Polypeptide Motions Are Dominated by Peptide Group Oscillations Resulting from Dihedral Angle Correlations between Nearest Neighbors
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- 作者：James E. Fitzgerald ; Abhishek K. Jha ; Tobin R. Sosnick ; Karl F. Freed
- 刊名：Biochemistry
- 出版年：2007
- 出版时间：January 23, 2007
- 年：2007
- 卷：46
- 期：3
- 页码：669 - 682
- 全文大小：541K
- 年卷期：v.46,no.3(January 23, 2007)
- ISSN：1520-4995
文摘
To identify basic local backbone motions in unfolded chains, simulations are performed for avariety of peptide systems using three popular force fields and for implicit and explicit solvent models.A dominant "crankshaft-like" motion is found that involves only a localized oscillation of the plane ofthe peptide group. This motion results in a strong anticorrelated motion of the 
fchars/Phi.gif" BORDER=0 > angle of the ith residue(fchars/Phi.gif" BORDER=0 >i) and the fchars/Psi.gif" BORDER=0 > angle of the residue i - 1 (fchars/Psi.gif" BORDER=0 >i-1) on the 0.1 ps time scale. Only a slight correlation isfound between the motions of the two backbone dihedral angles of the same residue. Aside from thespecial cases of glycine and proline, no correlations are found between backbone dihedral angles that areseparated by more than one torsion angle. These short time, correlated motions are found both in equilibriumfluctuations and during the transit process between Ramachandran basins, e.g., from the fchars/beta2.gif" BORDER=0 ALIGN="middle"> to the fchars/alpha.gif" BORDER=0> region.A residue's complete transit from one Ramachandran basin to another, however, occurs in a mannerindependent of its neighbors' conformational transitions. These properties appear to be intrinsic becausethey are robust across different force fields, solvent models, nonbonded interaction routines, and mostamino acids.
fchars/Phi.gif" BORDER=0 > angle of the ith residue(fchars/Phi.gif" BORDER=0 >i) and the fchars/Psi.gif" BORDER=0 > angle of the residue i - 1 (fchars/Psi.gif" BORDER=0 >i-1) on the 0.1 ps time scale. Only a slight correlation isfound between the motions of the two backbone dihedral angles of the same residue. Aside from thespecial cases of glycine and proline, no correlations are found between backbone dihedral angles that areseparated by more than one torsion angle. These short time, correlated motions are found both in equilibriumfluctuations and during the transit process between Ramachandran basins, e.g., from the fchars/beta2.gif" BORDER=0 ALIGN="middle"> to the fchars/alpha.gif" BORDER=0> region.A residue's complete transit from one Ramachandran basin to another, however, occurs in a mannerindependent of its neighbors' conformational transitions. These properties appear to be intrinsic becausethey are robust across different force fields, solvent models, nonbonded interaction routines, and mostamino acids.