Protein dynamics and ligand migration interplay as studied by computer simulation.
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplating this crucial characteristic results fundamental to allow revealing several aspects of their function. In this work, we present results obtained using classical mechanical atomistic simulation tools applied to understand the connection between protein dynamics and ligand migration. Firstly, we will present a review of the different sampling schemes used in the last years to obtain both ligand migration pathways and the thermodynamic information associated with the process. Secondly, we will focus on representative examples in which the schemes previously presented are employed, concerning the following: i) ligand migration, tunnels, and cavities in myoglobin and neuroglobin; ii) ligand migration in truncated hemoglobin members; iii) NO escape and conformational changes in nitrophorins; iv) ligand selectivity in catalase and hydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
Arroyo-Mañez
Pau
P
Departamento de Química Inorgánica, Analítica y Química-Física (INQUIMAE-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina.
Bikiel
Damián E
DE
Boechi
Leonardo
L
Capece
Luciana
L
Di Lella
Santiago
S
Estrin
Darío A
DA
Martí
Marcelo A
MA
Moreno
Diego M
DM
Nadra
Alejandro D
AD
Petruk
Ariel A
AA
D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*
D008024:Ligands; D011506:Proteins