title: Elasticity of peptide omega bonds.
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.
authors.affiliation: Department of Chemistry & Biochemistry, University of California-San Diego, La Jolla, CA 92093-0365, USA.
authors.forename: Tongye
authors.initials: T
authors.lastname: Shen
authors.forename: Donald
authors.initials: D
authors.lastname: Hamelberg
authors.forename: J Andrew
authors.initials: JA
authors.lastname: McCammon
mesh_terms: D001665:Binding Sites; D004151:Dipeptides / Q000737:chemistry*; D004548:Elasticity; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D013314:Stress, Mechanical
chemical_list: D004151:Dipeptides