Paper Citing NAMD - Abstract
Krishnan, Marimuthu; Smith, Jeremy C.
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 131:10083-10091, JUL 29 2009
Changes in the free energy barrier (Delta E), entropy, and motional parameters associated with the rotation of methyl groups in a protein (calmodulin (CaM)) on binding a ligand (the calmodulin-binding domain of smooth-muscle myosin (smMLCKp)) are investigated using molecular dynamics simulation. In both the bound and uncomplexed forms of CaM, the methyl rotational free energy barriers follow skewed-Gaussian distributions that are not altered significantly upon ligand binding. However, site-specific perturbations are found. Around 11% of the methyl groups in CaM exhibit changes in Delta E greater than 0.7 kcal/mol on binding. The rotational entropies of the methyl groups exhibit a nonlinear dependence on Delta E The relations are examined between motional parameters (the methyl rotational NMR order parameter and the relaxation time) and Delta E Low-barrier methyl group rotational order parameters deviate from ideal tetrahedrality by up to similar to 20%. There is a correlation between rotational barrier changes and proximity to the protein-peptide binding interface. Methyl groups that exhibit large changes in Delta E are found to report on elements in the protein undergoing structural change on binding.
