29 research outputs found
THE KINETICS OF MOLECULAR OXYGEN MIGRATION IN THE ISOLATED - CHAINS OF HEMOGLOBIN AS REVEALED BY MULTIPLE EXTENDED MOLECULAR DYNAMICS SIMULATIONS
A Diffusion-Based Approach to Geminate Recombination of Heme Proteins with Small Ligands
A model of postphotodissociative monomolecular (geminate) recombination of
heme proteins with small ligands (NO, O2 or CO) is represented. The
non-exponential decay with time for the probability to find a heme in unbound
state is interpreted in terms of diffusion-like migration of ligabs
physics/0212040 and between protein cavities. The temporal behavior for the
probability is obtained from numerical simulation and specified by two
parameters: the time \tau_{reb} of heme-ligand rebinding for the ligand
localized inside the heme pocket and the time \tau_{esc} of ligand escape from
the pocket. The model is applied in the analysis of available experimental data
for geminate reoxygenation of human hemoglobin HbA. Our simulation is in good
agreement with the measurements. The analysis shows that the variation in pH of
the solution (6.0<pH<9.4) results in considerable changes for \tau_{reb} from
0.36 ns (at pH=8.5) up to 0.5 ns (pH=6.0) but effects slightly on the time
\tau_{esc} (\tau_{esc} ~ 0.88 ns).Comment: 8 pages with 4 figures, submitted to Chem. Phy
Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study
Hemoglobin exhibits allosteric structural changes upon ligand binding due to
the dynamic interactions between the ligand binding sites, the amino acids
residues and some other solutes present under physiological conditions. In the
present study, the dynamical and quaternary structural changes occurring in two
unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures
of adult human hemoglobin were investigated with molecular dynamics. It is
shown that, in the sub-microsecond time scale, there is no marked difference in
the global dynamics of the amino acids residues in both the oxy- and the deoxy-
forms of the individual structures. In addition, the R, R2 are relatively
stable and do not present quaternary conformational changes within the time
scale of our simulations while the T structure is dynamically more flexible and
exhibited the T\rightarrow R quaternary conformational transition, which is
propagated by the relative rotation of the residues at the {\alpha}1{\beta}2
and {\alpha}2{\beta}1 interface.Comment: Reprinted (adapted) with permission from J. Phys. Chem. B
DOI:10.1021/jp3022908. Copyright (2012) American Chemical Societ