Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics.
All-atom, explicit water molecular dynamics simulations of calcium-loaded calmodulin complexed with a peptide corresponding to the smooth muscle myosin light chain kinase target were carried out at 295 and 346 K. Amide and side chain methyl angular generalized order parameters were calculated and analyzed in the context of the protein's structure and dynamics. The agreement between amide order parameters measured by NMR and those from the simulations was found to be good, especially at the higher temperature, indicating both better convergence for the latter and excellent transferrability of the CHARMM parameters to the higher temperature. Subtle dynamical features such as helix fraying were reproduced. A large range of order parameters for the nine calmodulin methionines was observed in the NMR, and reproduced quite well in the simulations. The major determinant of the methionine order parameter was found to be the proximity to side chains of aromatic residues. An upper bound estimate of the difference in backbone entropy between loop and helical regions was extracted from the order parameters using a model of motion in an effective potential. Although loop regions are more flexible than helical regions, it was found that the entropy loss per residue upon folding was only approximately 20% less for loops than for helices. Pairwise correlated motions, which could significantly lower entropy estimates obtained from order parameter analysis alone, were found to be largely absent.
Prabhu
Ninad V
NV
Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania, 3700 Hamilton Walk, Philadelphia, Pennsylvania 19104-6059, USA.
Lee
Andrew L
AL
Wand
A Joshua
AJ
Sharp
Kim A
KA
D000577:Amides; D000595:Amino Acid Sequence; D000818:Animals; D002147:Calmodulin / Q000737:chemistry*; D002645:Chickens; D003198:Computer Simulation; D019277:Entropy; D046911:Macromolecular Substances; D008956:Models, Chemical; D009130:Muscle, Smooth / Q000201:enzymology; D009219:Myosin-Light-Chain Kinase / Q000737:chemistry; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature; D013816:Thermodynamics
D000577:Amides; D002147:Calmodulin; D046911:Macromolecular Substances; D010446:Peptide Fragments; D009219:Myosin-Light-Chain Kinase