Small ligand–globin interactions: Reviewing lessons derived from computer simulation

In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented...

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Published in:Biochimica et biophysica acta Vol. 1834; no. 9; pp. 1722 - 1738
Main Authors: Capece, Luciana, Boechi, Leonardo, Perissinotti, Laura L., Arroyo-Mañez, Pau, Bikiel, Damián E., Smulevich, Giulietta, Marti, Marcelo A., Estrin, Dario A.
Format: Journal Article
Language:English
Published: Netherlands Elsevier B.V 01.09.2013
Subjects:
amino acids
Animals
carbon monoxide
Computer Simulation
fluorides
Globin
Globins - chemistry
Globins - metabolism
heme
Heme protein
Humans
Ligands
Molecular dynamics
nitric oxide
nitrites
oxygen
proteins
QM/MM
Quantum Theory
Globin
Molecular dynamics
Heme protein
QM/MM
Computer simulation
ISSN:1570-9639, 0006-3002, 1878-1454
Online Access:Get full text
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Summary:In this work we review the application of classical and quantum-mechanical atomistic computer simulation tools to the investigation of small ligand interaction with globins. In the first part, studies of ligand migration, with its connection to kinetic association rate constants (kon), are presented. In the second part, we review studies for a variety of ligands such as O2, NO, CO, HS−, F−, and NO2− showing how the heme structure, proximal effects, and the interactions with the distal amino acids can modulate proteinligand binding. The review presents mainly results derived from our previous works on the subject, in the context of other theoretical and experimental studies performed by others. The variety and extent of the presented data yield a clear example of how computer simulation tools have, in the last decade, contributed to our deeper understanding of small ligand interactions with globins. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. •We review the use of simulation tools to study ligand interactions with globins.•We describe ligand migration, entry and exit to/from the active site.•We describe, for different ligands, how the metalligand bond can be modulated.
Bibliography:http://dx.doi.org/10.1016/j.bbapap.2013.02.038
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ISSN:1570-9639
0006-3002
1878-1454
DOI:10.1016/j.bbapap.2013.02.038