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NASA NTRS · 20040089067

Molecular modeling of calmodulin: a comparison with crystallographic data

McDonald, J. J.·Rein, R.
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Abstract

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.

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NASA Discipline ExobiologyNon-NASA CenterComputer SimulationCalmodulin/chemistryModels, MolecularSoftwareHydrogen BondingAmino Acid SequenceCarbon/chemistrySupport, Non-U.S. Gov'tSupport, U.S. Gov't, Non-P.H.SProtein ConformationTroponin C/chemistryCalcium/chemistryMolecular StructureCrystallographyComparative Study

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McDonald, J. J., Rein, R.. 1989-01-01. Molecular modeling of calmodulin: a comparison with crystallographic data. https://ntrs.nasa.gov/citations/20040089067

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