A Nonradial Coarse-Grained Potential for Proteins Produces Naturally Stable Secondary Structure Elements
D Alemani and F Collu and M Cascella and M Dal Peraro, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 6, 315-324 (2010).
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 a-helical and beta-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 a-helices to helix-coil-helix or beta-hairpin assemblies. This novel scheme requires the structural information of C-alpha 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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