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Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term.
- Source :
-
Molecular Simulation . Feb2010, Vol. 36 Issue 2, p138-158. 21p. 6 Diagrams, 10 Charts, 3 Graphs. - Publication Year :
- 2010
-
Abstract
- We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase or decrease the α-helix-forming-tendencies by lowering or raising the torsion-energy surface in the α-helix region and likewise increase or decrease the β-sheet-forming tendencies by lowering or raising the surface in the β-sheet region in the Ramachandran space. We applied this torsion-energy modification method to six force fields, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM27, OPLS-AA and OPLS-AA/L, and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides. [ABSTRACT FROM AUTHOR]
- Subjects :
- *TORSION
*PROTEINS
*FORCE & energy
*PEPTIDES
*ORGANIC compounds
Subjects
Details
- Language :
- English
- ISSN :
- 08927022
- Volume :
- 36
- Issue :
- 2
- Database :
- Academic Search Index
- Journal :
- Molecular Simulation
- Publication Type :
- Academic Journal
- Accession number :
- 48041821
- Full Text :
- https://doi.org/10.1080/08927020903124601