INQUIMAE   12526
INSTITUTO DE QUIMICA, FISICA DE LOS MATERIALES, MEDIOAMBIENTE Y ENERGIA
Unidad Ejecutora - UE
artículos
Título:
Protein dynamics and ligand migration interplay as studied by computer simulation
Autor/es:
PAU ARROYO-MAÑEZ; DAMIÁN E. BIKIEL; LEONARDO BOECHI; LUCIANA CAPECE; SANTIAGO DI LELLA; DARÍO A. ESTRIN; MARCELO A. MARTÍ; DIEGO M. MORENO; ALEJANDRO D. NADRA; ARIEL A. PETRUK
Revista:
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
Editorial:
ELSEVIER SCIENCE BV
Referencias:
Año: 2010
ISSN:
1570-9639
Resumen:
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.