Journal
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Volume 68, Issue 2, Pages 480-487Publisher
WILEY
DOI: 10.1002/prot.21454
Keywords
molecular dynamics; QM/MM; ligand binding; heme protein; hydrogen bond; structure
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The binding of diatomic ligands, such as O-2, NO, and CO, to heme proteins is a process intimately related with their function. In this work, we analyzed by means of a combination of classical Molecular Dynamics (MD) and Hybrid Quantum-Classical (QM/MM) techniques the existence of multiple conformations in the distal. site of heme proteins and their influence on oxygen affinity regulation. We considered two representative examples: soybean leghemoglobin (Lba) and Paramecium caudatum truncated hemoglobin (PcHb). The results presented in this work provide a molecular interpretation for the kinetic, structural, and mutational data that cannot be obtained by assuming a single distal. conformation.
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