Proteinmorphosis: a mechanical model for protein conformational changes.

Meiyappan Solaiyappan, R. Raghavan, R. Viswanathan, Y. Yu, W. Lawton

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Proteinmorphosis is a physically-based interactive modeling system for simulating large or small conformational changes of proteins and protein complexes. It takes advantage of the cross-linked one-dimensional nature of protein chains. The user can, based on her chemical knowledge, pull pairs of points (lying either on a single protein or on different molecules) together by specifying geometric distance constraints. The resulting conformation(s) of the molecule(s) of interest is computed by an efficient finite element formalism taking into account elasticity of the protein backbone, van der Waals repulsions, hydrogen bonds, salt bridges and the imposed distance constraints. The conformational change is computed incrementally and the result can be visualized as an animation; complete interactivity is provided to position and view the proteins as desired by the user. Physical properties of regions on the protein can also be chosen interactively. The conformational change of calmodulin upon peptide binding is examined as a first experiment. It is found that the result is satisfactory in reproducing the conformational change that follows on peptide binding. We use Proteinmorphosis to study the cooperative hemoglobin oxygen binding mechanism in a second, more sophisticated, experiment. Different modeling strategies are designed to understand the allosteric (cooperative) binding process in this system and the results are found to be consistent with existing hypotheses.

Original languageEnglish (US)
Title of host publicationPacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
Pages341-353
Number of pages13
StatePublished - 1999
Externally publishedYes

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Proteins
Peptides
Elasticity
Calmodulin
Hydrogen
Hemoglobins
Salts
Oxygen

Cite this

Solaiyappan, M., Raghavan, R., Viswanathan, R., Yu, Y., & Lawton, W. (1999). Proteinmorphosis: a mechanical model for protein conformational changes. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (pp. 341-353)

Proteinmorphosis : a mechanical model for protein conformational changes. / Solaiyappan, Meiyappan; Raghavan, R.; Viswanathan, R.; Yu, Y.; Lawton, W.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1999. p. 341-353.

Research output: Chapter in Book/Report/Conference proceedingChapter

Solaiyappan, M, Raghavan, R, Viswanathan, R, Yu, Y & Lawton, W 1999, Proteinmorphosis: a mechanical model for protein conformational changes. in Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. pp. 341-353.
Solaiyappan M, Raghavan R, Viswanathan R, Yu Y, Lawton W. Proteinmorphosis: a mechanical model for protein conformational changes. In Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1999. p. 341-353
Solaiyappan, Meiyappan ; Raghavan, R. ; Viswanathan, R. ; Yu, Y. ; Lawton, W. / Proteinmorphosis : a mechanical model for protein conformational changes. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing. 1999. pp. 341-353
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