Oxygen diffusion in minihemoglobin from <Emphasis Type="Italic">Cerebratulus lacteus</Emphasis>: a locally enhanced sampling study |
| |
Authors: | Slawomir Orlowski Wieslaw Nowak |
| |
Institution: | (1) Theoretical Molecular Biophysics Group, Institute of Physics, N. Copernicus University, 87-100 Torun, Poland |
| |
Abstract: | Heme proteins serve as a source of oxygen in nervous tissue during anoxia. The functional routes of a dioxygen (O
2) diffusion in a novel structure of a minihemoglobin (CerHb) molecule present in worm Cerebratulus lacteus are not known. In this paper, the results of 1ns molecular dynamics simulations of this process are presented. The locally
enhanced sampling method (LES) and CHARMM force field were used for simulations of CerHb with 1–15 copies of O
2. It was found, that several alternative routes are possible. The dominant path consists of two steps. Firstly, ligands move
from the heme pocket to a different cavity through the barrier defined by the residues Phe10 and Tyr48. Secondly, ligands
leave the protein passing through the more complex barrier situated between the E/F loop and the H helix. We note that the
number of paths observed depends on a number of LES copies of (O
2). |
| |
Keywords: | Minihemoglobin Locally enhanced sampling Molecular dynamics |
本文献已被 SpringerLink 等数据库收录! |