Generating Conformations for Two Zinc-Binding Sites of HIV-1 Nucleocapsid Protein from Random Conformations by a Hierarchical Procedure and Polarizable Force Field

2003 ◽  
Vol 107 (20) ◽  
pp. 4862-4870 ◽  
Author(s):  
Nohad Gresh ◽  
Philippe Derreumaux
Keyword(s):  
Force Field ◽  
Binding Sites ◽  
Nucleocapsid Protein ◽  
Zinc Binding ◽  
Polarizable Force Field ◽  
Hiv 1

scholarly journals Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein NCp7 Using Extensive Polarizable Force Field Free-Energy Simulations

2020 ◽  
Vol 16 (4) ◽  
pp. 2013-2020 ◽  
Author(s):  
Léa El Khoury ◽  
Frédéric Célerse ◽  
Louis Lagardère ◽  
Luc-Henri Jolly ◽  
Etienne Derat ◽  
...  
Keyword(s):  
Free Energy ◽  
Force Field ◽  
Nucleocapsid Protein ◽  
Polarizable Force Field ◽  
Nmr Structures ◽  
Energy Simulations ◽  
Hiv 1

scholarly journals Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations

2020 ◽  
Author(s):  
Léa El Khoury ◽  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Luc-Henri Jolly ◽  
Étienne Derat ◽  
...  
Keyword(s):  
Free Energy ◽  
Nucleocapsid Protein ◽  
Extended Form ◽  
Polarizable Force Field ◽  
Relative Free Energy ◽  
Nmr Structures ◽  
Reference Protein ◽  
Energy Simulations ◽  
Hiv 1 ◽  
Most Probable Structure

Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free-energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.<br>

scholarly journals Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations

2020 ◽  
Author(s):  
Léa El Khoury ◽  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Luc-Henri Jolly ◽  
Étienne Derat ◽  
...  
Keyword(s):  
Free Energy ◽  
Nucleocapsid Protein ◽  
Extended Form ◽  
Polarizable Force Field ◽  
Relative Free Energy ◽  
Nmr Structures ◽  
Reference Protein ◽  
Energy Simulations ◽  
Hiv 1 ◽  
Most Probable Structure

Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free-energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.<br>

Site-Specific Characterization of HIV-1 Nucleocapsid Protein Binding to Oligonucleotides with Two Binding Sites†

Biochemistry ◽  
2009 ◽  
Vol 48 (11) ◽  
pp. 2422-2430 ◽  
Author(s):  
Sergiy V. Avilov ◽  
Julien Godet ◽  
Etienne Piémont ◽  
Yves Mély
Keyword(s):  
Protein Binding ◽  
Binding Sites ◽  
Nucleocapsid Protein ◽  
Site Specific ◽  
Hiv 1

Zinc Binding to the HIV-1 Nucleocapsid Protein:  A Thermodynamic Investigation by Fluorescence Spectroscopy†

Biochemistry ◽  
1996 ◽  
Vol 35 (16) ◽  
pp. 5175-5182 ◽  
Author(s):  
Y. Mély ◽  
H. De Rocquigny ◽  
N. Morellet ◽  
B. P. Roques ◽  
D. Gérard
Keyword(s):  
Fluorescence Spectroscopy ◽  
Nucleocapsid Protein ◽  
Protein A ◽  
Zinc Binding ◽  
Thermodynamic Investigation ◽  
Hiv 1

scholarly journals Reconciling NMR Structures of the HIV-1 Nucleocapsid Protein (NCp7) using Extensive Polarizable Force Field Free-Energy Simulations

2020 ◽  
Author(s):  
Léa El Khoury ◽  
Frédéric Célerse ◽  
Louis Lagardere ◽  
Luc-Henri Jolly ◽  
Étienne Derat ◽  
...  
Keyword(s):  
Free Energy ◽  
Nucleocapsid Protein ◽  
Extended Form ◽  
Polarizable Force Field ◽  
Relative Free Energy ◽  
Nmr Structures ◽  
Reference Protein ◽  
Energy Simulations ◽  
Hiv 1 ◽  
Most Probable Structure

Using polarizable (AMOEBA) and non-polarizable (CHARMM) force fields, we compare the relative free-energy stability of two extreme conformations of the HIV-1 NCp7 nucleocapsid that had been previously experimentally advocated to prevail in solution. Using accelerated sampling techniques, we show that they differ in stability by no more than 0.75-1.9 kcal/mol depending on the reference protein sequence. While the extended form appears to be the most probable structure, both forms should thus coexist in water explaining the differing NMR findings.<br>

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model

scholarly journals HIV-1 inactivation by 4-vinylpyridine is enhanced by dissociating Zn2+ from nucleocapsid protein

Virology ◽  
2008 ◽  
Vol 375 (1) ◽  
pp. 148-158 ◽  
Author(s):  
David R. Morcock ◽  
James A. Thomas ◽  
Raymond C. Sowder ◽  
Louis E. Henderson ◽  
Bruce J. Crise ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Hiv 1
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