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Kumar A, Sechi LA, Caboni P, Marrosu MG, Atzori L, Pieroni E. Dynamical insights into the differential characteristics of Mycobacterium avium subsp. paratuberculosis peptide binding to HLA-DRB1 proteins associated with multiple sclerosis. NEW J CHEM 2015. [DOI: 10.1039/c4nj01903b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Differential properties of MAP binding to HLA proteins in Sardinian MS patients.
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Affiliation(s)
- Amit Kumar
- CRS4 Science and Technology Park Polaris
- Biomedicine Dept
- Pula (CA)
- Italy
- Department of Biomedical Sciences
| | - Leonardo A. Sechi
- Department of Biomedical Sciences
- Microbiology and Virology Unit
- University of Sassari
- Sassari
- Italy
| | - Pierluigi Caboni
- Department of Life and Environmental Sciences
- University of Cagliari
- Cagliari
- Italy
| | - Maria Giovanna Marrosu
- Multiple Sclerosis Center
- Department of Public Health and Clinical and Molecular Medicine
- University of Cagliari
- Cagliari
- Italy
| | - Luigi Atzori
- Department of Biomedical Sciences
- Oncology and Molecular Pathology Unit
- University of Cagliari
- Cagliari
- Italy
| | - Enrico Pieroni
- CRS4 Science and Technology Park Polaris
- Biomedicine Dept
- Pula (CA)
- Italy
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2
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Bello M, Correa-Basurto J. Molecular dynamics simulations to provide insights into epitopes coupled to the soluble and membrane-bound MHC-II complexes. PLoS One 2013; 8:e72575. [PMID: 23977319 PMCID: PMC3747130 DOI: 10.1371/journal.pone.0072575] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/10/2013] [Indexed: 11/24/2022] Open
Abstract
Epitope recognition by major histocompatibility complex II (MHC-II) is essential for the activation of immunological responses to infectious diseases. Several studies have demonstrated that this molecular event takes place in the MHC-II peptide-binding groove constituted by the α and β light chains of the heterodimer. This MHC-II peptide-binding groove has several pockets (P1-P11) involved in peptide recognition and complex stabilization that have been probed through crystallographic experiments and in silico calculations. However, most of these theoretical calculations have been performed without taking into consideration the heavy chains, which could generate misleading information about conformational mobility both in water and in the membrane environment. Therefore, in absence of structural information about the difference in the conformational changes between the peptide-free and peptide-bound states (pMHC-II) when the system is soluble in an aqueous environment or non-covalently bound to a cell membrane, as the physiological environment for MHC-II is. In this study, we explored the mechanistic basis of these MHC-II components using molecular dynamics (MD) simulations in which MHC-II was previously co-crystallized with a small epitope (P7) or coupled by docking procedures to a large (P22) epitope. These MD simulations were performed at 310 K over 100 ns for the water-soluble (MHC-IIw, MHC-II-P7w, and MHC-II-P22w) and 150 ns for the membrane-bound species (MHC-IIm, MHC-II-P7m, and MHC-II-P22m). Our results reveal that despite the different epitope sizes and MD simulation environments, both peptides are stabilized primarily by residues lining P1, P4, and P6-7, and similar noncovalent intermolecular energies were observed for the soluble and membrane-bound complexes. However, there were remarkably differences in the conformational mobility and intramolecular energies upon complex formation, causing some differences with respect to how the two peptides are stabilized in the peptide-binding groove.
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Affiliation(s)
- Martiniano Bello
- Laboratorio de Modelado Molecular y Bioinformática de la Escuela Superior de Medicina, Instituto Politécnico Nacional, México, Plan de San Luis Y Diaz Mirón S/N, Col. Casco de Santo Tomas, Mexico City, México.
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3
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Doytchinova I, Petkov P, Dimitrov I, Atanasova M, Flower DR. HLA-DP2 binding prediction by molecular dynamics simulations. Protein Sci 2011; 20:1918-28. [PMID: 21898654 DOI: 10.1002/pro.732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 11/11/2022]
Abstract
Major histocompatibility complex (MHC) II proteins bind peptide fragments derived from pathogen antigens and present them at the cell surface for recognition by T cells. MHC proteins are divided into Class I and Class II. Human MHC Class II alleles are grouped into three loci: HLA-DP, HLA-DQ, and HLA-DR. They are involved in many autoimmune diseases. In contrast to HLA-DR and HLA-DQ proteins, the X-ray structure of the HLA-DP2 protein has been solved quite recently. In this study, we have used structure-based molecular dynamics simulation to derive a tool for rapid and accurate virtual screening for the prediction of HLA-DP2-peptide binding. A combinatorial library of 247 peptides was built using the "single amino acid substitution" approach and docked into the HLA-DP2 binding site. The complexes were simulated for 1 ns and the short range interaction energies (Lennard-Jones and Coulumb) were used as binding scores after normalization. The normalized values were collected into quantitative matrices (QMs) and their predictive abilities were validated on a large external test set. The validation shows that the best performing QM consisted of Lennard-Jones energies normalized over all positions for anchor residues only plus cross terms between anchor-residues.
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Affiliation(s)
- Irini Doytchinova
- School of Pharmacy, Medical University of Sofia, Sofia 1000, Bulgaria.
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Nojima H, Kanou K, Kamiya K, Atsuda K, Umeyama H, Takeda-Shitaka M. Dynamic influence of the two membrane-proximal immunoglobulin-like domains upon the peptide-binding platform domain in class I and class II major histocompatibility complexes: normal mode analysis. Chem Pharm Bull (Tokyo) 2010; 57:1193-9. [PMID: 19881266 DOI: 10.1248/cpb.57.1193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Major histocompatibility complexes (MHCs) mainly fall into class I and class II. The two classes have similar structures, with two membrane-proximal immunoglobulin-like domains and a peptide-binding platform domain, though their organizations are different. We simulated the dynamics of a whole and partial model deficient in either of the two membrane-proximal domains for class I and class II using normal mode analysis. Our study showed that the influence of the two membrane-proximal domains upon the dynamics of the platform domain were decisively different between class II and class I. Both membrane-proximal domains (the alpha2 and beta2 domains) of class II MHC, especially the alpha2 domain, influenced the most important pocket that accommodates a large hydrophobic anchor side chain of the N-terminal side of the bound peptide, though the pocket was not in the alpha2 domain neighborhood. By contrast, the two membrane-proximal domains (the alpha3 and beta2m domains) of class I MHC had little influence upon the most important pocket that accommodates the N-terminal residue of the bound peptide. These results suggest that the two membrane-proximal domains of class II MHC have a greater influence upon peptide-binding than those of class I MHC.
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Affiliation(s)
- Hiroyuki Nojima
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
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5
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Li Y, Yang Y, He P, Yang Q. QM/MM Study of Epitope Peptides Binding to HLA-A*0201: The Roles of Anchor Residues and Water. Chem Biol Drug Des 2009; 74:611-8. [DOI: 10.1111/j.1747-0285.2009.00896.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Yaneva R, Springer S, Zacharias M. Flexibility of the MHC class II peptide binding cleft in the bound, partially filled, and empty states: A molecular dynamics simulation study. Biopolymers 2009; 91:14-27. [DOI: 10.1002/bip.21078] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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Omasits U, Knapp B, Neumann M, Steinhauser O, Stockinger H, Kobler R, Schreiner W. Analysis of key parameters for molecular dynamics of pMHC molecules. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020802256298] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Nojima H, Takeda-Shitaka M, Kanou K, Kamiya K, Umeyama H. Dynamic Interaction among the Platform Domain and Two Membrane-Proximal Immunoglobulin-Like Domains of Class I Major Histocompatibility Complex: Normal Mode Analysis. Chem Pharm Bull (Tokyo) 2008; 56:635-41. [DOI: 10.1248/cpb.56.635] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Bui HH, Schiewe AJ, Haworth IS. WATGEN: an algorithm for modeling water networks at protein-protein interfaces. J Comput Chem 2007; 28:2241-51. [PMID: 17471455 DOI: 10.1002/jcc.20751] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Water molecules at protein-protein interfaces contribute to the close packing of atoms and ensure complementarity between the protein surfaces, as well as mediating polar interactions. Therefore, modeling of interface water is of importance in understanding the structural basis of biomolecular association. We present an algorithm, WATGEN, which predicts locations for water molecules at a protein-protein or protein-peptide interface, given the atomic coordinates of the protein and peptide. A key element of the WATGEN algorithm is the prediction of water sites that can form multiple hydrogen bonds that bridge the binding interface. Trial calculations were performed on water networks predicted by WATGEN at 126 protein-peptide interfaces (X-ray resolutions <or= 2.0 A), using different criteria for water placement. The energies of the predicted water networks were evaluated in AMBER8 and used in the choice of parameters for WATGEN. The 126 interfaces include 1264 experimentally determined bridging water sites, and the WATGEN algorithm predicts 72 and 88% of these sites within 1.5 and 2.0 A, respectively. The predicted number of water molecules at each interface was much higher than the number of water molecules identified experimentally. Therefore, random placement of the same number of water molecules as that predicted at each interface was performed as a control, and resulted in only 22 and 40% of water sites placed within 1.5 and 2.0 A of experimental sites, respectively. Based on these data, we conclude that WATGEN can accurately predict the location of water molecules at a protein-peptide interface, and this may be of value for understanding the energetics and specificity of biomolecular association.
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Affiliation(s)
- Huynh-Hoa Bui
- Division of Vaccine Discovery, La Jolla Institute of Allergy and Immunology, 9420 Athena Circle, La Jolla, California 92037, USA
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Sieker F, Springer S, Zacharias M. Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles. Protein Sci 2007; 16:299-308. [PMID: 17242432 PMCID: PMC2203297 DOI: 10.1110/ps.062568407] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Comparative unrestrained molecular dynamics simulations on the alpha(1)/alpha(2) peptide binding domains performed in the presence of bound peptides resulted in structures in close agreement with experiments for both alleles. In the absence of peptides, allele-specific conformational changes occurred in the first segment of the alpha(2)-helix that flanks the peptide C-terminal binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a shift toward an altered F-pocket structure deviating significantly from the bound form was observed. Subsequent free energy simulations on induced F-pocket opening in B*4402 confirmed a conformation that deviated significantly from the bound structure. For B*4405, a free energy minimum close to the bound structure was found. The simulations suggest that B*4405 has a greater tendency to adopt a peptide receptive conformation in the absence of peptide, allowing tapasin-independent peptide loading. A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles.
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Affiliation(s)
- Florian Sieker
- School of Engineering and Science, International University Bremen, D-28759 Bremen, Germany
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11
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Schiewe AJ, Haworth IS. Structure-based prediction of MHC-peptide association: algorithm comparison and application to cancer vaccine design. J Mol Graph Model 2007; 26:667-75. [PMID: 17493854 DOI: 10.1016/j.jmgm.2007.03.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Revised: 03/23/2007] [Accepted: 03/30/2007] [Indexed: 11/26/2022]
Abstract
Peptide vaccination for cancer immunotherapy requires identification of peptide epitopes derived from antigenic proteins associated with the tumor. Such peptides can bind to MHC proteins (MHC molecules) on the tumor-cell surface, with the potential to initiate a host immune response against the tumor. Computer prediction of peptide epitopes can be based on known motifs for peptide sequences that bind to a certain MHC molecule, on algorithms using experimental data as a training set, or on structure-based approaches. We have developed an algorithm, which we refer to as PePSSI, for flexible structural prediction of peptide binding to MHC molecules. Here, we have applied this algorithm to identify peptide epitopes (of nine amino acids, the common length) from the sequence of the cancer-testis antigen KU-CT-1, based on the potential of these peptides to bind to the human MHC molecule HLA-A2. We compared the PePSSI predictions with those of other algorithms and found that several peptides predicted to be strong HLA-A2 binders by PePSSI were similarly predicted by another structure-based algorithm, PREDEP. The results show how structure-based prediction can identify potential peptide epitopes without known binding motifs and suggest that side chain orientation in binding peptides may be obtained using PePSSI.
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Affiliation(s)
- Alexandra J Schiewe
- Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089-9121, USA
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12
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Meng WS, Bui HH, Haworth IS. Exploiting the Peptide — MHC Water Interface in the Computer-Aided Design of Non-Natural Peptides that Bind to the Class I MHC Molecule HLA-A2. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020008022372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Bui HH, Schiewe AJ, von Grafenstein H, Haworth IS. Structural prediction of peptides binding to MHC class I molecules. Proteins 2006; 63:43-52. [PMID: 16447245 DOI: 10.1002/prot.20870] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Peptide binding to class I major histocompatibility complex (MHCI) molecules is a key step in the immune response and the structural details of this interaction are of importance in the design of peptide vaccines. Algorithms based on primary sequence have had success in predicting potential antigenic peptides for MHCI, but such algorithms have limited accuracy and provide no structural information. Here, we present an algorithm, PePSSI (peptide-MHC prediction of structure through solvated interfaces), for the prediction of peptide structure when bound to the MHCI molecule, HLA-A2. The algorithm combines sampling of peptide backbone conformations and flexible movement of MHC side chains and is unique among other prediction algorithms in its incorporation of explicit water molecules at the peptide-MHC interface. In an initial test of the algorithm, PePSSI was used to predict the conformation of eight peptides bound to HLA-A2, for which X-ray data are available. Comparison of the predicted and X-ray conformations of these peptides gave RMSD values between 1.301 and 2.475 A. Binding conformations of 266 peptides with known binding affinities for HLA-A2 were then predicted using PePSSI. Structural analyses of these peptide-HLA-A2 conformations showed that peptide binding affinity is positively correlated with the number of peptide-MHC contacts and negatively correlated with the number of interfacial water molecules. These results are consistent with the relatively hydrophobic binding nature of the HLA-A2 peptide binding interface. In summary, PePSSI is capable of rapid and accurate prediction of peptide-MHC binding conformations, which may in turn allow estimation of MHCI-peptide binding affinity.
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Affiliation(s)
- Huynh-Hoa Bui
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089, USA
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14
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Joseph MA, Mitchell ML, Evanseck JD, Kovacs JR, Jia L, Shen H, Meng WS. Secondary anchor substitutions in an HLA-A*0201-restricted T-cell epitope derived from Her-2/neu. Mol Immunol 2006; 44:322-31. [PMID: 16597462 PMCID: PMC2430429 DOI: 10.1016/j.molimm.2006.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2006] [Accepted: 02/27/2006] [Indexed: 10/24/2022]
Abstract
We investigated analogues of GP2 (IISAVVGIL), an HLA-A*0201-restricted T-cell epitope derived from residues 654-662 in the tumor-associated antigen (TAA) Her-2/neu. One limiting factor of GP2 is its poor affinity for HLA-A*0201. Conformational analysis revealed the P5-P7 region in GP2 appears to be linked to the stability of P9 side chain interaction with the MHC molecule. To identify variants of GP2 with enhanced presentation to HLA-A*0201, we tested V6S, V6T, V6Q, G7P, G7F, T6F7, and Q6F7 for their capacity to stabilize cell surface HLA-A*0201 molecules. Of the mono-substituted variants, V6Q and G7F exhibited superior stabilization as compared to GP2. Molecular dynamics simulations suggest the improved binding can be attributed to concerted motions in the central and C-terminal regions of the peptide. These data support the notion that amino acids in HLA-A*0201 epitopes may be inter-dependent. Priming HLA-A*0201 transgenic mice with G7F-loaded syngeneic dendritic cells stimulated mouse T cells to produce a higher level of INFgamma than mice immunized with GP2.
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Affiliation(s)
- Matthew A. Joseph
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Megan L. Mitchell
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Jeffrey D. Evanseck
- Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA, United States
| | - Jeffrey R. Kovacs
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Liang Jia
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
| | - Hongmei Shen
- Department of Radiation Oncology, University of Pittsburgh Cancer Institute, Pittsburgh, PA, United States
| | - Wilson S. Meng
- Division of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA, United States
- Corresponding author at: Duquesne University, Mellon Hall 413, 600 Forbes Avenue, Pittsburgh, PA 15282, United States. Tel.: +1 412 396 6366; fax: +1 412 396 4660. E-mail address: (W.S. Meng)
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15
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Fagerberg T, Cerottini JC, Michielin O. Structural prediction of peptides bound to MHC class I. J Mol Biol 2005; 356:521-46. [PMID: 16368108 DOI: 10.1016/j.jmb.2005.11.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 11/16/2005] [Accepted: 11/17/2005] [Indexed: 11/29/2022]
Abstract
An ab initio structure prediction approach adapted to the peptide-major histocompatibility complex (MHC) class I system is presented. Based on structure comparisons of a large set of peptide-MHC class I complexes, a molecular dynamics protocol is proposed using simulated annealing (SA) cycles to sample the conformational space of the peptide in its fixed MHC environment. A set of 14 peptide-human leukocyte antigen (HLA) A0201 and 27 peptide-non-HLA A0201 complexes for which X-ray structures are available is used to test the accuracy of the prediction method. For each complex, 1000 peptide conformers are obtained from the SA sampling. A graph theory clustering algorithm based on heavy atom root-mean-square deviation (RMSD) values is applied to the sampled conformers. The clusters are ranked using cluster size, mean effective or conformational free energies, with solvation free energies computed using Generalized Born MV 2 (GB-MV2) and Poisson-Boltzmann (PB) continuum models. The final conformation is chosen as the center of the best-ranked cluster. With conformational free energies, the overall prediction success is 83% using a 1.00 Angstroms crystal RMSD criterion for main-chain atoms, and 76% using a 1.50 Angstroms RMSD criterion for heavy atoms. The prediction success is even higher for the set of 14 peptide-HLA A0201 complexes: 100% of the peptides have main-chain RMSD values < or =1.00 Angstroms and 93% of the peptides have heavy atom RMSD values < or =1.50 Angstroms. This structure prediction method can be applied to complexes of natural or modified antigenic peptides in their MHC environment with the aim to perform rational structure-based optimizations of tumor vaccines.
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Affiliation(s)
- Theres Fagerberg
- Ludwig Institute for Cancer Research, University of Lausanne, Epalinges, Switzerland
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16
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Zacharias M, Springer S. Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study. Biophys J 2005; 87:2203-14. [PMID: 15454423 PMCID: PMC1304646 DOI: 10.1529/biophysj.104.044743] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Major histocompatibility complex class I proteins play a key role in the recognition and presentation of peptide antigens to the host immune system. The structure of various major histocompatibility complex class I proteins has been determined experimentally in complex with several antigenic peptides. However, the structure in the unbound (empty) form is not known. To study the conformational dynamics of the empty major histocompatibility complex class I molecule comparative molecular dynamics simulations have been performed starting from the crystal structure of a peptide bound class I peptide-binding domain in the presence and absence of a peptide ligand. Simulations including the bound peptide stayed close to the experimental start structure at both simulation temperatures (300 and 355 K) during the entire simulation of 26 ns. Several independent simulations in the absence of peptide indicate that the empty domain may not adopt a single defined conformation but is conformationally significantly more heterogeneous in particular within the alpha-helices that flank the peptide binding cleft. The calculated conformational dynamics along the protein chain correlate well with available spectroscopic data and with the observed site-specific sensitivity of the empty class I protein to proteolytic digestion. During the simulations at 300 K the binding region for the peptide N-terminus stayed close to the conformation in the bound state, whereas the anchor region for the C-terminus showed significantly larger conformational fluctuations. This included a segment at the beginning of the second alpha-helix in the domain that is likely to be involved in the interaction with the chaperone protein tapasin during the peptide-loading process. The simulation studies further indicate that peptide binding at the C- and N-terminus may follow different mechanisms that involve different degrees of induced conformational changes in the peptide-binding domain. In particular binding of the peptide C-terminus may require conformational stabilization by chaperone proteins during peptide loading.
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Affiliation(s)
- Martin Zacharias
- International University Bremen, School of Engineering and Science, D-28759 Bremen, Germany.
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Wan S, Coveney P, Flower DR. Large-scale molecular dynamics simulations of HLA-A*0201 complexed with a tumor-specific antigenic peptide: can the alpha3 and beta2m domains be neglected? J Comput Chem 2004; 25:1803-13. [PMID: 15386470 DOI: 10.1002/jcc.20100] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Large-scale massively parallel molecular dynamics (MD) simulations of the human class I major histocompatibility complex (MHC) protein HLA-A*0201 bound to a decameric tumor-specific antigenic peptide GVYDGREHTV were performed using a scalable MD code on high-performance computing platforms. Such computational capabilities put us in reach of simulations of various scales and complexities. The supercomputing resources available for this study allow us to compare directly differences in the behavior of very large molecular models; in this case, the entire extracellular portion of the peptide-MHC complex vs. the isolated peptide binding domain. Comparison of the results from the partial and the whole system simulations indicates that the peptide is less tightly bound in the partial system than in the whole system. From a detailed study of conformations, solvent-accessible surface area, the nature of the water network structure, and the binding energies, we conclude that, when considering the conformation of the alpha1-alpha2 domain, the alpha3 and beta2m domains cannot be neglected.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, WC1H 0AJ, UK
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18
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Petrone PM, Garcia AE. MHC–Peptide Binding is Assisted by Bound Water Molecules. J Mol Biol 2004; 338:419-35. [PMID: 15066441 DOI: 10.1016/j.jmb.2004.02.039] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Revised: 02/02/2004] [Accepted: 02/02/2004] [Indexed: 10/26/2022]
Abstract
Water plays an important role in determining the high affinity of epitopes to the class I MHC complex. To study the energy and dynamics of water interactions in the complex we performed molecular dynamics simulation of the class I MHC-HLA2 complex bound to the HIV reverse transcriptase epitope, ILKEPVHGV, and in the absence of the epitope. Each simulation was extended for 5ns. We studied the processes of water penetration in the interface between MHC and peptide, and identified 14 water molecules that stay bound for periods longer than 1ns in regions previously identified by crystallography. These water molecules in the interface perform definite "tasks" contributing to the binding energy: hydrogen bond bridges between MHC and peptide and filling empty spaces in the groove which enhance affinity without contributing to epitope specificity. We calculate the binding energy for interfacial water molecules and find that there is an overall gain in free energy resulting from the formation of water clusters at the epitope-MHC interface. Water molecules serving the task of filling empty spaces bind at the interface with a net gain in entropy, relative to their entropy in bulk. We conclude that water molecules at the interface play the role of active mediators in the MHC-peptide interaction, and might be responsible for the large binding affinity of the MHC complex to a large number of epitope sequences.
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Affiliation(s)
- Paula M Petrone
- Theoretical Biology and Biophysics Group, T-10 MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Ogata K, Wodak SJ. Conserved water molecules in MHC class-I molecules and their putative structural and functional roles. Protein Eng Des Sel 2002; 15:697-705. [PMID: 12364585 DOI: 10.1093/protein/15.8.697] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A set of conserved water positions making direct contacts with the alpha1 and alpha2 domains of the MHC class-I protein was identified by a cluster analysis in 12 high-resolution crystal structures of proteins from different allele types and different species, comprising human, mouse and rat. The analysis revealed a total of 63 clusters, corresponding to water molecules, whose positions are conserved in half or more of the analyzed structures. Analysis of these clusters shows that the most conserved water positions-those appearing in the largest fraction of the structures-were also the most accurately defined, as measured by their normalized crystallographic B-factor. Not too surprisingly, these positions displayed better overlap and formed more H-bonds with the protein. In a second part of this work, a detailed analysis is presented of three of the most conserved water positions and their putative structural and functional roles are discussed. The most highly conserved of the three appears to play an important role in stabilizing the conformation of a twisted beta-turn between residues 118 and 122 (numbering of HLA-B3501, PDB code 1A1N). An equivalent water molecule was found to be associated with a similar beta-turn in 43 unrelated structures surveyed in the PDB, leading to the suggestion that this water molecule plays an important structural role in this type of turn. The second water molecule makes hydrogen bonds with residues lining pocket B in the peptide-binding groove and is suggested to play a role in modulating peptide recognition. The third highly conserved water molecule is located at the first kink of the alpha2 helix, possibly playing a role in determining the position of the N-terminal segment of that helix, which also carries side chains in contact with the bound peptide. This information on conserved water positions in MHC class-I molecules should be helpful in modeling interactions with bound peptide antigens and in designing new peptides with tailor-made affinities.
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Affiliation(s)
- Koji Ogata
- Service de Conformation de Macromolécules Biologiques, Centre de Biologie Structurale et Bioinformatique, Université Libre de Bruxelles,av. F.D. Roosevelt 50, CP160/16, B-1050 Brussels, Belgium
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Abstract
Administration of synthetic peptides derived from proteins uniquely or overexpressed in tumor cells (tumor-associated antigens) can elicit tumor-specific immune responses in vivo. This is because cytotoxic T lymphocytes can recognize and lyse tumor cells that display peptides derived from tumor-associated antigens (TAAs) in the context of class I major histocompatibility complex (MHC) molecules. TAA peptides, in contrast to peptides of viral origin, generally bind weakly to the MHC molecule. In many cases, this explains the poor magnitude of T cell response directed at the tumor in vivo. Improving MHC binding as a strategy to upregulate antigen recognition can convert low affinity TAA peptides into useful tools in clinical trial settings. High-resolution structures of class I MHC molecules reported over the past two decades provided the framework for designing peptides that can induce optimal T cell response. This review will discuss the basic and clinical aspects of modifying native TAA peptides as tumor vaccines.
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Affiliation(s)
- Wilson S Meng
- Division of Pharmaceutical Sciences, Duquesne University, Mylan School of Pharmacy, Pittsburgh, Pennsylvania 15282, USA.
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Meng WS, Butterfield LH, Ribas A, Heller JB, Dissette VB, Glaspy JA, McBride WH, Economou JS. Fine specificity analysis of an HLA-A2.1-restricted immunodominant T cell epitope derived from human alpha-fetoprotein. Mol Immunol 2000; 37:943-50. [PMID: 11395133 DOI: 10.1016/s0161-5890(01)00017-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Human alpha-fetoprotein (AFP) is a potentially important target for the immunotherapy of hepatocellular carcinoma (HCC). AFP(542-550) (GVALQTMKQ) is one of several HLA-A2.1-restricted immunodominant AFP peptides that consistently generate AFP-specific T cell responses in human T cell cultures and in HLA-A2.1/K(b) transgenic (A2.1 tg) mice. We performed a fine specificity analysis of this nonamer to determine which amino acid side chains were critical for T cell priming and recognition. Using peptide-pulsed dendritic cells (DC) as an immunization strategy, we characterized the effects of AFP(542-550) amino acid substitutions on priming and recognition in A2.1 tg mice. Replacing the glutamine at anchor position 9 with a leucine enhanced MHC binding and AFP-specific T cell responses. Substitution of leucine at non-anchor position 4 with an alanine did not alter binding but greatly diminished T cell recognition. Computer-generated three-dimensional models provided the structural rationale for these observed effects in MHC binding and T cell responses resulted from the modifications in the AFP(542-550) sequence.
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Affiliation(s)
- W S Meng
- Room 54-140 CHS, Division of Surgical Oncology, UCLA School of Medicine, University of California at Los Angeles, 10833 Le Conte Avenue, 90095-1782, Los Angeles, CA, USA
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Toh H, Savoie CJ, Kamikawaji N, Muta S, Sasazuki T, Kuhara S. Changes at the floor of the peptide-binding groove induce a strong preference for proline at position 3 of the bound peptide: molecular dynamics simulations of HLA-A*0217. Biopolymers 2000; 54:318-27. [PMID: 10935972 DOI: 10.1002/1097-0282(20001015)54:5<318::aid-bip30>3.0.co;2-t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We report on molecular dynamics simulations of major histocompatibility complex (MHC)-peptide complexes. Class I MHC molecules play an important role in cellular immunity by presenting antigenic peptides to cytotoxic T cells. Pockets in the peptide-binding groove of MHC molecules accommodate anchor side chains of the bound peptide. Amino acid substitutions in MHC affect differences in the peptide-anchor motifs. HLA-A*0217, human MHC class I molecule, differs from HLA-A*0201 only by three amino acid residues substitutions (positions 95, 97, and 99) at the floor of the peptide-binding groove. A*0217 showed a strong preference for Pro at position 3 (p3) and accepted Phe at p9 of its peptide ligands, but these preferences have not been found in other HLA-A2 ligands. To reveal the structural mechanism of these observations, the A*0217-peptide complexes were simulated by 1000 ps molecular dynamics at 300 K with explicit solvent molecules and compared with those of the A*0201-peptide complexes. We examined the distances between the anchor side chain of the bound peptide and the pocket, and the rms fluctuations of the bound peptides and the HLA molecules. On the basis of the results from our simulations, we propose that Pro at p3 serves as an optimum residue to lock the dominant anchor residue (p9) tightly into pocket F and to hold the peptide in the binding groove, rather than a secondary anchor residue fitting optimally the complementary pocket. We also found that Phe at p9 is used to occupy the space created by replacements of three amino acid residues at the floor within the groove. These findings would provide a novel understanding in the peptide-binding motifs of class I MHC molecules.
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Affiliation(s)
- H Toh
- Graduate School of Genetic Resources Technology, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Meng WS, von Grafenstein H, Haworth IS. Water dynamics at the binding interface of four different HLA-A2-peptide complexes. Int Immunol 2000; 12:949-57. [PMID: 10882406 DOI: 10.1093/intimm/12.7.949] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Because only a limited number of MHC molecules are available for presentation of a large number of peptides, each of these MHC molecules must be able to bind promiscuously many different peptides at an affinity sufficient for stable presentation. Here we show, for the MHC molecule HLA-A2, that this ability may be facilitated by a flexible water network that forms an interface between the MHC molecule and the peptide. Using the SURFNET program we have computed the 'gaps' present in the peptide-binding groove in the X-ray structures of complexes of HLA-A2 with four different bound peptides. The volume of these gaps increases with increasing peptide hydrophilicity. Using molecular dynamics simulations, we show that the water molecules in the binding groove of complexes of HLA-A2 with the more hydrophilic peptides are largely disordered, but a number of defined water-binding sites are also discernable. Conversely, for complexes of HLA-A2 with the more hydrophobic peptides, the water molecules are more rigidly bound at the MHC-peptide interface and a number of well-defined water-binding sites exist. However, even these well-defined sites may not be permanently occupied by the same water molecule and in the dynamics calculations we observed exchange of water molecules between such sites.
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Affiliation(s)
- W S Meng
- Department of Pharmaceutical Sciences, University of Southern California, 1985 Zonal Avenue, Los Angeles, CA 90089-9121, USA
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Toh H, Kamikawaji N, Tana T, Muta S, Sasazuki T, Kuhara S. Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: molecular dynamics simulations of HLA-DR4 (DRB1*0405) complexed with analogue peptide. PROTEIN ENGINEERING 2000; 13:423-9. [PMID: 10877853 DOI: 10.1093/protein/13.6.423] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In our model system, we generated T cell clones specific for the HLA-DR4 (DRB1*0405)-index peptide (YWALEAAAD) complex. Based on response patterns of the T cell clones, analogue peptides containing single amino acid substitutions of the index peptide were classified into three types, agonists, antagonists or null peptides (non-agonistic and non-antagonistic peptides). Subtle structural changes induced by the antagonists in the T-cell receptor (TCR) binding regions have already been explained using the root mean square (r.m.s.) deviations from the DR4-index peptide complex in the molecular dynamics (MD) trajectory. In this work, we performed additional MD simulations at 300 K with explicit solvent molecules to reveal the structural character of the HLA-DR4 complexed with the analogue peptides. We examined the r.m.s. deviations of the TCR-binding sites and the exposed areas of the bound peptides. Remarkable differences of the r.m.s. deviations among the DR4-antagonist complexes, together with our previous data, suggest that the magnitude of structural changes of TCR-binding regions would determine the strength of TCR antagonism. The simulations also indicate that TCR could discriminate null peptides from other ligands mainly through the changes of exposed side chains of the bound peptide, rather than the conformational changes of TCR-binding surfaces on HLA molecule.
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Affiliation(s)
- H Toh
- Graduate School of Genetic Resources Technology, Kyushu University, Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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Gurlo T, Meng WS, Bui HH, Haworth IS, von Grafenstein H. Experimental evidence for the presence of a water network at the peptide-MHC interface. Immunol Lett 1999; 70:139-41. [PMID: 10656665 DOI: 10.1016/s0165-2478(99)00150-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- T Gurlo
- University of Southern California, School of Pharmacy, Department of Pharmaceutical Sciences, Los Angeles 90033, USA
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Abstract
MHC molecules are crucially involved in controlling the specific immune system. They are highly polymorphic receptors sampling peptides from the cellular environment and presenting these peptides for scrutiny by immune cells. Recent advances in combinatorial peptide chemistry have improved the description and prediction of peptide-MHC binding. It is envisioned that a complete mapping of human immune reactivities will be possible.
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Affiliation(s)
- S Buus
- Institute of Medical Microbiology and Immunology, Panum Building 18.3.22, Blegdamsvej 3, 2200, Copenhagen N, Denmark.
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