Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca2+Positions Determined by a Genetic Algorithm†

Leping Li; Thomas A. Darden; Steven J. Freedman; Barbara C. Furie; Bruce Furie; James D. Baleja; Howard Smith; Richard G. Hiskey; Lee G. Pedersen

doi:10.1021/bi962250r

Refinement of the NMR Solution Structure of the γ-Carboxyglutamic Acid Domain of Coagulation Factor IX Using Molecular Dynamics Simulation with Initial Ca2+Positions Determined by a Genetic Algorithm†

Biochemistry ◽

10.1021/bi962250r ◽

1997 ◽

Vol 36 (8) ◽

pp. 2132-2138 ◽

Cited By ~ 38

Author(s):

Leping Li ◽

Thomas A. Darden ◽

Steven J. Freedman ◽

Barbara C. Furie ◽

Bruce Furie ◽

...

Keyword(s):

Genetic Algorithm ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Coagulation Factor ◽

Factor Ix ◽

Dynamics Simulation ◽

Coagulation Factor Ix ◽

Carboxyglutamic Acid ◽

Acid Domain

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In Silico Mutation and Binding Studies of Human FVIIa γ-Carboxyglutamic Acid-Domain to Endothelial Protein C Receptor: A Molecular Dynamics Simulation Approach

ACS Omega ◽

10.1021/acsomega.8b02647 ◽

2019 ◽

Vol 4 (1) ◽

pp. 496-508

Author(s):

Suparna Banerjee ◽

Ramesh Prasad ◽

Prosenjit Sen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

In Silico ◽

Protein C ◽

Dynamics Simulation ◽

Simulation Approach ◽

Endothelial Protein C Receptor ◽

Binding Studies ◽

Carboxyglutamic Acid ◽

Acid Domain

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In vitro gamma-carboxylation of a 59-residue recombinant peptide including the propeptide and the gamma-carboxyglutamic acid domain of coagulation factor IX. Effect of mutations near the propeptide cleavage site.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(19)38275-4 ◽

1990 ◽

Vol 265 (22) ◽

pp. 13124-13129

Author(s):

S M Wu ◽

B A Soute ◽

C Vermeer ◽

D W Stafford

Keyword(s):

Cleavage Site ◽

Coagulation Factor ◽

Factor Ix ◽

Recombinant Peptide ◽

Coagulation Factor Ix ◽

Carboxyglutamic Acid ◽

Acid Domain

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Effects of Urea, Tetramethyl Urea, and TrimethylamineN-Oxide on Aqueous Solution Structure and Solvation of Protein Backbones: A Molecular Dynamics Simulation Study

The Journal of Physical Chemistry B ◽

10.1021/jp9084926 ◽

2010 ◽

Vol 114 (1) ◽

pp. 557-568 ◽

Cited By ~ 128

Author(s):

Haiyan Wei ◽

Yubo Fan ◽

Yi Qin Gao

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Solution Structure ◽

Dynamics Simulation ◽

Protein Backbones

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Solution Structure of a Type 1 H Antigen Trisaccharide at a Micellar Surface: NMR Relaxation and Molecular Dynamics Simulation Studies

The Journal of Physical Chemistry B ◽

10.1021/jp0136462 ◽

2002 ◽

Vol 106 (20) ◽

pp. 5275-5280 ◽

Cited By ~ 9

Author(s):

Kristina Lycknert ◽

Torgny Rundlöf ◽

Göran Widmalm

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Nmr Relaxation ◽

Dynamics Simulation ◽

Simulation Studies

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Molecular Dynamics Simulation of the Solution Structure near the Solid−Liquid Interface between the NaCl(100) and NaCl−KCl−H2O Solutions

Crystal Growth & Design ◽

10.1021/cg025513r ◽

2003 ◽

Vol 3 (2) ◽

pp. 209-213 ◽

Cited By ~ 8

Author(s):

Hirohisa Uchida ◽

Hiroshi Takiyama ◽

Masakuni Matsuoka

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Liquid Interface ◽

Dynamics Simulation ◽

Solid Liquid Interface ◽

Solid Liquid

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The entire γ-carboxyglutamic acid- and helical stack-domains of human coagulation factor IX are required for optimal binding to its endothelial cell receptor

International journal of peptide & protein research ◽

10.1111/j.1399-3011.1996.tb00842.x ◽

2009 ◽

Vol 48 (3) ◽

pp. 281-285 ◽

Cited By ~ 4

Author(s):

MARY PROROK ◽

JIE-PING GENG ◽

SCOTT E. WARDER ◽

FRANCIS J. CASTELLINO

Keyword(s):

Endothelial Cell ◽

Coagulation Factor ◽

Cell Receptor ◽

Factor Ix ◽

Coagulation Factor Ix ◽

Carboxyglutamic Acid

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Designing Sequence-Specific Copolymer Compatibilizers Using a Molecular-Dynamics-Simulation-Based Genetic Algorithm

Macromolecules ◽

10.1021/acs.macromol.6b01747 ◽

2017 ◽

Vol 50 (3) ◽

pp. 1155-1166 ◽

Cited By ~ 21

Author(s):

Venkatesh Meenakshisundaram ◽

Jui-Hsiang Hung ◽

Tarak K. Patra ◽

David S. Simmons

Keyword(s):

Genetic Algorithm ◽

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Simulation Based

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Solution structure of α-conotoxin MI determined by -NMR spectroscopy and molecular dynamics simulation with the explicit solvent water

Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology ◽

10.1016/s0167-4838(97)00140-4 ◽

1997 ◽

Vol 1343 (2) ◽

pp. 327-334 ◽

Cited By ~ 18

Author(s):

Hiroaki Gouda ◽

Ken-ichi Yamazaki ◽

Jun Hasegawa ◽

Yuji Kobayashi ◽

Yuji Nishiuchi ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Nmr Spectroscopy ◽

Solution Structure ◽

Dynamics Simulation ◽

Solvent Water ◽

Explicit Solvent

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Solution structure of a conserved DNA sequence from the HIV-1 genome: Restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra

Biochemistry ◽

10.1021/bi00212a007 ◽

1993 ◽

Vol 32 (49) ◽

pp. 13419-13431 ◽

Cited By ~ 47

Author(s):

Anwer Mujeeb ◽

Sean M. Kerwin ◽

George L. Kenyon ◽

Thomas L. James

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Dna Sequence ◽

Torsion Angle ◽

Nmr Spectra ◽

Solution Structure ◽

Dynamics Simulation ◽

Two Dimensional ◽

Hiv 1 ◽

Restrained Molecular Dynamics

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Solution Structure of HIV-1 Protease Flaps Probed by Comparison of Molecular Dynamics Simulation Ensembles and EPR Experiments

Journal of the American Chemical Society ◽

10.1021/ja800893d ◽

2008 ◽

Vol 130 (23) ◽

pp. 7184-7185 ◽

Cited By ~ 48

Author(s):

Fangyu Ding ◽

Melinda Layten ◽

Carlos Simmerling

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Solution Structure ◽

Dynamics Simulation ◽

Epr Experiments ◽

Hiv 1

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