메뉴 건너뛰기




Volumn 118, Issue 1, 2014, Pages 69-80

The gp41659-671 HIV-1 antibody epitope: A structurally challenging small peptide

Author keywords

[No Author keywords available]

Indexed keywords

CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; MONOCLONAL ANTIBODIES; PEPTIDES; SOLUTIONS; X RAY CRYSTALLOGRAPHY;

EID: 84892565540     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp409355r     Document Type: Article
Times cited : (7)

References (58)
  • 1
    • 0030970693 scopus 로고    scopus 로고
    • Core Structure of gp41 from the HIV Envelope Glycoprotein
    • Chan, D. C.; Fass, D.; Berger, J. M.; Kim, P. S. Core Structure of gp41 from the HIV Envelope Glycoprotein Cell 1997, 89, 263-273
    • (1997) Cell , vol.89 , pp. 263-273
    • Chan, D.C.1    Fass, D.2    Berger, J.M.3    Kim, P.S.4
  • 5
    • 0035912191 scopus 로고    scopus 로고
    • Challenges and Opportunities for Development of an AIDS Vaccine
    • Nabel, G. J. Challenges and Opportunities for Development of an AIDS Vaccine Nature 2001, 410, 1002-1007
    • (2001) Nature , vol.410 , pp. 1002-1007
    • Nabel, G.J.1
  • 6
    • 0037159248 scopus 로고    scopus 로고
    • A Monomeric 3(10)-Helix is Formed in Water by a 13-residue Peptide Representing the Neutralizing Determinant of HIV-1 on gp41
    • Biron, Z.; Khare, S.; Samson, A.; Hayek, Y.; Naider, F.; Anglister, J. A Monomeric 3(10)-Helix is Formed in Water by a 13-residue Peptide Representing the Neutralizing Determinant of HIV-1 on gp41 Biochemistry 2002, 41, 12687-12696
    • (2002) Biochemistry , vol.41 , pp. 12687-12696
    • Biron, Z.1    Khare, S.2    Samson, A.3    Hayek, Y.4    Naider, F.5    Anglister, J.6
  • 8
    • 0034755554 scopus 로고    scopus 로고
    • Fine Definition of the Epitope on the gp41 Glycoprotein of Human Immunodeficiency Virus Type 1 for the Neutralizing Monoclonal Antibody 2F5
    • Parker, C. E.; Deterding, L. J.; Hager-Braun, C.; Binley, J. M.; Schulke, N.; Katinger, H.; Moore, J. P.; Tomer, K. B. Fine Definition of the Epitope on the gp41 Glycoprotein of Human Immunodeficiency Virus Type 1 for the Neutralizing Monoclonal Antibody 2F5 J. Virol. 2001, 75, 10906-10911
    • (2001) J. Virol. , vol.75 , pp. 10906-10911
    • Parker, C.E.1    Deterding, L.J.2    Hager-Braun, C.3    Binley, J.M.4    Schulke, N.5    Katinger, H.6    Moore, J.P.7    Tomer, K.B.8
  • 9
    • 0028801450 scopus 로고
    • Epitope Exposure on Functional, Oligomeric HIV-1 GP41 Molecules
    • Sattentau, Q. J.; Zollapazner, S.; Poignard, P. Epitope Exposure on Functional, Oligomeric HIV-1 GP41 Molecules Virology 1995, 206, 713-717
    • (1995) Virology , vol.206 , pp. 713-717
    • Sattentau, Q.J.1    Zollapazner, S.2    Poignard, P.3
  • 11
    • 33746603928 scopus 로고    scopus 로고
    • UV Resonance Raman Investigation of a 3(10)-helical Peptide Reveals a Rough Energy Landscape
    • Ahmed, Z.; Asher, S. A. UV Resonance Raman Investigation of a 3(10)-helical Peptide Reveals a Rough Energy Landscape Biochemistry 2006, 45, 9068-9073
    • (2006) Biochemistry , vol.45 , pp. 9068-9073
    • Ahmed, Z.1    Asher, S.A.2
  • 13
    • 4544379899 scopus 로고    scopus 로고
    • Structure and Mechanistic Analysis of the Anti-human Immunodeficiency Virus Type 1 Antibody 2F5 in Complex with its gp41 Epitope
    • Ofek, G.; Tang, M.; Sambor, A.; Katinger, H.; Mascola, J. R.; Wyatt, R.; Kwong, P. D. Structure and Mechanistic Analysis of the Anti-human Immunodeficiency Virus Type 1 Antibody 2F5 in Complex with its gp41 Epitope J. Virol. 2004, 78, 10724-10737
    • (2004) J. Virol. , vol.78 , pp. 10724-10737
    • Ofek, G.1    Tang, M.2    Sambor, A.3    Katinger, H.4    Mascola, J.R.5    Wyatt, R.6    Kwong, P.D.7
  • 17
    • 42149132659 scopus 로고    scopus 로고
    • T-20 and T-1249 HIV Fusion Inhibitors' Structure and Conformation in Solution: A Molecular Dynamics Study
    • Martins Do Canto, A. M. T.; Carvalho, A. J. P.; Ramalho, J. P. P.; Loura, L. M. S. T-20 and T-1249 HIV Fusion Inhibitors' Structure and Conformation in Solution: a Molecular Dynamics Study J. Pept. Sci. 2008, 14, 442-447
    • (2008) J. Pept. Sci. , vol.14 , pp. 442-447
    • Martins Do Canto, A.M.T.1    Carvalho, A.J.P.2    Ramalho, J.P.P.3    Loura, L.M.S.4
  • 18
    • 68949107624 scopus 로고    scopus 로고
    • Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes
    • Matthes, D.; de Groot, B. L. Secondary Structure Propensities in Peptide Folding Simulations: A Systematic Comparison of Molecular Mechanics Interaction Schemes Biophys. J. 2009, 97, 599-608
    • (2009) Biophys. J. , vol.97 , pp. 599-608
    • Matthes, D.1    De Groot, B.L.2
  • 21
    • 2442480826 scopus 로고    scopus 로고
    • Distinguish Protein Decoys by Using a Scoring Function Based on a New Amber Force Field, Short Molecular Dynamics Simulations, and the Generalized Born Solvent Model
    • Lee, M. C.; Duan, Y. Distinguish Protein Decoys by Using a Scoring Function Based on a New Amber Force Field, Short Molecular Dynamics Simulations, and the Generalized Born Solvent Model Proteins 2004, 55, 620-634
    • (2004) Proteins , vol.55 , pp. 620-634
    • Lee, M.C.1    Duan, Y.2
  • 22
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
    • Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins 2006, 65, 712-725
    • (2006) Proteins , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 23
    • 78650126176 scopus 로고    scopus 로고
    • Autonomous Folding in the Membrane Proximal HIV Peptide gp41(659-671): PH Tuneability at Micelle Interfaces
    • Gregor, C. R.; Cerasoli, E.; Tulip, P. R.; Ryadnov, M. G.; Martyna, G. J.; Crain, J. Autonomous Folding in the Membrane Proximal HIV Peptide gp41(659-671): pH Tuneability at Micelle Interfaces Phys. Chem. Chem. Phys. 2011, 13, 127-135
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 127-135
    • Gregor, C.R.1    Cerasoli, E.2    Tulip, P.R.3    Ryadnov, M.G.4    Martyna, G.J.5    Crain, J.6
  • 26
    • 84865088597 scopus 로고    scopus 로고
    • Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations
    • Cino, E. A.; Choy, W.-Y.; Karttunen, M. Comparison of Secondary Structure Formation Using 10 Different Force Fields in Microsecond Molecular Dynamics Simulations J. Chem. Theory Comput. 2012, 8, 2725-2740
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2725-2740
    • Cino, E.A.1    Choy, W.-Y.2    Karttunen, M.3
  • 27
    • 84858779824 scopus 로고    scopus 로고
    • Residue-Specific alpha-Helix Propensities from Molecular Simulation
    • Best, R. B.; de Sancho, D.; Mittal, J. Residue-Specific alpha-Helix Propensities from Molecular Simulation Biophys. J. 2012, 102, 1462-1467
    • (2012) Biophys. J. , vol.102 , pp. 1462-1467
    • Best, R.B.1    De Sancho, D.2    Mittal, J.3
  • 29
    • 20644449471 scopus 로고    scopus 로고
    • Modification of the Generalized Born Model Suitable for Macromolecules
    • Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 2000, 104, 3712-3720
    • (2000) J. Phys. Chem. B , vol.104 , pp. 3712-3720
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 30
    • 0000408363 scopus 로고    scopus 로고
    • Approximate Atomic Surfaces from Linear Combinations of Pairwise Overlaps (LCPO)
    • Weiser, J.; Shenkin, P. S.; Still, W. C. Approximate Atomic Surfaces from Linear Combinations of Pairwise Overlaps (LCPO) J. Comput. Chem. 1999, 20, 217-230
    • (1999) J. Comput. Chem. , vol.20 , pp. 217-230
    • Weiser, J.1    Shenkin, P.S.2    Still, W.C.3
  • 31
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model Proteins 2004, 55, 383-394
    • (2004) Proteins , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 32
    • 0004016501 scopus 로고
    • Comparison of Simple Potential Functions for Simulating Liquid Water
    • Jorgensen, W. L.; Chandrasekhar, J.; Madura, J.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
    • (1983) J. Chem. Phys. , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.3    Klein, M.L.4
  • 33
    • 33846823909 scopus 로고
    • Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
    • Darden, T. A.; York, D. M.; Pedersen, L. G. Particle Mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.A.1    York, D.M.2    Pedersen, L.G.3
  • 36
    • 0029619259 scopus 로고
    • Knowledge-Based Secondary Structure Assignment
    • Frishman, D.; Argos, P. Knowledge-Based Secondary Structure Assignment Proteins 1995, 23, 566-579
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 37
    • 0020997912 scopus 로고
    • Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features
    • Kabsch, W.; Sander, C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features Biopolymers 1983, 22, 2577-2637
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 39
    • 80051673221 scopus 로고    scopus 로고
    • SHIFTX2: Significantly Improved Protein Chemical Shift Prediction
    • Han, B.; Liu, Y.; Ginzinger, S. W.; Wishart, D. S. SHIFTX2: Significantly Improved Protein Chemical Shift Prediction J. Biomol. NMR 2011, 50, 43-57
    • (2011) J. Biomol. NMR , vol.50 , pp. 43-57
    • Han, B.1    Liu, Y.2    Ginzinger, S.W.3    Wishart, D.S.4
  • 40
    • 37849000389 scopus 로고    scopus 로고
    • HIV-1 Broadly Neutralizing Antibody Extracts Its Epitope from a Kinked gp41 Ectodomain Region on the Viral Membrane
    • Sun, Z.-Y. J.; Oh, K. J.; Kim, M.; Yu, J.; Brusic, V.; Song, L.; Qiao, Z.; huai Wang, J.; Wagner, G.; Reinherz, E. L. HIV-1 Broadly Neutralizing Antibody Extracts Its Epitope from a Kinked gp41 Ectodomain Region on the Viral Membrane Immunity 2008, 28, 52-63
    • (2008) Immunity , vol.28 , pp. 52-63
    • Sun, Z.-Y.J.1    Oh, K.J.2    Kim, M.3    Yu, J.4    Brusic, V.5    Song, L.6    Qiao, Z.7    Huai Wang, J.8    Wagner, G.9    Reinherz, E.L.10
  • 41
    • 0035859948 scopus 로고    scopus 로고
    • The Membrane-proximal Tryptophan-Rich Region of the HIV Glycoprotein, gp41, Forms a Well-Defined Helix in Dodecylphosphocholine Micelles
    • Schibli, D. J.; Montelara, R. C.; Vogel, H. J. The Membrane-proximal Tryptophan-Rich Region of the HIV Glycoprotein, gp41, Forms a Well-Defined Helix in Dodecylphosphocholine Micelles Biochemistry 2001, 40, 9570-9578
    • (2001) Biochemistry , vol.40 , pp. 9570-9578
    • Schibli, D.J.1    Montelara, R.C.2    Vogel, H.J.3
  • 42
    • 65249185539 scopus 로고    scopus 로고
    • Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation
    • Liu, J.; Deng, Y.; Dey, A. K.; Moore, J. P.; Lu, M. Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation Biochemistry 2009, 48, 2915-2923
    • (2009) Biochemistry , vol.48 , pp. 2915-2923
    • Liu, J.1    Deng, Y.2    Dey, A.K.3    Moore, J.P.4    Lu, M.5
  • 43
    • 74949118437 scopus 로고    scopus 로고
    • Role of a Putative gp41 Dimerization Domain in Human Immunodeficiency Virus Type 1 Membrane Fusion
    • Liu, J.; Deng, Y.; Li, Q.; Dey, A. K.; Moore, J. P.; Lu, M. Role of a Putative gp41 Dimerization Domain in Human Immunodeficiency Virus Type 1 Membrane Fusion J. Virol. 2010, 84, 201-209
    • (2010) J. Virol. , vol.84 , pp. 201-209
    • Liu, J.1    Deng, Y.2    Li, Q.3    Dey, A.K.4    Moore, J.P.5    Lu, M.6
  • 44
    • 77954059555 scopus 로고    scopus 로고
    • Crystal Structure of HIV-1 gp41 Including Both Fusion Peptide and Membrane Proximal External Regions
    • Buzon, V.; Natrajan, G.; Schibli, D.; Campelo, F.; Kozlov, M. M.; Weissenhorn, W. Crystal Structure of HIV-1 gp41 Including Both Fusion Peptide and Membrane Proximal External Regions PLoS Pathog. 2010, 6, 880
    • (2010) PLoS Pathog. , vol.6 , pp. 880
    • Buzon, V.1    Natrajan, G.2    Schibli, D.3    Campelo, F.4    Kozlov, M.M.5    Weissenhorn, W.6
  • 45
    • 58149087854 scopus 로고    scopus 로고
    • In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes
    • Lapelosa, M.; Gallicchio, E.; Arnold, G. F.; Arnold, E.; Levy, R. M. In Silico Vaccine Design Based on Molecular Simulations of Rhinovirus Chimeras Presenting HIV-1 gp41 Epitopes J. Mol. Biol. 2009, 385, 675-691
    • (2009) J. Mol. Biol. , vol.385 , pp. 675-691
    • Lapelosa, M.1    Gallicchio, E.2    Arnold, G.F.3    Arnold, E.4    Levy, R.M.5
  • 46
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides
    • Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides J. Phys. Chem. B 2001, 105, 6474-6487
    • (2001) J. Phys. Chem. B , vol.105 , pp. 6474-6487
    • Kaminski, G.A.1    Friesner, R.A.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 47
    • 0029912748 scopus 로고    scopus 로고
    • Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids
    • Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 48
    • 33748539347 scopus 로고    scopus 로고
    • Conformational Equilibrium in Alanine-Rich Peptides Probed by Reversible Stretching Simulations
    • Henin, J.; Schulten, K.; Chipot, C. Conformational Equilibrium in Alanine-Rich Peptides Probed by Reversible Stretching Simulations J. Phys. Chem. B 2006, 110, 16718-16723
    • (2006) J. Phys. Chem. B , vol.110 , pp. 16718-16723
    • Henin, J.1    Schulten, K.2    Chipot, C.3
  • 50
    • 14744302119 scopus 로고
    • Helix-Coil Transition of Polypeptides under an External Force
    • Saito, N.; Go, M. Helix-Coil Transition of Polypeptides under an External Force J. Phys. Soc. Jpn. 1968, 24, 376-379
    • (1968) J. Phys. Soc. Jpn. , vol.24 , pp. 376-379
    • Saito, N.1    Go, M.2
  • 51
    • 0015959823 scopus 로고
    • Helix-Coil Transition under External Forces
    • Doi, M. Helix-Coil Transition under External Forces Polym. J. (Tokyo, Jpn.) 1974, 6, 222-229
    • (1974) Polym. J. (Tokyo, Jpn.) , vol.6 , pp. 222-229
    • Doi, M.1
  • 52
    • 84856195985 scopus 로고    scopus 로고
    • Tensile Mechanics of α-Helical Coil Springs
    • Ikai, A. Tensile Mechanics of α-Helical Coil Springs Adv. Polym. Sci. 2010, 232, 65-96
    • (2010) Adv. Polym. Sci. , vol.232 , pp. 65-96
    • Ikai, A.1
  • 54
    • 33646169744 scopus 로고    scopus 로고
    • Mechanically Induced Helix-Coil Transition in Biopolymer Networks
    • Courty, S.; Gornall, J. L.; Terentjev, E. M. Mechanically Induced Helix-Coil Transition in Biopolymer Networks Biophys. J. 2006, 90, 1019-1027
    • (2006) Biophys. J. , vol.90 , pp. 1019-1027
    • Courty, S.1    Gornall, J.L.2    Terentjev, E.M.3
  • 55
    • 33748580683 scopus 로고    scopus 로고
    • Nonlinear Elasticity of an Alpha-helical Polypeptide: Monte Carlo Studies
    • Chakrabarti, B.; Levine, A. J. Nonlinear Elasticity of an Alpha-helical Polypeptide: Monte Carlo Studies Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. 2006, 74, 031903-1-031903-11
    • (2006) Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys. , vol.74 , pp. 0319031-03190311
    • Chakrabarti, B.1    Levine, A.J.2
  • 56
    • 61549123336 scopus 로고    scopus 로고
    • Tensile Mechanics of Alanine-Based Helical Polypeptide: Force Spectroscopy versus Computer Simulations
    • Afrin, R.; Takahashi, I.; Shiga, K.; Ikai, A. Tensile Mechanics of Alanine-Based Helical Polypeptide: Force Spectroscopy versus Computer Simulations Biophys. J. 2009, 96, 1105-1114
    • (2009) Biophys. J. , vol.96 , pp. 1105-1114
    • Afrin, R.1    Takahashi, I.2    Shiga, K.3    Ikai, A.4
  • 57
    • 3042681600 scopus 로고    scopus 로고
    • Nature of Structural Inhomogeneities on Folding a Helix and their Influence on Spectral Measurements
    • Gnanakaran, S.; Hochstrasser, R. M.; Garcia, A. E. Nature of Structural Inhomogeneities on Folding a Helix and their Influence on Spectral Measurements Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 9229-9234
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 9229-9234
    • Gnanakaran, S.1    Hochstrasser, R.M.2    Garcia, A.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.