Secondary-structure design of proteins by a backbone torsion energy

Sakae Yoshitake

Okamoto Yuko

Journal of the Physical Society of Japan

We propose a new backbone-torsion-energy term in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, 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/decrease the α-helix-forming tendencies by lowering/raising the torsion-energy surface in the α-helix region and likewise increase/decrease the β-sheet-forming tendencies by lowering/raising the surface in the β-sheet region in the Ramachandran space. We applied our approach to AMBER parm94 and AMBER parm96 force fields 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.

protein folding

force field

torsion energy

simulated annealing

biomolecular simulation

Physics [ 420 ]

eng

the Physical Society of Japan

Copyright (c) 2006 The Physical Society of Japan

[NCID] AA00704814

[ISSN] 0031-9015

[DOI] 10.1143/JPSJ.75.054802

[DOI] http://dx.doi.org/10.1143/JPSJ.75.054802 isVersionOf