title: Modeling truncated hemoglobin vibrational dynamics.
abstract: 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 Calphas for all residues but glycines in the coarse-graining procedure, without leading to an increase in the degrees of freedom (beta 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.
authors.affiliation: International School for Advanced Studies (S.I.S.S.A.), Trieste, Italy. marsella@sissa.it
authors.forename: Luca
authors.initials: L
authors.lastname: Marsella
mesh_terms: D000818:Animals; D001665:Binding Sites; D005914:Globins / Q000737:chemistry / Q000378:metabolism; D005998:Glycine; D006418:Heme / Q000378:metabolism; D006454:Hemoglobins / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D048488:Paramecium caudatum; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D015800:Protozoan Proteins / Q000737:chemistry* / Q000378:metabolism*; D054793:Truncated Hemoglobins; D014732:Vibration
chemical_list: D006454:Hemoglobins; D010446:Peptide Fragments; D015800:Protozoan Proteins; D054793:Truncated Hemoglobins; D006418:Heme; D005914:Globins; D005998:Glycine