Modeling truncated hemoglobin vibrational dynamics
| dc.creator | Marsella, Luca | |
| dc.date | 2004-12-23 | |
| dc.date | 2005-04-25 | |
| dc.date.accessioned | 2026-07-07T03:02:55Z | |
| dc.date.available | 2026-07-07T03:02:55Z | |
| dc.description | 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-alphas for all residues but glycines in the coarse-graining procedure, without leading to an increase in the degrees of freedom (betaGaussian Model). Normalized covariance matrix and deformation along slowest modes with collective character are analyzed, pointing out anti-correlations 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. | |
| dc.description | 23 pages, 7 figures | |
| dc.identifier | https://arxiv.org/abs/cond-mat/0412661 | |
| dc.identifier | http://arxiv.org/abs/cond-mat/0412661 | |
| dc.identifier.uri | http://salesiana.dossiersoluciones.com/handle/123456789/25569 | |
| dc.subject | Soft Condensed Matter | |
| dc.subject | Biomolecules | |
| dc.title | Modeling truncated hemoglobin vibrational dynamics | |
| dc.type | text |