Mapping All-Atom Models onto One-Bead Coarse-Grained Models:  General Properties and Applications to a Minimal Polypeptide Model

Valentina Tozzini*
NEST Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
Walter Rocchia
Scuola Normale Superiore, Piazza dei Cavalieri, 7 I-56126 Pisa, Italy
J. Andrew McCammon
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093
J. Chem. Theory Comput., 2006, 2 (3), pp 667–673
DOI: 10.1021/ct050294k
Publication Date (Web): April 18, 2006
Copyright © 2006 American Chemical Society
*

 Corresponding author fax:  +39-050-509417; e-mail:  tozzini@ nest.sns.it.

Abstract

In the one- and two-bead coarse-grained (CG) models for proteins, the two conformational dihedrals phi and ψ that describe the backbone geometry are no longer present as explicit internal coordinates; thus, the information contained in the Ramachandran plot cannot be used directly. We derive an analytical mapping between these dihedrals and the internal variable describing the backbone conformation in the one- (two-) bead CG models, namely, the pseudo-bond angle and pseudo-dihedral between subsequent Cα's. This is used to derive a new density plot that contains the same information as the Ramachandran plot and can be used with the one- (two-) bead CG models. The use of this mapping is then illustrated with a new one-bead polypeptide model that accounts for transitions between α helices and β sheets.

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History

  • Published In Issue May 09, 2006
  • Received November 29, 2005

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