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  4. A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
 
research article

A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements

Alemani, Davide  
•
Collu, Francesca
•
Cascella, Michele  
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2010
Journal of Chemical Theory and Computation

We introduce a nonradial potential term for coarse-grained (CG) molecular simulations of proteins. This term mimics the backbone dipole−dipole interactions and accounts for the needed directionality to form stable folded secondary structure elements. We show that α-helical and β-sheet peptide chains are correctly described in dynamics without the need of introducing any a priori bias potentials or ad hoc parametrizations, which limit broader applicability of CG simulations for proteins. Moreover, our model is able to catch the formation of supersecondary structural motifs, like transitions from long single α-helices to helix−coil−helix or β-hairpin assemblies. This novel scheme requires the structural information of Cα beads only; it does not introduce any additional degrees of freedom to the system and has a general formulation, which allows it to be used in synergy with various CG protocols, leading to an improved description of the structural and dynamic properties of protein assemblies and networks.

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Type
research article
DOI
10.1021/ct900457z
Web of Science ID

WOS:000274757000031

Author(s)
Alemani, Davide  
Collu, Francesca
Cascella, Michele  
Dal Peraro, Matteo  
Date Issued

2010

Published in
Journal of Chemical Theory and Computation
Volume

6

Issue

1

Start page

315

End page

324

Subjects

coarse-grain

•

molecular

•

dynamics

•

dipole

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
UPDALPE  
Available on Infoscience
January 27, 2010
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/46182
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