1
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Symmetry of Post-Translational Modifications in a Human Enzyme. Symmetry (Basel) 2022. [DOI: 10.3390/sym14020212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Paraoxonase 2 (PON2) is a member of a small family of human lactonases. Recently, post-translational modifications (PTMs) of PON2 were highlighted, one of which involved the modulation of the enzyme activity. Furthermore, two important single nucleotide polymorphisms (SNPs) involved in type 2 diabetes and its consequences, were found to modulate the enzyme activity as well. The position on the PON2 structural model of both residues corresponding to SNPs and PTMs suggested a symmetry of the molecule. By sequence and structure superposition we were able to confirm this finding. The result will be discussed in light of the evolution of symmetry in biological molecules and their function.
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2
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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3
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Boyer B, Laurent B, Robert CH, Prévost C. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio Protoc 2021; 11:e4097. [PMID: 34395733 DOI: 10.21769/bioprotoc.4097] [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: 11/22/2020] [Revised: 03/28/2021] [Accepted: 04/22/2021] [Indexed: 11/02/2022] Open
Abstract
Protein filaments are dynamic entities that respond to external stimuli by slightly or substantially modifying the internal binding geometries between successive protomers. This results in overall changes in the filament architecture, which are difficult to model due to the helical character of the system. Here, we describe how distortions in RecA nucleofilaments and their consequences on the filament-DNA and bound DNA-DNA interactions at different stages of the homologous recombination process can be modeled using the PTools/Heligeom software and subsequent molecular dynamics simulation with NAMD. Modeling methods dealing with helical macromolecular objects typically rely on symmetric assemblies and take advantage of known symmetry descriptors. Other methods dealing with single objects, such as MMTK or VMD, do not integrate the specificities of regular assemblies. By basing the model building on binding geometries at the protomer-protomer level, PTools/Heligeom frees the building process from a priori knowledge of the system topology and enables irregular architectures and symmetry disruption to be accounted for. Graphical abstract: Model of ATP hydrolysis-induced distortions in the recombinant nucleoprotein, obtained by combining RecA-DNA and two RecA-RecA binding geometries.
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Affiliation(s)
- Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Université de Paris, F-75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Benoist Laurent
- CNRS, FR 550, Institut de Biologie Physico-Chimique, Paris, France
| | - Charles H Robert
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Université de Paris, F-75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Université de Paris, F-75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
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4
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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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5
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Bonjack M, Avnir D. The near-symmetry of protein oligomers: NMR-derived structures. Sci Rep 2020; 10:8367. [PMID: 32433550 PMCID: PMC7239866 DOI: 10.1038/s41598-020-65097-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/18/2020] [Indexed: 02/07/2023] Open
Abstract
The majority of oligomeric proteins form clusters which have rotational or dihedral symmetry. Despite the many advantages of symmetric packing, protein oligomers are only nearly symmetric, and the origin of this phenomenon is still in need to be fully explored. Here we apply near-symmetry analyses by the Continuous Symmetry Measures methodology of protein homomers to their natural state, namely their structures in solution. NMR-derived structural data serves us for that purpose. We find that symmetry deviations of proteins are by far higher in solution, compared to the crystalline state; that much of the symmetry distortion is due to amino acids along the interface between the subunits; that the distortions are mainly due to hydrophilic amino acids; and that distortive oligomerization processes such as the swap-domain mechanism can be identified by the symmetry analysis. Most of the analyses were carried out on distorted C2-symmetry dimers, but C3 and D2 cases were analyzed as well. Our NMR analysis supports the idea that the crystallographic B-factor represents non-classical crystals, in which different conformers pack in the crystal, perhaps from the conformers which the NMR analysis provides.
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Affiliation(s)
- Maayan Bonjack
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - David Avnir
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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6
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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7
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Boyer B, Ezelin J, Poulain P, Saladin A, Zacharias M, Robert CH, Prévost C. An integrative approach to the study of filamentous oligomeric assemblies, with application to RecA. PLoS One 2015; 10:e0116414. [PMID: 25785454 PMCID: PMC4364692 DOI: 10.1371/journal.pone.0116414] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 12/09/2014] [Indexed: 11/19/2022] Open
Abstract
Oligomeric macromolecules in the cell self-organize into a wide variety of geometrical motifs such as helices, rings or linear filaments. The recombinase proteins involved in homologous recombination present many such assembly motifs. Here, we examine in particular the polymorphic characteristics of RecA, the most studied member of the recombinase family, using an integrative approach that relates local modes of monomer/monomer association to the global architecture of their screw-type organization. In our approach, local modes of association are sampled via docking or Monte Carlo simulations. This enables shedding new light on fiber morphologies that may be adopted by the RecA protein. Two distinct RecA helical morphologies, the so-called "extended" and "compressed" forms, are known to play a role in homologous recombination. We investigate the variability within each form in terms of helical parameters and steric accessibility. We also address possible helical discontinuities in RecA filaments due to multiple monomer-monomer association modes. By relating local interface organization to global filament morphology, the strategies developed here to study RecA self-assembly are particularly well suited to other DNA-binding proteins and to filamentous protein assemblies in general.
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Affiliation(s)
- Benjamin Boyer
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Johann Ezelin
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Pierre Poulain
- DSIMB team, Inserm UMR-S 665 and Univ. Paris Diderot, Sorbonne Paris Cité, INTS, 6 rue Alexandre Cabanel, 75015 Paris, France
- Ets Poulain, Pointe-Noire, Republic of Congo
| | - Adrien Saladin
- MTI, INSERM UMR-M 973, Université Paris Diderot-Paris 7, Bât Lamarck, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Martin Zacharias
- Technische Universität München, Physik-Department, James-Franck-Str. 1, 85748 Garching, Germany
| | - Charles H. Robert
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Chantal Prévost
- Laboratoire de Biochimie Théorique, CNRS, UPR 9080, Univ Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
- * E-mail:
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8
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Bonjack-Shterengartz M, Avnir D. The near-symmetry of proteins. Proteins 2015; 83:722-34. [PMID: 25354765 DOI: 10.1002/prot.24706] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/06/2014] [Accepted: 10/18/2014] [Indexed: 11/07/2022]
Abstract
The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
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9
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Huang SY. Search strategies and evaluation in protein–protein docking: principles, advances and challenges. Drug Discov Today 2014; 19:1081-96. [DOI: 10.1016/j.drudis.2014.02.005] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/04/2014] [Accepted: 02/24/2014] [Indexed: 01/10/2023]
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10
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Kuzu G, Keskin O, Nussinov R, Gursoy A. Modeling protein assemblies in the proteome. Mol Cell Proteomics 2014; 13:887-96. [PMID: 24445405 PMCID: PMC3945916 DOI: 10.1074/mcp.m113.031294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 12/13/2013] [Indexed: 11/06/2022] Open
Abstract
Most (if not all) proteins function when associated in multimolecular assemblies. Attaining the structures of protein assemblies at the atomic scale is an important aim of structural biology. Experimentally, structures are increasingly available, and computations can help bridge the resolution gap between high- and low-resolution scales. Existing computational methods have made substantial progress toward this aim; however, current approaches are still limited. Some involve manual adjustment of experimental data; some are automated docking methods, which are computationally expensive and not applicable to large-scale proteome studies; and still others exploit the symmetry of the complexes and thus are not applicable to nonsymmetrical complexes. Our study aims to take steps toward overcoming these limitations. We have developed a strategy for the construction of protein assemblies computationally based on binary interactions predicted by a motif-based protein interaction prediction tool, PRISM (Protein Interactions by Structural Matching). Previously, we have shown its power in predicting pairwise interactions. Here we take a step toward multimolecular assemblies, reflecting the more prevalent cellular scenarios. With this method we are able to construct homo-/hetero-complexes and symmetric/asymmetric complexes without a limitation on the number of components. The method considers conformational changes and is applicable to large-scale studies. We also exploit electron microscopy density maps to select a solution from among the predictions. Here we present the method, illustrate its results, and highlight its current limitations.
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Affiliation(s)
- Guray Kuzu
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ozlem Keskin
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
| | - Ruth Nussinov
- §Cancer and Inflammation Program, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702
- ¶Sackler Institute of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Attila Gursoy
- From the ‡Center for Computational Biology and Bioinformatics and College of Engineering, Koc University Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
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11
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Macromolecular symmetric assembly prediction using swarm intelligence dynamic modeling. Structure 2014; 21:1097-1106. [PMID: 23810695 DOI: 10.1016/j.str.2013.05.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 05/21/2013] [Accepted: 05/22/2013] [Indexed: 11/23/2022]
Abstract
Proteins often assemble in multimeric complexes to perform a specific biologic function. However, trapping these high-order conformations is difficult experimentally. Therefore, predicting how proteins assemble using in silico techniques can be of great help. The size of the associated conformational space and the fact that proteins are intrinsically flexible structures make this optimization problem extremely challenging. Nonetheless, known experimental spatial restraints can guide the search process, contributing to model biologically relevant states. We present here a swarm intelligence optimization protocol able to predict the arrangement of protein symmetric assemblies by exploiting a limited amount of experimental restraints and steric interactions. Importantly, within this scheme the native flexibility of each protein subunit is taken into account as extracted from molecular dynamics (MD) simulations. We show that this is a key ingredient for the prediction of biologically functional assemblies when, upon oligomerization, subunits explore activated states undergoing significant conformational changes.
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12
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Spiga E, Degiacomi MT, Dal Peraro M. New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:77-111. [DOI: 10.1016/bs.apcsb.2014.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Popov P, Ritchie DW, Grudinin S. DockTrina: docking triangular protein trimers. Proteins 2013; 82:34-44. [PMID: 23775700 DOI: 10.1002/prot.24344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/30/2013] [Accepted: 05/31/2013] [Indexed: 11/06/2022]
Abstract
In spite of the abundance of oligomeric proteins within a cell, the structural characterization of protein-protein interactions is still a challenging task. In particular, many of these interactions involve heteromeric complexes, which are relatively difficult to determine experimentally. Hence there is growing interest in using computational techniques to model such complexes. However, assembling large heteromeric complexes computationally is a highly combinatorial problem. Nonetheless the problem can be simplified greatly by considering interactions between protein trimers. After dimers and monomers, triangular trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) are the most frequently observed quaternary structural motifs according to the three-dimensional (3D) complex database. This article presents DockTrina, a novel protein docking method for modeling the 3D structures of nonsymmetrical triangular trimers. The method takes as input pair-wise contact predictions from a rigid body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation test. Finally, it ranks the predictions using a scoring function which combines triples of pair-wise contact terms and a geometric clash penalty term. The overall approach takes less than 2 min per complex on a modern desktop computer. The method is tested and validated using a benchmark set of 220 bound and seven unbound protein trimer structures. DockTrina will be made available at http://nano-d.inrialpes.fr/software/docktrina.
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Affiliation(s)
- Petr Popov
- NANO-D, INRIA Grenoble-Rhone-Alpes, 38334 Saint Ismier Cedex, Montbonnot, France; Laboratoire Jean Kuntzmann, B.P. 53, 38041 Grenoble Cedex 9, France
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14
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Melquiond AS, Karaca E, Kastritis PL, Bonvin AM. Next challenges in protein-protein docking: from proteome to interactome and beyond. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.91] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Mashiach-Farkash E, Nussinov R, Wolfson HJ. SymmRef: a flexible refinement method for symmetric multimers. Proteins 2011; 79:2607-23. [PMID: 21721046 PMCID: PMC3155011 DOI: 10.1002/prot.23082] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 05/02/2011] [Accepted: 05/04/2011] [Indexed: 11/11/2022]
Abstract
Symmetric protein complexes are abundant in the living cell. Predicting their atomic structure can shed light on the mechanism of many important biological processes. Symmetric docking methods aim to predict the structure of these complexes given the unbound structure of a single monomer, or its model. Symmetry constraints reduce the search-space of these methods and make the prediction easier compared to asymmetric protein-protein docking. However, the challenge of modeling the conformational changes that the monomer might undergo is a major obstacle. In this article, we present SymmRef, a novel method for refinement and reranking of symmetric docking solutions. The method models backbone and side-chain movements and optimizes the rigid-body orientations of the monomers. The backbone movements are modeled by normal modes minimization and the conformations of the side-chains are modeled by selecting optimal rotamers. Since solved structures of symmetric multimers show asymmetric side-chain conformations, we do not use symmetry constraints in the side-chain optimization procedure. The refined models are re-ranked according to an energy score. We tested the method on a benchmark of unbound docking challenges. The results show that the method significantly improves the accuracy and the ranking of symmetric rigid docking solutions. SymmRef is available for download at http:// bioinfo3d.cs.tau.ac.il/SymmRef/download.html.
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Affiliation(s)
- Efrat Mashiach-Farkash
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Nussinov
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI - Frederick, Frederick, MD 21702, USA
- Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Haim J. Wolfson
- Blavatnik School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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16
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Lasker K, Sali A, Wolfson HJ. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins 2011; 78:3205-11. [PMID: 20827723 DOI: 10.1002/prot.22845] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. Determining these structures is a major challenge for experimental techniques, such as X-ray crystallography, NMR spectroscopy and electron microscopy (EM). Thus, computational modeling techniques, including molecular docking, are required. The development of most molecular docking methods has so far been focused on modeling of binary complexes. We have recently introduced the MultiFit method for modeling the structure of a multisubunit complex by simultaneously optimizing the fit of the model into an EM density map of the entire complex and the shape complementarity between interacting subunits. Here, we report algorithmic advances of the MultiFit method that result in an efficient and accurate assembly of the input subunits into their density map. The successful predictions and the increasing number of complexes being characterized by EM suggests that the CAPRI challenge could be extended to include docking-based modeling of macromolecular assemblies guided by EM.
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Affiliation(s)
- Keren Lasker
- Raymond and Beverly Sackler Faculty of Exact Sciences, Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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17
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Stein A, Mosca R, Aloy P. Three-dimensional modeling of protein interactions and complexes is going 'omics. Curr Opin Struct Biol 2011; 21:200-8. [PMID: 21320770 DOI: 10.1016/j.sbi.2011.01.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/11/2011] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
High-throughput interaction discovery initiatives have revealed the existence of hundreds of multiprotein complexes whose functions are regulated through thousands of protein-protein interactions (PPIs). However, the structural details of these interactions, often necessary to understand their function, are only available for a tiny fraction, and the experimental difficulties surrounding complex structure determination make computational modeling techniques paramount. In this manuscript, we critically review some of the most recent developments in the field of structural bioinformatics applied to the modeling of protein interactions and complexes, from large macromolecular machines to domain-domain and peptide-mediated interactions. In particular, we place a special emphasis on those methods that can be applied in a proteome-wide manner, and discuss how they will help in the ultimate objective of building 3D interactome networks.
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Affiliation(s)
- Amelie Stein
- Institute for Research in Biomedicine (IRB Barcelona), Joint IRB-BSC Program in Computational Biology, c/Baldiri i Reixac 10-12, 08028 Barcelona, Spain
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18
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Zrimi J, Ng Ling A, Giri-Rachman Arifin E, Feverati G, Lesieur C. Cholera toxin B subunits assemble into pentamers--proposition of a fly-casting mechanism. PLoS One 2010; 5:e15347. [PMID: 21203571 PMCID: PMC3006222 DOI: 10.1371/journal.pone.0015347] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 11/11/2010] [Indexed: 11/18/2022] Open
Abstract
The cholera toxin B pentamer (CtxB5), which belongs to the AB5 toxin family, is used as a model study for protein assembly. The effect of the pH on the reassembly of the toxin was investigated using immunochemical, electrophoretic and spectroscopic methods. Three pH-dependent steps were identified during the toxin reassembly: (i) acquisition of a fully assembly-competent fold by the CtxB monomer, (ii) association of CtxB monomer into oligomers, (iii) acquisition of the native fold by the CtxB pentamer. The results show that CtxB5 and the related heat labile enterotoxin LTB5 have distinct mechanisms of assembly despite sharing high sequence identity (84%) and almost identical atomic structures. The difference can be pinpointed to four histidines which are spread along the protein sequence and may act together. Thus, most of the toxin B amino acids appear negligible for the assembly, raising the possibility that assembly is driven by a small network of amino acids instead of involving all of them.
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Affiliation(s)
- Jihad Zrimi
- LAPTH, Université de Savoie, CNRS, Annecy le Vieux, France
| | - Alicia Ng Ling
- National University of Singapore, Physics Department, Singapore, Singapore
| | | | | | - Claire Lesieur
- LAPTH, Université de Savoie, CNRS, Annecy le Vieux, France
- National University of Singapore, Physics Department, Singapore, Singapore
- CEA-CNRS-Université Joseph Fourier, IRTSV, LBBSI, Grenoble, France
- * E-mail:
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19
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Karaca E, Melquiond ASJ, de Vries SJ, Kastritis PL, Bonvin AMJJ. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server. Mol Cell Proteomics 2010; 9:1784-94. [PMID: 20305088 PMCID: PMC2938057 DOI: 10.1074/mcp.m000051-mcp201] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Over the last years, large scale proteomics studies have generated a wealth of information of biomolecular complexes. Adding the structural dimension to the resulting interactomes represents a major challenge that classical structural experimental methods alone will have difficulties to confront. To meet this challenge, complementary modeling techniques such as docking are thus needed. Among the current docking methods, HADDOCK (High Ambiguity-Driven DOCKing) distinguishes itself from others by the use of experimental and/or bioinformatics data to drive the modeling process and has shown a strong performance in the critical assessment of prediction of interactions (CAPRI), a blind experiment for the prediction of interactions. Although most docking programs are limited to binary complexes, HADDOCK can deal with multiple molecules (up to six), a capability that will be required to build large macromolecular assemblies. We present here a novel web interface of HADDOCK that allows the user to dock up to six biomolecules simultaneously. This interface allows the inclusion of a large variety of both experimental and/or bioinformatics data and supports several types of cyclic and dihedral symmetries in the docking of multibody assemblies. The server was tested on a benchmark of six cases, containing five symmetric homo-oligomeric protein complexes and one symmetric protein-DNA complex. Our results reveal that, in the presence of either bioinformatics and/or experimental data, HADDOCK shows an excellent performance: in all cases, HADDOCK was able to generate good to high quality solutions and ranked them at the top, demonstrating its ability to model symmetric multicomponent assemblies. Docking methods can thus play an important role in adding the structural dimension to interactomes. However, although the current docking methodologies were successful for a vast range of cases, considering the variety and complexity of macromolecular assemblies, inclusion of some kind of experimental information (e.g. from mass spectrometry, nuclear magnetic resonance, cryoelectron microscopy, etc.) will remain highly desirable to obtain reliable results.
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Affiliation(s)
- Ezgi Karaca
- Bijvoet Center for Biomolecular Research, Science Faculty, Utrecht University, Utrecht, The Netherlands
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20
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Abstract
The quaternary structure (QS) of a protein is determined by measuring its molecular weight in solution. The data have to be extracted from the literature, and they may be missing even for proteins that have a crystal structure reported in the Protein Data Bank (PDB). The PDB and other databases derived from it report QS information that either was obtained from the depositors or is based on an analysis of the contacts between polypeptide chains in the crystal, and this frequently differs from the QS determined in solution.The QS of a protein can be predicted from its sequence using either homology or threading methods. However, a majority of the proteins with less than 30% sequence identity have different QSs. A model of the QS can also be derived by docking the subunits when their 3D structure is independently known, but the model is likely to be incorrect if large conformation changes take place when the oligomer assembles.
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Affiliation(s)
- Anne Poupon
- Yeast Structural Genomics, IBBMC UMR 8619 CNRS, Université Paris-Sud, Orsay, France
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21
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Abstract
AbstractProtein–protein recognition plays an essential role in structure and function. Specific non-covalent interactions stabilize the structure of macromolecular assemblies, exemplified in this review by oligomeric proteins and the capsids of icosahedral viruses. They also allow proteins to form complexes that have a very wide range of stability and lifetimes and are involved in all cellular processes. We present some of the structure-based computational methods that have been developed to characterize the quaternary structure of oligomeric proteins and other molecular assemblies and analyze the properties of the interfaces between the subunits. We compare the size, the chemical and amino acid compositions and the atomic packing of the subunit interfaces of protein–protein complexes, oligomeric proteins, viral capsids and protein–nucleic acid complexes. These biologically significant interfaces are generally close-packed, whereas the non-specific interfaces between molecules in protein crystals are loosely packed, an observation that gives a structural basis to specific recognition. A distinction is made within each interface between a core that contains buried atoms and a solvent accessible rim. The core and the rim differ in their amino acid composition and their conservation in evolution, and the distinction helps correlating the structural data with the results of site-directed mutagenesis and in vitro studies of self-assembly.
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22
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Lapidot A, Berchanski A, Borkow G. Insight into the mechanisms of aminoglycoside derivatives interaction with HIV-1 entry steps and viral gene transcription. FEBS J 2008; 275:5236-57. [PMID: 18803669 DOI: 10.1111/j.1742-4658.2008.06657.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In recent years, based on peptide models of HIV-1 RNA binding, NMR structures of Tat-responsive element-ligand complexes and aminoglycoside-RNA interactions, and HIV-1 Tat structure, we have designed and synthesized aminoglycoside-arginine conjugates (AACs) and aminoglycoside poly-arginine conjugates (APACs), to serve as Tat mimetics. These novel molecules inhibit HIV-1 infectivity with 50% effective concentration values in the low micromolar range, the most potent compounds being the hexa-arginine-neomycin B and nona-D-arginine-neomycin conjugates. Importantly, these compounds, in addition to acting as Tat antagonists, inhibit HIV-1 infectivity by blocking several steps in HIV-1 cell entry. The AACs and APACs inhibit HIV-1 cell entry by interacting with gp120 at the CD4-binding site, by interacting with CXCR4 at the binding site of the CXCR4 mAb 12G5, and apparently by interacting with transient structures of the ectodomain of gp41. In the current review, we discuss the mechanisms of anti-HIV-1 activities of these AACs, APACs and other aminoglycoside derivatives in detail. Targeting several key processes in the viral life cycle by the same compound not only may increase its antiviral efficacy, but more importantly, may reduce the capacity of the virus to develop resistance to the compound. AACs and APACs may thus serve as leading compounds for the development of multitargeting novel HIV-1 inhibitors.
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Affiliation(s)
- Aviva Lapidot
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel.
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23
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Casciari D, Dell’Orco D, Fanelli F. Homodimerization of Neurotensin 1 Receptor Involves Helices 1, 2, and 4: Insights from Quaternary Structure Predictions and Dimerization Free Energy Estimations. J Chem Inf Model 2008; 48:1669-78. [DOI: 10.1021/ci800048d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Daniele Casciari
- Department of Chemistry and Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Daniele Dell’Orco
- Department of Chemistry and Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - Francesca Fanelli
- Department of Chemistry and Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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24
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Heifetz A, Pal S, Smith GR. Protein-protein docking: progress in CAPRI rounds 6-12 using a combination of methods: the introduction of steered solvated molecular dynamics. Proteins 2008; 69:816-22. [PMID: 17803214 DOI: 10.1002/prot.21734] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In recent rounds of CAPRI, the Bii group has employed a combination of techniques for the prediction of the structure of protein-protein complexes. We currently use third-party software for rigid-body and semiflexible docking (MolFit, 3D-Dock, RosettaDock), and our own steered molecular dynamics (SMD) technique for flexible refinement. SMD has also been found to be useful for discriminating near-native from false positive docking decoys. In addition to this, a variety of sources of information, including multiple descriptors of interface quality combined with a QSAR-like technique, published biological information, and continuum electrostatics calculations, are also used in the assessment of candidate complexes. We shall concentrate on results for CAPRI rounds 9-11 (targets 24-27). In these rounds, the Bii group has been successful in submitting a medium quality model for each of CAPRI targets 25 and 26, and a model of acceptable quality for target 27.
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Affiliation(s)
- Alexander Heifetz
- Protein-Protein Interactions Group, Biosystems Informatics Institute, Marlborough House, Marlborough Crescent, Newcastle upon Tyne NE1 4EE, United Kingdom
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25
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Abstract
Biological supramolecular systems are commonly built up by the self-assembly of identical protein subunits to produce symmetrical oligomers with cyclical, icosahedral, or helical symmetry that play roles in processes ranging from allosteric control and molecular transport to motor action. The large size of these systems often makes them difficult to structurally characterize using experimental techniques. We have developed a computational protocol to predict the structure of symmetrical protein assemblies based on the structure of a single subunit. The method carries out simultaneous optimization of backbone, side chain, and rigid-body degrees of freedom, while restricting the search space to symmetrical conformations. Using this protocol, we can reconstruct, starting from the structure of a single subunit, the structure of cyclic oligomers and the icosahedral virus capsid of satellite panicum virus using a rigid backbone approximation. We predict the oligomeric state of EscJ from the type III secretion system both in its proposed cyclical and crystallized helical form. Finally, we show that the method can recapitulate the structure of an amyloid-like fibril formed by the peptide NNQQNY from the yeast prion protein Sup35 starting from the amino acid sequence alone and searching the complete space of backbone, side chain, and rigid-body degrees of freedom.
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26
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Abstract
Computational prediction of protein complex structures through docking offers a means to gain a mechanistic understanding of protein interactions that mediate biological processes. This is particularly important as the number of experimentally determined structures of isolated proteins exceeds the number of structures of complexes. A comprehensive docking procedure is described in which efficient sampling of conformations is achieved by matching surface normal vectors, fast filtering for shape complementarity, clustering by RMSD, and scoring the docked conformations using a supervised machine learning approach. Contacting residue pair frequencies, residue propensities, evolutionary conservation, and shape complementarity score for each docking conformation are used as input data to a Random Forest classifier. The performance of the Random Forest approach for selecting correctly docked conformations was assessed by cross-validation using a nonredundant benchmark set of X-ray structures for 93 heterodimer and 733 homodimer complexes. The single highest rank docking solution was the correct (near-native) structure for slightly more than one third of the complexes. Furthermore, the fraction of highly ranked correct structures was significantly higher than the overall fraction of correct structures, for almost all complexes. A detailed analysis of the difficult to predict complexes revealed that the majority of the homodimer cases were explained by incorrect oligomeric state annotation. Evolutionary conservation and shape complementarity score as well as both underrepresented and overrepresented residue types and residue pairs were found to make the largest contributions to the overall prediction accuracy. Finally, the method was also applied to docking unbound subunit structures from a previously published benchmark set.
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Affiliation(s)
- Andrew J Bordner
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6173, USA.
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27
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Berchanski A, Lapidot A. Prediction of HIV-1 entry inhibitors neomycin-arginine conjugates interaction with the CD4-gp120 binding site by molecular modeling and multistep docking procedure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2107-19. [PMID: 17560540 DOI: 10.1016/j.bbamem.2007.04.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2006] [Revised: 04/04/2007] [Accepted: 04/19/2007] [Indexed: 10/23/2022]
Abstract
Developing of multi-target HIV-1 entry inhibitors represents an important avenue of drug therapy. Two such inhibitors are hexa-arginine-neomycin-conjugate (NeoR6) and nona-d-arginine-neomycin-conjugate (Neo-r9). Our findings that NeoR6-resistant mutations appear in the gp120 constant regions; and NeoR6 is not CCR5 antagonist, but inhibits CXCR4 and CCR5 HIV-1 using isolates, led us to suggest that NeoR6 may inhibit HIV-1 entry by interfering with the CD4-gp120 binding. To support this notion, we constructed a homology model of unliganded HIV-1(IIIB) gp120 and docked NeoR6 and Neo-r9 to it, using a multistep docking procedure: geometric-electrostatic docking by MolFit; flexible ligand docking by Autodock3 and final refinement of the obtained complexes by Discover3. Binding free energies were calculated by MM-PBSA methodology. The model predicts competitive inhibition of CD4-gp120 binding by NeoR6 and Neo-r9. We determined plausible binding sites between constructed CD4-bound gp120 trimer and homology modeled membranal CXCR4, and tested NeoR6 and Neo-r9 interfering with this interaction. These models support our notion that another mechanism of anti-HIV-1 activity of NeoR6 is inhibition of gp120-CXCR4 binding. These structural models and interaction of NeoR6 and Neo-r9 with gp120 and CXCR4 provide a powerful approach for structural based drug design for selective targeting of HIV-1 entry and/or for inhibition of other retroviruses with similar mechanism of entry.
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Affiliation(s)
- Alexander Berchanski
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, 76100, Israel
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28
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Casciari D, Seeber M, Fanelli F. Quaternary structure predictions of transmembrane proteins starting from the monomer: a docking-based approach. BMC Bioinformatics 2006; 7:340. [PMID: 16836758 PMCID: PMC1590055 DOI: 10.1186/1471-2105-7-340] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Accepted: 07/12/2006] [Indexed: 12/03/2022] Open
Abstract
Background We introduce a computational protocol for effective predictions of the supramolecular organization of integral transmembrane proteins, starting from the monomer. Despite the demonstrated constitutive and functional importance of supramolecular assemblies of transmembrane subunits or proteins, effective tools for structure predictions of such assemblies are still lacking. Our computational approach consists in rigid-body docking samplings, starting from the docking of two identical copies of a given monomer. Each docking run is followed by membrane topology filtering and cluster analysis. Prediction of the native oligomer is therefore accomplished by a number of progressive growing steps, each made of one docking run, filtering and cluster analysis. With this approach, knowledge about the oligomerization status of the protein is required neither for improving sampling nor for the filtering step. Furthermore, there are no size-limitations in the systems under study, which are not limited to the transmembrane domains but include also the water-soluble portions. Results Benchmarks of the approach were done on ten homo-oligomeric membrane proteins with known quaternary structure. For all these systems, predictions led to native-like quaternary structures, i.e. with Cα-RMSDs lower than 2.5 Å from the native oligomer, regardless of the resolution of the structural models. Conclusion Collectively, the results of this study emphasize the effectiveness of the prediction protocol that will be extensively challenged in quaternary structure predictions of other integral membrane proteins.
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Affiliation(s)
- D Casciari
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - M Seeber
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | - F Fanelli
- Department of Chemistry, Dulbecco Telethon Institute (DTI), University of Modena e Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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29
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Ben-Zeev E, Kowalsman N, Ben-Shimon A, Segal D, Atarot T, Noivirt O, Shay T, Eisenstein M. Docking to single-domain and multiple-domain proteins: Old and new challenges. Proteins 2005; 60:195-201. [PMID: 15981268 DOI: 10.1002/prot.20557] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The diverse selection of targets in the CAPRI experiments provides grounds for determining the limits of our rigid-body docking program MolFit, and for extending it. We find that the sensitivity of MolFit is high, enabling it to produce reasonably accurate docking solutions when the structures undergo moderate local conformation changes upon complex formation or when the docked molecules are modeled. Yet the ranks of these solutions are sometimes too low to meet the requirements of CAPRI assessment. This indicates that the selectivity of MolFit, which was optimized for docking of unbound X-ray structures, and which relies on the availability of external data from biochemical and bioinformatic sources, needs readjustment in order to meet the challenges presented by NMR or modeled structures. A different challenge is presented by large global conformation changes such as movements of domains. We show that such changes can be accommodated within the rigid-body approximation by employing rigid multibody multistage docking procedures. We also address the difficulty of ranking results from 2-body and multibody docking scans in cases in which there are no external data favoring one option over the other.
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Affiliation(s)
- E Ben-Zeev
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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