ct5004059_si_001.pdf (1.11 MB)
Minimalist Model for the Dynamics of Helical Polypeptides: A Statistic-Based Parametrization
journal contribution
posted on 2014-09-09, 00:00 authored by Giulia
Lia Beatrice Spampinato, Giuseppe Maccari, Valentina TozziniLow-resolution models
are often used to address macroscopic time
and size scales in molecular dynamics simulations of biomolecular
systems. Coarse graining is often coupled to knowledge-based parametrization
to obtain empirical potentials able to reproduce the system thermodynamic
behavior. Here, a minimalist coarse grained (GC) model for the helical
structures of proteins is reported. A knowledge-based parametrization
strategy is coupled to the explicit inclusion of hydrogen-bonding-related
terms, resulting in an accurate reproduction of the structure and
dynamics of each single helical type, as well as the internal conformational
variables correlation. The proposed strategy of basing the force field
terms on real physicochemical interactions is transferable to different
secondary structures. Thus, this work, though conclusive for helices,
is to be considered the first of a series devoted to the application
of the knowledge-based, physicochemical model to extended secondary
structures and unstructured proteins.