Elasticity of Peptide Omega Bonds.
From: Department of Chemistry & Biochemistry, University of California-San Diego, La Jolla, CA 92093-0365, USA.
Physical review. E, Statistical, nonlinear, and soft matter physics
- Publish Date: Apr 2006
- ISSN: 1539-3755
- Volume: 73
- Issue: 4 Pt 1
- Pages: 041908
- Medium: Print
- Language: English
- Citation (JAMA): Shen Tongye, Hamelberg Donald, McCammon J Andrew, et al. Elasticity of Peptide Omega Bonds.. Apr 2006;73:041908
Abstract
We calculated the changes of the free energy profile of the peptidyl-prolyl torsional angle of the dipeptide valine-proline under pulling forces by simulations. Using a dynamic model built on the equilibrium properties of this system and previously studied dynamic properties of cis-trans isomerization of other dipeptides, we calculated the dynamic viscoelasticity of this degree of freedom. The results show significant differences between how thermal and mechanical forces alter the equilibrium and the dynamics of the isomerization transition. The former does not change the barrier heights but changes the prefactor of the kinetics owing to temperature effects, while the latter changes minima and thus the population. The force that is required to “excite” this degree of freedom is small. Compared to other systems, we found that this degree of freedom becomes already quite rigid at several hertz, which is a much lower value due to the high barrier of the cis-trans isomerization. We also found that the tensile elastic modulus of densely packed omega bonds is at the order of GPa, which is comparable to that of polymer materials. These results give mechanical properties of polyproline elasticity of a local nature and provide guidance for future experimental designs.
Mesh Headings (Keywords): Binding Sites, Dipeptides, Elasticity, Models, Chemical, Models, Molecular, Protein Binding, Protein Conformation, Stress, Mechanical
Check for Full Text / PubMed Unique Identifier (PMID): 16711837
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