INSTITUTO DE QUIMICA, FISICA DE LOS MATERIALES, MEDIOAMBIENTE Y ENERGIA
Unidad Ejecutora - UE
Protein dynamics and ligand migration interplay as studied by computer simulation.
PAU ARROYO MAÑEZ; DAMIAN E BIKIEL; LEONARDO BOECHI; LUCIANA CAPECE; SANTIAGO DI LELLA; DARIO A ESTRIN; MARCELO A. MARTI; DIEGO M MORENO; ALEJANDRO D NADRA; ARIEL A PETRUK
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
ELSEVIER SCIENCE BV
Since proteins are dynamic systems in living organisms, the employment of methodologies contemplatingthis crucial characteristic results fundamental to allow revealing several aspects of their function. In thiswork, we present results obtained using classical mechanical atomistic simulation tools applied tounderstand the connection between protein dynamics and ligand migration. Firstly, we will present a reviewof the different sampling schemes used in the last years to obtain both ligand migration pathways and thethermodynamic information associated with the process. Secondly, we will focus on representative examplesin 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 andhydrogenase; and v) larger ligand migration: the P450 and haloalkane dehalogenase cases.