Calculating the Na + translocating V-ATPase catalytic site affinity for substrate binding by homology modeled NtpA monomer using molecular dynamics/free energy calculation

Journal of Molecular Graphics and Modelling

Volumn 37, Issue , 2012, Pages 59-66

  Muhammed, Zahed ^a   Arai, Satoshi ^a   Saijo, Shinya ^a   Yamato, Ichiro ^a   Murata, Takeshi ^c   Suenaga, Atsushi ^b  

^a TOKYO UNIVERSITY OF SCIENCE   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c CHIBA UNIVERSITY   (Japan)

Author keywords

Free energy calculation; Homology modeling; Molecular dynamics; Nucleotide binding; V ATPase

Indexed keywords

ATOMIC LEVELS; BINDING FREE ENERGY; CATALYTIC DOMAINS; CATALYTIC SITES; ELECTROSTATIC CONTRIBUTIONS; ENERGY CALCULATION; ENERGY TRANSDUCTION MECHANISM; EXPERIMENTAL DATA; FREE-ENERGY CALCULATIONS; HOMOLOGY MODELING; INTEGRAL MEMBRANE; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NUCLEOTIDE BINDING; SUBSTRATE BINDING; THERMODYNAMIC INTEGRATION; TRIPHOSPHATE; V-ATPASE; VACUOLAR ATPASE;

BACILLI; FREE ENERGY; MODEL STRUCTURES; MOLECULAR DYNAMICS; MONOMERS; NUCLEOTIDES; SODIUM;

BINDING ENERGY;

ADENOSINE DERIVATIVE; BACTERIAL ENZYME; BACTERIAL PROTEIN; MONOMER; NTPA PROTEIN; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR; UNCLASSIFIED DRUG; VACULOAR ATPASE;

ARTICLE; BINDING AFFINITY; CHEMICAL STRUCTURE; ENERGY; ENERGY TRANSFER; ENZYME ACTIVE SITE; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN INTERACTION; PROTEIN SUBUNIT; SEQUENCE HOMOLOGY; SIMULATION; STATIC ELECTRICITY; THERMODYNAMICS;

ADENOSINE TRIPHOSPHATASES; ADENYLYL IMIDODIPHOSPHATE; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; CATION TRANSPORT PROTEINS; ENTEROCOCCUS; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, PROTEIN; THERMODYNAMICS;

ENTEROCOCCUS HIRAE;

EID: 84861210888     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2012.03.006     Document Type: Article

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