Molecular modeling of calmodulin:  a comparison with crystallographic data.
Two methods of side-chain placement on a modeled protein have been examined.  Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule.  A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules.  In the first model, side chains were initially constructed in an extended conformation.  In the second model, a conformational grid search technique was employed.  Calcium ions were treated explicitly during energy optimization using CHARMM.  The models are compared to a recently published refined crystal structure of calmodulin.  The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure.  The conformational differences are discussed.  Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.
McDonald
J J
JJ
Roswell Park Memorial Institute, Buffalo, New York 14263, USA.
Rein
R
R
D000595:Amino Acid Sequence; D002118:Calcium / Q000737:chemistry; D002147:Calmodulin / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry; D003198:Computer Simulation; D003461:Crystallography; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D012984:Software; D019209:Troponin C / Q000737:chemistry
D002147:Calmodulin; D019209:Troponin C; D002244:Carbon; D002118:Calcium