Abstract
Analytical studies have several advantages for an understanding of the
mechanisms of protein folding such as the interplay between geometrical
and energetic effects. In this paper, we introduce a Gaussian filament
with a C-alpha structure-based (G (o) over bar) potential as a new
theoretical scheme based on a Hamiltonian approach. This model takes
into account geometrical information in a realistic fashion without the
need of phenomenological descriptions. In order to make this model more
appropriate for comparison with protein folding simulations and
experiments, we introduce a many-body interaction into the potential
term to enhance cooperativity. We apply our new analytical model to a
beta-hairpin-type peptide and compare our results with a molecular
dynamics simulation of a structure-based model. (c) 2008 American
Institute of Physics.
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