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Modeling truncated hemoglobin vibrational dynamics
Author(s) -
Marsella Luca
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20707
Subject(s) - statistical physics , gaussian , molecular dynamics , covariance , degrees of freedom (physics and chemistry) , globin , biological system , gaussian network model , physics , relaxation (psychology) , matrix (chemical analysis) , chemical physics , chemistry , hemoglobin , mathematics , computational chemistry , thermodynamics , biology , statistics , biochemistry , chromatography , neuroscience
We present a study on the near equilibrium dynamics of two small proteins in the family of truncated hemoglobins, developed under the framework of a Gaussian network approach. Effective beta carbon atoms are taken into account besides C α s for all residues but glycines in the coarse‐graining procedure, without leading to an increase in the degrees of freedom (β Gaussian Model). Normalized covariance matrix and deformation along slowest modes with collective character are analyzed, pointing out anticorrelations between functionally relevant sites for the proteins under study. In particular, we underline the functional motions of an extended tunnel‐cavity system running inside the protein matrix, which provide a pathway for small ligands binding with the iron in the heme group. We give a rough estimate of the order of magnitude of the relaxation times of the slowest two overdamped modes and compare results with previous studies on globins. Proteins 2006. © 2005 Wiley‐Liss, Inc.