CO escape from myoglobin with metadynamics simulations.
The relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure-function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data.
Ceccarelli
Matteo
M
CNR-INFM Slacs and Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy. matteo.ceccarelli@dsf.unica.it
Anedda
Roberto
R
Casu
Mariano
M
Ruggerone
Paolo
P
D000465:Algorithms; D000818:Animals; D002248:Carbon Monoxide / Q000737:chemistry* / Q000378:metabolism; D003198:Computer Simulation; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D055672:Static Electricity; D014907:Whales
D009211:Myoglobin; C055547:deoxymyoglobin; D002248:Carbon Monoxide