Paper Info
Title
Calculation Of The Relative Free Energy Of Oxidation Of Azurin At Ph 5 And Ph 9
Abstract
Free energy calculations are described for the small copper-containing redox protein Azurin from Pseudomonas aeruginosa. A thermodynamic cycle connecting the reduced and oxidized states at pH 5 and pH 9 is considered, allowing for an assessment of convergence in terms of hysteresis and cycle closure. Previously published thermodynamic integration (TI) data is compared to Hamiltonian replica exchange TI (RE-TI) simulations using different simulation setups. The effects of varying simulation length, initial structure, position restraints on particular atoms, and the strength of temperature coupling are studied. Although the overall simulation times are too short to observe an experimentally described peptide plane rotation, it is found that RE-TI simulations do stimulate the distribution of conformational changes over the relevant values of the TI coupling parameter ?. This results in significantly improved values for hysteresis and cycle closure when compared to regular TI. (c) 2012 Wiley Periodicals, Inc.
Year
DOI
Venue
2012
10.1002/jcc.22972
JOURNAL OF COMPUTATIONAL CHEMISTRY
Keywords
Field
DocType
protein, molecular dynamics simulation, Hamiltonian replica exchange, Azurin, free energy calculation
Azurin,Hamiltonian (quantum mechanics),Computational chemistry,Hysteresis,Chemistry,Atom,Molecular dynamics,Coupling parameter,Thermodynamic cycle,Thermodynamic integration
Journal
Volume
Issue
ISSN
33
17
0192-8651
Citations 
PageRank 
References 
0
0.34
2
Authors
3
Name
Order
Citations
PageRank
Denise Steiner130.78
Chris Oostenbrink229738.41
Wilfred F. Van Gunsteren356484.80