-
1
-
-
0037159248
-
10-Helix Is Formed in Water by a 13-Residue Peptide Representing the Neutralizing Determinant of HIV-1 on gp41
-
10-Helix Is Formed in Water by a 13-Residue Peptide Representing the Neutralizing Determinant of HIV-1 on gp41 Biochemistry 2002, 41, 12687
-
(2002)
Biochemistry
, vol.41
, pp. 12687
-
-
Biron, Z.1
Khare, S.2
Samson, A.3
Heyak, Y.4
Naider, F.5
Anglister, J.6
-
2
-
-
0032980413
-
A Conserved Tryptophan-Rich Motif in the Membrane-Proximal Region of the Human Immunodeficiency Virus Type 1 gp41 Ectodomain Is Important for Env-Mediated Fusion and Virus Infectivity
-
Salzwedel, K.; West, J.; Hunter, E. A Conserved Tryptophan-Rich Motif in the Membrane-Proximal Region of the Human Immunodeficiency Virus Type 1 gp41 Ectodomain Is Important for Env-Mediated Fusion and Virus Infectivity J. Virol. 1999, 73, 2469-2480
-
(1999)
J. Virol.
, vol.73
, pp. 2469-2480
-
-
Salzwedel, K.1
West, J.2
Hunter, E.3
-
3
-
-
0037195784
-
Enhancement of α-Helicity in the HIV-1 Inhibitory Peptide DP178 Leads to an Increased Affinity for Human Monoclonal Antibody 2F5 but Does Not Elicit Neutralizing Responses in Vitro
-
Joyce, J.; Hurni, W.; Bogusky, M.; Garsky, V.; Liang, X.; Citron, M.; Danzeisen, R.; Miller, M.; Shiver, J.; Keller, P. Enhancement of α-Helicity in the HIV-1 Inhibitory Peptide DP178 Leads to an Increased Affinity for Human Monoclonal Antibody 2F5 but Does Not Elicit Neutralizing Responses in Vitro J. Biol. Chem. 2002, 277, 45811-45820
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 45811-45820
-
-
Joyce, J.1
Hurni, W.2
Bogusky, M.3
Garsky, V.4
Liang, X.5
Citron, M.6
Danzeisen, R.7
Miller, M.8
Shiver, J.9
Keller, P.10
-
4
-
-
0028865465
-
Cross-clade neutralization of primary isolates of human immunodeficiency virus type 1 by human monoclonal antibodies and tetrameric CD4-IgG
-
Trkola, A.; Pomales, A.; Yuan, H.; Korber, B.; Maddon, P.; Allaway, G.; Kattinger, H.; Barbas, C.; Burton, D.; Ho, D.; Moore, J. Cross-clade neutralization of primary isolates of human immunodeficiency virus type 1 by human monoclonal antibodies and tetrameric CD4-IgG J. Virol. 1995, 69, 6609-6617
-
(1995)
J. Virol.
, vol.69
, pp. 6609-6617
-
-
Trkola, A.1
Pomales, A.2
Yuan, H.3
Korber, B.4
Maddon, P.5
Allaway, G.6
Kattinger, H.7
Barbas, C.8
Burton, D.9
Ho, D.10
Moore, J.11
-
5
-
-
11144227042
-
Anti-Human Immunodeficiency Virus Type 1 (HIV-1) Antibodies 2F5 and 4E10 Require Surprisingly Few Crucial Residues in the Membrane-Proximal External Region of Glycoprotein gp41 to Neutralize HIV-1
-
Zwick, M.; Jensen, R.; Church, S.; Wang, M.; Steigler, G.; Kunert, R.; Katinger, H.; Burton, D. Anti-Human Immunodeficiency Virus Type 1 (HIV-1) Antibodies 2F5 and 4E10 Require Surprisingly Few Crucial Residues in the Membrane-Proximal External Region of Glycoprotein gp41 To Neutralize HIV-1 J. Virol. 2005, 79, 1252-1261
-
(2005)
J. Virol.
, vol.79
, pp. 1252-1261
-
-
Zwick, M.1
Jensen, R.2
Church, S.3
Wang, M.4
Steigler, G.5
Kunert, R.6
Katinger, H.7
Burton, D.8
-
6
-
-
1242342052
-
Binding of the 2F5Monoclonal Antibody to Native and Fusion-Intermediate Forms of Human Immunodeficiency Virus Type 1 gp41: Implications for Fusion-Inducing Conformational Changes
-
de Rosny, E.; Vassell, R.; Jiang, S.; Kunert, R.; Weiss, C. Binding of the 2F5Monoclonal Antibody to Native and Fusion-Intermediate Forms of Human Immunodeficiency Virus Type 1 gp41: Implications for Fusion-Inducing Conformational Changes J. Virol. 2004, 78, 2627
-
(2004)
J. Virol.
, vol.78
, pp. 2627
-
-
De Rosny, E.1
Vassell, R.2
Jiang, S.3
Kunert, R.4
Weiss, C.5
-
7
-
-
0038351790
-
Structural Analysis of the Epitope of the Anti-HIV Antibody 2F5 Sheds Light into Its Mechanism of Neutralization and HIV Fusion
-
Barbato, G.; Bianchi, E.; Ingallinella, P.; Hurni, W.; Miller, M. D.; Ciliberto, G.; Cortese, R.; Bazzo, R.; Shiver, J. W.; Pessi, A. Structural Analysis of the Epitope of the Anti-HIV Antibody 2F5 Sheds Light into Its Mechanism of Neutralization and HIV Fusion J. Mol. Biol. 2003, 330, 1101
-
(2003)
J. Mol. Biol.
, vol.330
, pp. 1101
-
-
Barbato, G.1
Bianchi, E.2
Ingallinella, P.3
Hurni, W.4
Miller, M.D.5
Ciliberto, G.6
Cortese, R.7
Bazzo, R.8
Shiver, J.W.9
Pessi, A.10
-
8
-
-
33746603928
-
10-Helical Peptide Reveals a Rough Energy Landscape
-
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.2
-
9
-
-
42149132659
-
T-20 and T-1249 HIV fusion inhibitors' structure and conformation in solution: A molecular dynamics study
-
Martins do Canto, A. M. T.; Palace Carvalho, A. J.; Prates Ramalho, J. 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. 2007, 14, 442-447
-
(2007)
J. Pept. Sci.
, vol.14
, pp. 442-447
-
-
Martins Do Canto, A.M.T.1
Palace Carvalho, A.J.2
Prates Ramalho, J.P.3
Loura, L.M.S.4
-
10
-
-
58149087854
-
In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes
-
Lapelosa, M.; Gallicchio, E.; Arnold, G. F.; Arnold, G. F.; 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, G.F.4
Levy, R.M.5
-
11
-
-
0035859948
-
The Membrane-Proximal Tryptophan-Rich Region of the HIV Glycoprotein, gp41, Forms a Well-Defined Helix in Dodecylphosphocholine Micelles
-
Schibli, D.; Montelero, R.; Vogel, H. The Membrane-Proximal Tryptophan-Rich Region of the HIV Glycoprotein, gp41, Forms a Well-Defined Helix in Dodecylphosphocholine Micelles Biochemistry 2001, 40, 9570
-
(2001)
Biochemistry
, vol.40
, pp. 9570
-
-
Schibli, D.1
Montelero, R.2
Vogel, H.3
-
12
-
-
0036467163
-
Structure of met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu, K. Y.; Garcia, A. E. Structure of met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics Proteins: Struct., Funct., Genet. 2002, 46, 225-234
-
(2002)
Proteins: Struct., Funct., Genet.
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
14
-
-
0025737751
-
-
Siligardi, G.; Drake, A.; Mascagni, P.; Rowlands, D.; Brown, F.; Gibbons, W. Eur. J. Biochem. 1991, 199, 545-551
-
(1991)
Eur. J. Biochem.
, vol.199
, pp. 545-551
-
-
Siligardi, G.1
Drake, A.2
Mascagni, P.3
Rowlands, D.4
Brown, F.5
Gibbons, W.6
-
15
-
-
0041784950
-
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
-
MacKerell, A.; Bashford, D.; Bellott, M.; Dunbrack, R.; Evanseck, J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.; Prodhom, B.; Reiher, W.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586
-
-
MacKerell, A.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.18
Prodhom, B.19
Reiher, W.20
Roux, B.21
Schlenkrich, M.22
Smith, J.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
16
-
-
0034625286
-
Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers
-
Tuckerman, M. E.; A Yarne, D.; Samuelson, S. O.; Hughes, A. L.; Martyna, G. J. Exploiting multiple levels of parallelism in Molecular Dynamics based calculations via modern techniques and software paradigms on distributed memory computers Comput. Phys. Commun. 2000, 128, 333
-
(2000)
Comput. Phys. Commun.
, vol.128
, pp. 333
-
-
Tuckerman, M.E.1
Yarne D, A.2
Samuelson, S.O.3
Hughes, A.L.4
Martyna, G.J.5
-
17
-
-
36449000062
-
Nosé-Hoover chains - The canonical ensemble via continuous dynamics
-
Martyna, G. J.; Klein, M. L.; Tuckerman, M. Nosé-Hoover chains-the canonical ensemble via continuous dynamics J. Chem. Phys. 1992, 97, 2635
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 2635
-
-
Martyna, G.J.1
Klein, M.L.2
Tuckerman, M.3
-
18
-
-
0000026966
-
Explicit reversible integrators for extended systems dynamics
-
Martyna, G. J.; Tuckerman, M. E.; Tobias, D. J.; Klein, M. L. Explicit reversible integrators for extended systems dynamics Mol. Phys. 1996, 87, 1117
-
(1996)
Mol. Phys.
, vol.87
, pp. 1117
-
-
Martyna, G.J.1
Tuckerman, M.E.2
Tobias, D.J.3
Klein, M.L.4
-
19
-
-
28844454252
-
Parallel tempering: Theory, applications, and new perspectives
-
Earl, D. J.; Deem, M. W. Parallel tempering: Theory, applications, and new perspectives Phys. Chem. Chem. Phys. 2005, 23, 3910
-
(2005)
Phys. Chem. Chem. Phys.
, vol.23
, pp. 3910
-
-
Earl, D.J.1
Deem, M.W.2
-
20
-
-
24944462252
-
Virtual-move parallel tempering
-
Coluzza, I.; Frenkel, D. Virtual-move parallel tempering Chem. Phys. Chem 2005, 6, 1779
-
(2005)
Chem. Phys. Chem
, vol.6
, pp. 1779
-
-
Coluzza, I.1
Frenkel, D.2
-
21
-
-
0031232794
-
Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters and Bulk Water
-
Samuelson, S. O.; Tobias, D. J.; Martyna, G. J. Modern Computational Methodology Applied to the Simulation of Blocked Trialanine Peptide in Vacuo, Water Clusters and Bulk Water J. Phys. Chem. B 1997, 101, 7592-7603
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 7592-7603
-
-
Samuelson, S.O.1
Tobias, D.J.2
Martyna, G.J.3
-
22
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
Frishman, D.; Argos, P. Knowledge-based protein secondary structure assignment Proteins: Struct., Funct., Genet. 1995, 23, 566-579
-
(1995)
Proteins: Struct., Funct., Genet.
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
23
-
-
68949107624
-
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
-
24
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a Β-hairpin folding in water
-
Zhou, R.; Berne, B. J. Can a continuum solvent model reproduce the free energy landscape of a Β-hairpin folding in water Proc. Natl. Acad. Sci. 2002, 99, 12777-12782
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
-
25
-
-
46749127364
-
Are current molecular dynamics force fields too helical
-
Best, R. B.; Buchete, N.-V.; Hummer, G. Are current molecular dynamics force fields too helical Biophys. J. 2008, 95, L07-L09
-
(2008)
Biophys. J.
, vol.95
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
26
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
Mackerell, A. D., Jr.; Feig, M.; Brooks, C. L., III Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 2004, 25, 1400
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
27
-
-
4444351490
-
Empirical Force Fields for Biological Macromolecules: Overview and Issues
-
Mackerell, A., Jr. Empirical Force Fields for Biological Macromolecules: Overview and Issues J. Comput. Chem. 2004, 25, 1583
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1583
-
-
Mackerell Jr., A.1
-
28
-
-
1642576012
-
Improved Treatment of the Protein Backbone in Empirical Force Fields
-
Mackerell, A., Jr.; Feig, M.; Brooks, C. L., III Improved Treatment of the Protein Backbone in Empirical Force Fields J. Am. Chem. Soc. 2004, 126, 698-699
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 698-699
-
-
Mackerell Jr., A.1
Feig, M.2
Brooks III, C.L.3
-
29
-
-
32544446167
-
Peptide Secondary Structure Folding Reaction Coordinate: Correlation between UV Raman Amide III Frequency, Î̈ Ramachandran Angle, and Hydrogen Bonding
-
Mikhonin, A.; Bykov, S.; Myshakina, N.; Asher, S. Peptide Secondary Structure Folding Reaction Coordinate: Correlation between UV Raman Amide III Frequency, Î̈ Ramachandran Angle, and Hydrogen Bonding J. Phys. Chem. B 2006, 110, 1928
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 1928
-
-
Mikhonin, A.1
Bykov, S.2
Myshakina, N.3
Asher, S.4
-
30
-
-
0036828955
-
Folding Plasticity
-
Muñoz, V. Folding Plasticity Nat. Struct. Biol. 2002, 9, 792-794
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 792-794
-
-
Muñoz, V.1
-
31
-
-
35848935407
-
A biological cosmos of parallel universes: Does protein structural plasticity facilitate evolution
-
Meier, S.; Özbek, S. A biological cosmos of parallel universes: does protein structural plasticity facilitate evolution BioEssays 2007, 29, 1095-1104
-
(2007)
BioEssays
, vol.29
, pp. 1095-1104
-
-
Meier, S.1
Özbek, S.2
-
32
-
-
31944434700
-
Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: Two ways to promote multifunctionality
-
Ikura, M.; Ames, J. B. Genetic polymorphism and protein conformational plasticity in the calmodulin superfamily: two ways to promote multifunctionality Proc. Natl. Acad. Sci. 2006, 103, 1159-1164
-
(2006)
Proc. Natl. Acad. Sci.
, vol.103
, pp. 1159-1164
-
-
Ikura, M.1
Ames, J.B.2
-
33
-
-
0034257929
-
2+-bound calmodulin: An analysis of disorder and implications for functionally relevant plasticity
-
2+-bound calmodulin: an analysis of disorder and implications for functionally relevant plasticity J. Mol. Biol. 2000, 301, 1237-1256
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 1237-1256
-
-
Wilson, M.A.1
Brunger, A.T.2
-
34
-
-
44349088854
-
The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis
-
Laine, E.; Yoneda, J. D.; Blondel, A.; Malliavin, T. E. The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis Proteins 2008, 71, 1813-1829
-
(2008)
Proteins
, vol.71
, pp. 1813-1829
-
-
Laine, E.1
Yoneda, J.D.2
Blondel, A.3
Malliavin, T.E.4
-
36
-
-
34547652634
-
Structure and plasticity of the human immunodeficiency virus gp41 fusion domain in lipd micelles and bilayers
-
Li, Y.; Tamm, L. K. Structure and plasticity of the human immunodeficiency virus gp41 fusion domain in lipd micelles and bilayers Biophys. J. 2007, 93, 876-885
-
(2007)
Biophys. J.
, vol.93
, pp. 876-885
-
-
Li, Y.1
Tamm, L.K.2
-
37
-
-
11244328066
-
Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers
-
Vaccaro, L.; Cross, K. J.; Kleinjung, J.; Straus, S. K.; Thomas, D. J.; Wharton, S. A.; Skehl, J. J.; Fraternali, F. Plasticity of influenza haemagglutinin fusion peptides and their interaction with lipid bilayers Biophys. J. 2005, 88, 25-36
-
(2005)
Biophys. J.
, vol.88
, pp. 25-36
-
-
Vaccaro, L.1
Cross, K.J.2
Kleinjung, J.3
Straus, S.K.4
Thomas, D.J.5
Wharton, S.A.6
Skehl, J.J.7
Fraternali, F.8
-
38
-
-
0038054912
-
Force Field Influence on the Observation of φ-Helical Protein Structures in Molecular Dynamics Simulations
-
Feig, M.; Mackerell, A., Jr.; Brooks, C. L., III Force Field Influence on the Observation of φ-Helical Protein Structures in Molecular Dynamics Simulations J. Phys. Chem. B 2003, 107, 2831-2836
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 2831-2836
-
-
Feig, M.1
Mackerell Jr., A.2
Brooks III, C.L.3
-
39
-
-
0024970049
-
Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein
-
Tatham, A. S.; Drake, A. F.; Shewry, P. R. Conformational studies of a synthetic peptide corresponding to the repeat motif of C hordein Biophys. J. 1989, 259, 471-476
-
(1989)
Biophys. J.
, vol.259
, pp. 471-476
-
-
Tatham, A.S.1
Drake, A.F.2
Shewry, P.R.3
-
40
-
-
1642546383
-
Computation and analysis of protein circular dichroism spectra
-
Academic Press, San Diego,; Vol. 383, pp-351
-
Sreerama, N.; Woody, R. W. Computation and analysis of protein circular dichroism spectra. Numerical Methods, Part D, Methods in Enzymology; Academic Press, San Diego, 2004; Vol. 383, pp 383-351.
-
(2004)
Numerical Methods, Part D, Methods in Enzymology
, pp. 383
-
-
Sreerama, N.1
Woody, R.W.2
-
41
-
-
84906397330
-
Computation and analysis of protein circular dichroism spectra
-
Sreerama, N.; Woody, R. W. Computation and analysis of protein circular dichroism spectra Protein Sci. 1996, 5, 1108-1117
-
(1996)
Protein Sci.
, vol.5
, pp. 1108-1117
-
-
Sreerama, N.1
Woody, R.W.2
-
46
-
-
0032514771
-
Trifluoroethanol Promotes Helix Formation by Destabilizing Backbone Exposure: Desolvation Rather than Native Hydrogen Bonding Defines the Kinetic Pathway of Dimeric Coiled Coil Folding
-
Kentsis, A.; Sosnick, T. Trifluoroethanol Promotes Helix Formation by Destabilizing Backbone Exposure: Desolvation Rather than Native Hydrogen Bonding Defines the Kinetic Pathway of Dimeric Coiled Coil Folding Biochemistry 1998, 37, 14613-14622
-
(1998)
Biochemistry
, vol.37
, pp. 14613-14622
-
-
Kentsis, A.1
Sosnick, T.2
-
47
-
-
0032444658
-
Trifluorethanol and colleagues: Cosolvents come of age. Recent studies with peptides and proteins
-
Buck, M. Trifluorethanol and colleagues: cosolvents come of age. Recent studies with peptides and proteins Q. Rev. Biophys. 1998, 31, 297-355
-
(1998)
Q. Rev. Biophys.
, vol.31
, pp. 297-355
-
-
Buck, M.1
|