Quantifying the importance of protein conformation on ligand migration in myoglobin.

ABSTRACT: Myoglobin (Mb) is a model system for ligand binding and migration. The energy barriers (ΔG) for ligand migration in Mb have been studied in the past by experiment and theory and significant differences between different approaches were found. From experiment, it is known that Mb can assume a large number of conformational substates. In this work, these substates are investigated as a possible source of the differences in migration barriers. We show that the initial structure significantly affects the calculated ΔG for a particular transition and that fluctuations in barrier heights δΔG are of similar magnitude as the free energy barriers themselves. The sensitivity of ΔG to the initial structure is compared to other sources of errors. Different protein structures can affect the calculated

SUBMITTER: Plattner N 

PROVIDER: S-EPMC3260668 | biostudies-literature | 2012 Jan

REPOSITORIES: biostudies-literature