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Molecular modeling of calmodulin: a comparison with crystallographic dataTwo 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.
Document ID
20040089067
Acquisition Source
Legacy CDMS
Document Type
Reprint (Version printed in journal)
Authors
McDonald, J. J.
(Roswell Park Memorial Institute Buffalo, New York 14263, United States)
Rein, R.
Date Acquired
August 21, 2013
Publication Date
January 1, 1989
Publication Information
Publication: International journal of quantum chemistry. Quantum biology symposium : proceedings of the International Symposium on Quantum Biology and Quantum Pharmacology. International Symposium on Quantum Biology and Quantum Pharmacology
Volume: 16
ISSN: 0360-8832
Subject Category
Exobiology
Funding Number(s)
CONTRACT_GRANT: NSG-7305
Distribution Limits
Public
Copyright
Other
Keywords
NASA Discipline Exobiology
Non-NASA Center

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