ABSTRACT
The methods of molecular dynamics were used to study the influence of peptide matrix and conformational relaxation on the thermal effects of redox reactions of two proteins containing Fe4S4 clusters with sharply differing redox potential values. It was shown that the depth of immersion of the Fe4S4 cluster in the protein globule affects the parameters of chemical equilibrium. It was found that the peptide matrix makes a determining contribution to the compensation of the Coulomb repulsion energy in Fe4S4 clusters.
Subject(s)
Bacterial Proteins/chemistry , Ferredoxins/chemistry , Iron-Sulfur Proteins/chemistry , Iron/chemistry , Peptides/chemistry , Photosynthetic Reaction Center Complex Proteins , Sulfur/chemistry , Betaproteobacteria/chemistry , Models, Chemical , Models, Molecular , Oxidation-Reduction , Thermodynamics , Thermotoga maritima/chemistryABSTRACT
The method of molecular dynamics investigations of the particularities of macromolecule physical-chemical properties is discussed. The results, obtained from the calculations of modified dipeptides in different regimes (different temperatures, length of trajectories and ways of thermostat simulation) are compared. The optimal conditions for this peptides calculations are determined: collisional dynamics regime, trajectories not less than 5000 ps, temperature about 1000 K. In this case the figurative point is able to scan the molecule configuration space and the statistically reliable results could be obtained.
