1
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Wang J, Youkharibache P, Marchler-Bauer A, Lanczycki C, Zhang D, Lu S, Madej T, Marchler GH, Cheng T, Chong LC, Zhao S, Yang K, Lin J, Cheng Z, Dunn R, Malkaram SA, Tai CH, Enoma D, Busby B, Johnson NL, Tabaro F, Song G, Ge Y. iCn3D: From Web-Based 3D Viewer to Structural Analysis Tool in Batch Mode. Front Mol Biosci 2022; 9:831740. [PMID: 35252351 PMCID: PMC8892267 DOI: 10.3389/fmolb.2022.831740] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
iCn3D was initially developed as a web-based 3D molecular viewer. It then evolved from visualization into a full-featured interactive structural analysis software. It became a collaborative research instrument through the sharing of permanent, shortened URLs that encapsulate not only annotated visual molecular scenes, but also all underlying data and analysis scripts in a FAIR manner. More recently, with the growth of structural databases, the need to analyze large structural datasets systematically led us to use Python scripts and convert the code to be used in Node. js scripts. We showed a few examples of Python scripts at https://github.com/ncbi/icn3d/tree/master/icn3dpython to export secondary structures or PNG images from iCn3D. Users just need to replace the URL in the Python scripts to export other annotations from iCn3D. Furthermore, any interactive iCn3D feature can be converted into a Node. js script to be run in batch mode, enabling an interactive analysis performed on one or a handful of protein complexes to be scaled up to analysis features of large ensembles of structures. Currently available Node. js analysis scripts examples are available at https://github.com/ncbi/icn3d/tree/master/icn3dnode. This development will enable ensemble analyses on growing structural databases such as AlphaFold or RoseTTAFold on one hand and Electron Microscopy on the other. In this paper, we also review new features such as DelPhi electrostatic potential, 3D view of mutations, alignment of multiple chains, assembly of multiple structures by realignment, dynamic symmetry calculation, 2D cartoons at different levels, interactive contact maps, and use of iCn3D in Jupyter Notebook as described at https://pypi.org/project/icn3dpy.
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Affiliation(s)
- Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
- *Correspondence: Jiyao Wang,
| | | | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Christopher Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Dachuan Zhang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Shennan Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Gabriele H. Marchler
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Li Chuin Chong
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Turkey
| | | | - Kevin Yang
- University of Maryland, College Park, MD, United States
| | - Jack Lin
- University of Washington, Tacoma, WA, United States
| | - Zhiyu Cheng
- University of California, Irvine, Irvine, CA, United States
| | - Rachel Dunn
- University of British Columbia, Vancouver, BC, Canada
| | | | - Chin-Hsien Tai
- National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Ben Busby
- DNAnexus, Pittsburgh, PA, United States
| | - Nicholas L. Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
| | - Francesco Tabaro
- European Molecular Biology Laboratory, EMBL Rome, Monterotondo, Italy
| | - Guangfeng Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Yuchen Ge
- Johns Hopkins University, Baltimore, MD, United States
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2
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Thaker TM, Mishra S, Zhou W, Mohan M, Tang Q, Faraldo-Goméz JD, Mchaourab HS, Tomasiak TM. Asymmetric drug binding in an ATP-loaded inward-facing state of an ABC transporter. Nat Chem Biol 2022; 18:226-235. [PMID: 34931066 PMCID: PMC9242650 DOI: 10.1038/s41589-021-00936-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/26/2021] [Indexed: 12/24/2022]
Abstract
Substrate efflux by ATP-binding cassette (ABC) transporters, which play a major role in multidrug resistance, entails the ATP-powered interconversion between transporter intermediates. Despite recent progress in structure elucidation, a number of intermediates have yet to be visualized and mechanistically interpreted. Here, we combine cryogenic-electron microscopy (cryo-EM), double electron-electron resonance spectroscopy and molecular dynamics simulations to profile a previously unobserved intermediate of BmrCD, a heterodimeric multidrug ABC exporter from Bacillus subtilis. In our cryo-EM structure, ATP-bound BmrCD adopts an inward-facing architecture featuring two molecules of the substrate Hoechst-33342 in a striking asymmetric head-to-tail arrangement. Deletion of the extracellular domain capping the substrate-binding chamber or mutation of Hoechst-coordinating residues abrogates cooperative stimulation of ATP hydrolysis. Together, our findings support a mechanistic role for symmetry mismatch between the nucleotide binding and the transmembrane domains in the conformational cycle of ABC transporters and is of notable importance for rational design of molecules for targeted ABC transporter inhibition.
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Affiliation(s)
- Tarjani M Thaker
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
- St Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenchang Zhou
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michael Mohan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Qingyu Tang
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - José D Faraldo-Goméz
- Theoretical Molecular Biophysics Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA.
| | - Thomas M Tomasiak
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.
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3
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Sayers EW, Bolton EE, Brister JR, Canese K, Chan J, Comeau DC, Connor R, Funk K, Kelly C, Kim S, Madej T, Marchler-Bauer A, Lanczycki C, Lathrop S, Lu Z, Thibaud-Nissen F, Murphy T, Phan L, Skripchenko Y, Tse T, Wang J, Williams R, Trawick BW, Pruitt KD, Sherry ST. Database resources of the national center for biotechnology information. Nucleic Acids Res 2021; 50:D20-D26. [PMID: 34850941 DOI: 10.1093/nar/gkab1112] [Citation(s) in RCA: 917] [Impact Index Per Article: 305.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/20/2021] [Accepted: 11/18/2021] [Indexed: 11/14/2022] Open
Abstract
The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.
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Affiliation(s)
- Eric W Sayers
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kathi Canese
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jessica Chan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Donald C Comeau
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Ryan Connor
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kathryn Funk
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Chris Kelly
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Tom Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Christopher Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stacy Lathrop
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Terence Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Lon Phan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Yuri Skripchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Tony Tse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Rebecca Williams
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Barton W Trawick
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Stephen T Sherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA
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4
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Youkharibache P. Topological and Structural Plasticity of the Single Ig Fold and the Double Ig Fold Present in CD19. Biomolecules 2021; 11:biom11091290. [PMID: 34572502 PMCID: PMC8470474 DOI: 10.3390/biom11091290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/18/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
The Ig fold has had a remarkable success in vertebrate evolution, with a presence in over 2% of human genes. The Ig fold is not just the elementary structural domain of antibodies and TCRs, it is also at the heart of a staggering 30% of immunologic cell surface receptors, making it a major orchestrator of cell–cell interactions. While BCRs, TCRs, and numerous Ig-based cell surface receptors form homo- or heterodimers on the same cell surface (in cis), many of them interface as ligand-receptors (checkpoints) on interacting cells (in trans) through their Ig domains. New Ig-Ig interfaces are still being discovered between Ig-based cell surface receptors, even in well-known families such as B7. What is largely ignored, however, is that the Ig fold itself is pseudosymmetric, a property that makes the Ig domain a versatile self-associative 3D structure and may, in part, explain its success in evolution, especially through its ability to bind in cis or in trans in the context of cell surface receptor–ligand interactions. In this paper, we review the Ig domains’ tertiary and quaternary pseudosymmetries, with particular attention to the newly identified double Ig fold in the solved CD19 molecular structure to highlight the underlying fundamental folding elements of Ig domains, i.e., Ig protodomains. This pseudosymmetric property of Ig domains gives us a decoding frame of reference to understand the fold, relate all Ig domain forms, single or double, and suggest new protein engineering avenues.
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5
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Caillat C, Guilligay D, Torralba J, Friedrich N, Nieva JL, Trkola A, Chipot CJ, Dehez FL, Weissenhorn W. Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies. eLife 2021; 10:65005. [PMID: 33871352 PMCID: PMC8084527 DOI: 10.7554/elife.65005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 04/18/2021] [Indexed: 12/19/2022] Open
Abstract
The HIV-1 gp120/gp41 trimer undergoes a series of conformational changes in order to catalyze gp41-induced fusion of viral and cellular membranes. Here, we present the crystal structure of gp41 locked in a fusion intermediate state by an MPER-specific neutralizing antibody. The structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides and the transmembrane regions pointing into different directions. Hinge regions located adjacent to the fusion peptide and the transmembrane region facilitate the conformational flexibility that allows high-affinity binding of broadly neutralizing anti-MPER antibodies. Molecular dynamics simulation of the MPER Ab-stabilized gp41 conformation reveals a possible transition pathway into the final post-fusion conformation with the central fusion peptides forming a hydrophobic core with flanking transmembrane regions. This suggests that MPER-specific broadly neutralizing antibodies can block final steps of refolding of the fusion peptide and the transmembrane region, which is required for completing membrane fusion.
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Affiliation(s)
- Christophe Caillat
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Delphine Guilligay
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
| | - Johana Torralba
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Jose L Nieva
- Instituto Biofisika (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Christophe J Chipot
- Laboratoire de Physique et Chimie Théoriques (LPCT), University of Lorraine, Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé, CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-lès-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - François L Dehez
- Laboratoire de Physique et Chimie Théoriques (LPCT), University of Lorraine, Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé, CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-lès-Nancy, France
| | - Winfried Weissenhorn
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), Grenoble, France
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6
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Shalit Y, Tuvi-Arad I. Side chain flexibility and the symmetry of protein homodimers. PLoS One 2020; 15:e0235863. [PMID: 32706779 PMCID: PMC7380632 DOI: 10.1371/journal.pone.0235863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
A comprehensive analysis of crystallographic data of 565 high-resolution protein homodimers comprised of over 250,000 residues suggests that amino acids form two groups that differ in their tendency to distort or symmetrize the structure of protein homodimers. Residues of the first group tend to distort the protein homodimer and generally have long or polar side chains. These include: Lys, Gln, Glu, Arg, Asn, Met, Ser, Thr and Asp. Residues of the second group contribute to protein symmetry and are generally characterized by short or aromatic side chains. These include: Ile, Pro, His, Val, Cys, Leu, Trp, Tyr, Phe, Ala and Gly. The distributions of the continuous symmetry measures of the proteins and the continuous chirality measures of their building blocks highlight the role of side chain geometry and the interplay between entropy and symmetry in dictating the conformational flexibility of proteins.
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Affiliation(s)
- Yaffa Shalit
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, Raanana, Israel
- * E-mail:
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7
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Sarti E, Aleksandrova AA, Ganta SK, Yavatkar AS, Forrest LR. EncoMPASS: an online database for analyzing structure and symmetry in membrane proteins. Nucleic Acids Res 2020; 47:D315-D321. [PMID: 30357403 PMCID: PMC6323976 DOI: 10.1093/nar/gky952] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/05/2018] [Indexed: 12/21/2022] Open
Abstract
The EncoMPASS online database (http://encompass.ninds.nih.gov) collects, organizes, and presents information about membrane proteins of known structure, emphasizing their structural similarities as well as their quaternary and internal symmetries. Unlike, e.g. SCOP, the EncoMPASS database does not aim for a strict classification of membrane proteins, but instead is organized as a protein chain-centric network of sequence and structural homologues. The online server for the EncoMPASS database provides tools for comparing the structural features of its entries, making it a useful resource for homology modeling and active site identification studies. The database can also be used for inferring functionality, which for membrane proteins often involves symmetry-related mechanisms. To this end, the online database also provides a comprehensive description of both the quaternary and internal symmetries in known membrane protein structures, with a particular focus on their orientation relative to the membrane.
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Affiliation(s)
- Edoardo Sarti
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Antoniya A Aleksandrova
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Srujan K Ganta
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amarendra S Yavatkar
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lucy R Forrest
- Computational Structural Biology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Tuvi-Arad I, Alon G. Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis. J Cheminform 2019; 11:39. [PMID: 31172379 PMCID: PMC6551912 DOI: 10.1186/s13321-019-0360-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 05/28/2019] [Indexed: 12/12/2022] Open
Abstract
Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation. Analysis of the symmetry of several sets of protein homomers, with various degrees of rotational symmetry is presented. The new methodology lays the foundations for accurate, efficient and reliable large scale symmetry analysis of protein structure and can be used as a collective variable that describes changes of the protein geometry along various processes, both at the backbone level and for the complete protein structure.
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Affiliation(s)
- Inbal Tuvi-Arad
- Department of Natural Sciences, The Open University of Israel, 4353701, Raanana, Israel.
| | - Gil Alon
- Department of Mathematics and Computer Science, The Open University of Israel, 4353701, Raanana, Israel.
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9
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MacCarthy E, Perry D, Kc DB. Advances in Protein Super-Secondary Structure Prediction and Application to Protein Structure Prediction. Methods Mol Biol 2019; 1958:15-45. [PMID: 30945212 DOI: 10.1007/978-1-4939-9161-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the advancement in various sequencing technologies, the gap between the number of protein sequences and the number of experimental protein structures is ever increasing. Community-wide initiatives like CASP have resulted in considerable efforts in the development of computational methods to accurately model protein structures from sequences. Sequence-based prediction of super-secondary structure has direct application in protein structure prediction, and there have been significant efforts in the prediction of super-secondary structure in the last decade. In this chapter, we first introduce the protein structure prediction problem and highlight some of the important progress in the field of protein structure prediction. Next, we discuss recent methods for the prediction of super-secondary structures. Finally, we discuss applications of super-secondary structure prediction in structure prediction/analysis of proteins. We also discuss prediction of protein structures that are composed of simple super-secondary structure repeats and protein structures that are composed of complex super-secondary structure repeats. Finally, we also discuss the recent trends in the field.
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Affiliation(s)
- Elijah MacCarthy
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Derrick Perry
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA
| | - Dukka B Kc
- Department of Computational Science and Engineering, North Carolina A&T State University, Greensboro, NC, USA.
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10
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Youkharibache P. Protodomains: Symmetry-Related Supersecondary Structures in Proteins and Self-Complementarity. Methods Mol Biol 2019; 1958:187-219. [PMID: 30945220 PMCID: PMC8323591 DOI: 10.1007/978-1-4939-9161-7_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We will consider in this chapter supersecondary structures (SSS) as a set of secondary structure elements (SSEs) found in protein domains. Some SSS arrangements/topologies have been consistently observed within known tertiary structural domains. We use them in the context of repeating supersecondary structures that self-assemble in a symmetric arrangement to form a domain. We call them protodomains (or protofolds). Protodomains are some of the most interesting and insightful SSSs. Within a given 3D protein domain/fold, recognizing such sets may give insights into a possible evolutionary process of duplication, fusion, and coevolution of these protodomains, pointing to possible original protogenes. On protein folding itself, pseudosymmetric domains may point to a "directed" assembly of pseudosymmetric protodomains, directed by the only fact that they are tethered together in a protein chain. On function, tertiary functional sites often occur at protodomain interfaces, as they often occur at domain-domain interfaces in quaternary arrangements.First, we will briefly review some lessons learned from a previously published census of pseudosymmetry in protein domains (Myers-Turnbull, D. et al., J Mol Biol. 426:2255-2268, 2014) to introduce protodomains/protofolds. We will observe that the most abundant and diversified folds, or superfolds, in the currently known protein structure universe are indeed pseudosymmetric. Then, we will learn by example and select a few domain representatives of important pseudosymmetric folds and chief among them the immunoglobulin (Ig) fold and go over a pseudosymmetry supersecondary structure (protodomain) analysis in tertiary and quaternary structures. We will point to currently available software tools to help in identifying pseudosymmetry, delineating protodomains, and see how the study of pseudosymmetry and the underlying supersecondary structures can enrich a structural analysis. This should potentially help in protein engineering, especially in the development of biologics and immunoengineering.
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11
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A Rahaman SN, Mat Yusop J, Mohamed-Hussein ZA, Aizat WM, Ho KL, Teh AH, Waterman J, Tan BK, Tan HL, Li AY, Chen ES, Ng CL. Crystal structure and functional analysis of human C1ORF123. PeerJ 2018; 6:e5377. [PMID: 30280012 PMCID: PMC6166629 DOI: 10.7717/peerj.5377] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022] Open
Abstract
Proteins of the DUF866 superfamily are exclusively found in eukaryotic cells. A member of the DUF866 superfamily, C1ORF123, is a human protein found in the open reading frame 123 of chromosome 1. The physiological role of C1ORF123 is yet to be determined. The only available protein structure of the DUF866 family shares just 26% sequence similarity and does not contain a zinc binding motif. Here, we present the crystal structure of the recombinant human C1ORF123 protein (rC1ORF123). The structure has a 2-fold internal symmetry dividing the monomeric protein into two mirrored halves that comprise of distinct electrostatic potential. The N-terminal half of rC1ORF123 includes a zinc-binding domain interacting with a zinc ion near to a potential ligand binding cavity. Functional studies of human C1ORF123 and its homologue in the fission yeast Schizosaccharomyces pombe (SpEss1) point to a role of DUF866 protein in mitochondrial oxidative phosphorylation.
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Affiliation(s)
| | - Jastina Mat Yusop
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia.,Center for Frontier Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Wan Mohd Aizat
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Bayan Lepas, Penang, Malaysia
| | - Jitka Waterman
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, England, United Kingdom
| | - Boon Keat Tan
- Division of Human Biology, School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur, Malaysia
| | - Hwei Ling Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Adelicia Yongling Li
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chyan Leong Ng
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
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12
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Granell M, Namura M, Alvira S, Kanamaru S, van Raaij MJ. Crystal Structure of the Carboxy-Terminal Region of the Bacteriophage T4 Proximal Long Tail Fiber Protein Gp34. Viruses 2017; 9:v9070168. [PMID: 28665339 PMCID: PMC5537660 DOI: 10.3390/v9070168] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/23/2017] [Accepted: 06/27/2017] [Indexed: 12/22/2022] Open
Abstract
Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894–1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744–1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877. A triple-helical neck connects to an extended triple β-helix domain (amino acids 900–1127) punctuated by two β-prism domains. Next, a β-prism domain decorated with short helices and extended β-helices is present (residues 1146–1238), while the C-terminal end is capped with another short β-helical region and three β-hairpins. The structure provides insight into the stability of the fibrous gp34 protein.
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Affiliation(s)
- Meritxell Granell
- Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain
| | - Mikiyoshi Namura
- Department of Life Science and Technology, Tokyo Institute of Technology, M6-11 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550, Japan.
| | - Sara Alvira
- Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain
- Departmento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Shuji Kanamaru
- Department of Life Science and Technology, Tokyo Institute of Technology, M6-11 2-12-1 Ookayama, Meguro-ku Tokyo 152-8550, Japan.
| | - Mark J van Raaij
- Departmento de Estructura de Macromoleculas, Centro Nacional de Biotecnologia (CNB-CSIC), Calle Darwin 3, E-28049 Madrid, Spain.
- Departmento Bioquimica y Biologia Molecular, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain.
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13
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Parallel-SymD: A Parallel Approach to Detect Internal Symmetry in Protein Domains. BIOMED RESEARCH INTERNATIONAL 2016; 2016:4628592. [PMID: 27747230 PMCID: PMC5056246 DOI: 10.1155/2016/4628592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/25/2016] [Indexed: 11/24/2022]
Abstract
Internally symmetric proteins are proteins that have a symmetrical structure in their monomeric single-chain form. Around 10–15% of the protein domains can be regarded as having some sort of internal symmetry. In this regard, we previously published SymD (symmetry detection), an algorithm that determines whether a given protein structure has internal symmetry by attempting to align the protein to its own copy after the copy is circularly permuted by all possible numbers of residues. SymD has proven to be a useful algorithm to detect symmetry. In this paper, we present a new parallelized algorithm called Parallel-SymD for detecting symmetry of proteins on clusters of computers. The achieved speedup of the new Parallel-SymD algorithm scales well with the number of computing processors. Scaling is better for proteins with a larger number of residues. For a protein of 509 residues, a speedup of 63 was achieved on a parallel system with 100 processors.
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14
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The bacterial dicarboxylate transporter VcINDY uses a two-domain elevator-type mechanism. Nat Struct Mol Biol 2016; 23:256-63. [PMID: 26828963 PMCID: PMC5215794 DOI: 10.1038/nsmb.3166] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/30/2015] [Indexed: 11/11/2022]
Abstract
Secondary transporters use alternating access mechanisms to couple uphill substrate movement to downhill ion flux. Most known transporters utilize a “rocking bundle” motion, where the protein moves around an immobile substrate binding site. However, the glutamate transporter homolog, GltPh, translocates its substrate binding site vertically across the membrane, an “elevator” mechanism. Here, we used the “repeat swap” approach to computationally predict the outward-facing state of the Na+/succinate transporter VcINDY, from Vibrio cholerae. Our model predicts a substantial “elevator”-like movement of vcINDY’s substrate binding site, with a vertical translation of ~15 Å and a rotation of ~43°; multiple disulfide crosslinks which completely inhibit transport provide experimental confirmation and demonstrate that such movement is essential. In contrast, crosslinks across the VcINDY dimer interface preserve transport, revealing an absence of large scale coupling between protomers.
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15
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Stonefish toxin defines an ancient branch of the perforin-like superfamily. Proc Natl Acad Sci U S A 2015; 112:15360-5. [PMID: 26627714 DOI: 10.1073/pnas.1507622112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lethal factor in stonefish venom is stonustoxin (SNTX), a heterodimeric cytolytic protein that induces cardiovascular collapse in humans and native predators. Here, using X-ray crystallography, we make the unexpected finding that SNTX is a pore-forming member of an ancient branch of the Membrane Attack Complex-Perforin/Cholesterol-Dependent Cytolysin (MACPF/CDC) superfamily. SNTX comprises two homologous subunits (α and β), each of which comprises an N-terminal pore-forming MACPF/CDC domain, a central focal adhesion-targeting domain, a thioredoxin domain, and a C-terminal tripartite motif family-like PRY SPla and the RYanodine Receptor immune recognition domain. Crucially, the structure reveals that the two MACPF domains are in complex with one another and arranged into a stable early prepore-like assembly. These data provide long sought after near-atomic resolution insights into how MACPF/CDC proteins assemble into prepores on the surface of membranes. Furthermore, our analyses reveal that SNTX-like MACPF/CDCs are distributed throughout eukaryotic life and play a broader, possibly immune-related function outside venom.
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16
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Vergara-Jaque A, Fenollar-Ferrer C, Kaufmann D, Forrest LR. Repeat-swap homology modeling of secondary active transporters: updated protocol and prediction of elevator-type mechanisms. Front Pharmacol 2015; 6:183. [PMID: 26388773 PMCID: PMC4560100 DOI: 10.3389/fphar.2015.00183] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/13/2015] [Indexed: 12/04/2022] Open
Abstract
Secondary active transporters are critical for neurotransmitter clearance and recycling during synaptic transmission and uptake of nutrients. These proteins mediate the movement of solutes against their concentration gradients, by using the energy released in the movement of ions down pre-existing concentration gradients. To achieve this, transporters conform to the so-called alternating-access hypothesis, whereby the protein adopts at least two conformations in which the substrate binding sites are exposed to one or other side of the membrane, but not both simultaneously. Structures of a bacterial homolog of neuronal glutamate transporters, GltPh, in several different conformational states have revealed that the protein structure is asymmetric in the outward- and inward-open states, and that the conformational change connecting them involves a elevator-like movement of a substrate binding domain across the membrane. The structural asymmetry is created by inverted-topology repeats, i.e., structural repeats with similar overall folds whose transmembrane topologies are related to each other by two-fold pseudo-symmetry around an axis parallel to the membrane plane. Inverted repeats have been found in around three-quarters of secondary transporter folds. Moreover, the (a)symmetry of these systems has been successfully used as a bioinformatic tool, called “repeat-swap modeling” to predict structural models of a transporter in one conformation using the known structure of the transporter in the complementary conformation as a template. Here, we describe an updated repeat-swap homology modeling protocol, and calibrate the accuracy of the method using GltPh, for which both inward- and outward-facing conformations are known. We then apply this repeat-swap homology modeling procedure to a concentrative nucleoside transporter, VcCNT, which has a three-dimensional arrangement related to that of GltPh. The repeat-swapped model of VcCNT predicts that nucleoside transport also occurs via an elevator-like mechanism.
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Affiliation(s)
- Ariela Vergara-Jaque
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Cristina Fenollar-Ferrer
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Desirée Kaufmann
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
| | - Lucy R Forrest
- Computational Structural Biology Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke - National Institutes of Health, Bethesda, MD USA
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