta strand of a beta sheet in the receptor. Using the Rosetta FlexPepDock peptide docking protocol we generated top-performing, high-accuracy models for targets 134 and 135, involving an interaction between a peptide derived from L-MAG with DLC8. In addition, we were able to generate the only medium-accuracy models for a particularly challenging target, T121. In contrast to the classical peptide-mediated interaction, in which receptor side chains contact both peptide backbone and side chains, beta-sheet complementation involves a major contribution to binding by hydrogen bonds between main chain atoms. To establish how binding affinity and specificity are established in this special class of peptide-protein interactions, we extracted PeptiDBeta, a benchmark of solved structures of different protein domains that are bound by peptides via beta-sheet complementation, and tested our protocol for global peptide-docking PIPER-FlexPepDock on this dataset. We find that the beta-strand part of the peptide is sufficient to generate approximate and even high resolution models of many interactions, but inclusion of adjacent motif residues often provides additional information necessary to achieve high resolution model quality.
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Affiliation(s)
- Alisa Khramushin
- Department of Microbiologyand Molecular Genetics, Institute
for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University,
Jerusalem, Israel
| | - Orly Marcu
- Department of Microbiologyand Molecular Genetics, Institute
for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University,
Jerusalem, Israel
| | - Nawsad Alam
- Department of Microbiologyand Molecular Genetics, Institute
for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University,
Jerusalem, Israel
| | - Orly Shimony
- Department of Microbiologyand Molecular Genetics, Institute
for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University,
Jerusalem, Israel
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony
Brook University, New York, New York
- Laufer Center for Physical and Quantitative Biology, Stony
Brook University, New York, New York
| | - Emiliano Brini
- Laufer Center for Physical and Quantitative Biology, Stony
Brook University, New York, New York
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony
Brook University, New York, New York
- Department of Physics and Astronomy, Stony Brook
University, New York, New York
- Department of Chemistry, Stony Brook University, New York,
New York
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University,
Boston, Massachusetts
- Department of Chemistry, Boston University, Boston,
Massachusetts
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony
Brook University, New York, New York
- Laufer Center for Physical and Quantitative Biology, Stony
Brook University, New York, New York
| | - Ora Schueler-Furman
- Department of Microbiologyand Molecular Genetics, Institute
for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University,
Jerusalem, Israel
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Tao H, Zhang Y, Huang SY. Improving Protein-Peptide Docking Results via Pose-Clustering and Rescoring with a Combined Knowledge-Based and MM-GBSA Scoring Function. J Chem Inf Model 2020; 60:2377-2387. [PMID: 32267149 DOI: 10.1021/acs.jcim.0c00058] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein-peptide docking, which predicts the complex structure between a protein and a peptide, is a valuable computational tool in peptide therapeutics development and the mechanistic investigation of peptides involved in cellular processes. Although current peptide docking approaches are often able to sample near-native peptide binding modes, correctly identifying those near-native modes from decoys is still challenging because of the extremely high complexity of the peptide binding energy landscape. In this study, we have developed an efficient postdocking rescoring protocol using a combined scoring function of knowledge-based ITScorePP potentials and physics-based MM-GBSA energies. Tested on five benchmark/docking test sets, our postdocking strategy showed an overall significantly better performance in binding mode prediction and score-rmsd correlation than original docking approaches. Specifically, our postdocking protocol outperformed original docking approaches with success rates of 15.8 versus 10.5% for pepATTRACT on the Global_57 benchmark, 5.3 versus 5.3% for CABS-dock on the Global_57 benchmark, 17.0 versus 11.3% for FlexPepDock on the LEADS-PEP data set, 40.3 versus 33.9% for HPEPDOCK on the Local_62 benchmark, and 64.2 versus 52.8% for HPEPDOCK on the LEADS-PEP data set when the top prediction was considered. These results demonstrated the efficacy and robustness of our postdocking protocol.
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Affiliation(s)
- Huanyu Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Yanjun Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
| | - Sheng-You Huang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P. R. China
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Abstract
Many of the biological functions of the cell are driven by protein-protein interactions. However, determining which proteins interact and exactly how they do so to enable their functions, remain major research questions. Functional interactions are dependent on a number of complicated factors; therefore, modeling the three-dimensional structure of protein-protein complexes is still considered a complex endeavor. Nevertheless, the rewards for modeling protein interactions to atomic level detail are substantial, and there are numerous examples of how models can provide useful information for drug design, protein engineering, systems biology, and understanding of the immune system. Here, we provide practical guidelines for docking proteins using the web-server, SwarmDock, a flexible protein-protein docking method. Moreover, we provide an overview of the factors that need to be considered when deciding whether docking is likely to be successful.
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Affiliation(s)
- Iain H Moal
- European Bioinformatics Institute, Hinxton, UK
| | | | | | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK.
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Shen Y, Mevius DE, Caliandro R, Carrozzini B, Roh Y, Kim J, Kim S, Ha SC, Morishita M, di Luccio E. Set7 Is a H3K37 Methyltransferase in Schizosaccharomyces pombe and Is Required for Proper Gametogenesis. Structure 2019; 27:631-638.e8. [DOI: 10.1016/j.str.2019.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 11/23/2018] [Accepted: 01/18/2019] [Indexed: 11/15/2022]
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Abstract
The atomic structures of protein complexes can provide useful information for drug design, protein engineering, systems biology, and understanding pathology. Obtaining this information experimentally can be challenging. However, if the structures of the subunits are known, then it is often possible to model the complex computationally. This chapter provide practical guidelines for docking proteins using the SwarmDock flexible protein-protein docking method, providing an overview of the factors that need to be considered when deciding whether docking is likely to be successful, the preparation of structural input, generation of docked poses, analysis and ranking of docked poses, and the validation of models using external data.
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Affiliation(s)
- Iain H Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.
| | | | - Paul A Bates
- Biomolecular Modelling Laboratory, The Francis Crick Institute, London, UK
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