A Novel Coarse-Grained Description of Protein Structure and Folding by UNRES Force Field and Discrete Nonlinear Schrödinger Equation
Pp. 257-289 (33)
Adam Liwo, Antti Niemi, Xubiao Peng and Adam K. Sieradzan
The UNited RESidue (UNRES) force field has been developed for over two
decades. This force field has been derived carefully as a potential of mean force of the
system studied, which is further expressed in terms of the Kubo cluster-cumulant functions.
New terms in the energy function to improve loop structures have been introduced recently.
On the other hand, new concept was developed, in which wave-analysis physics is applied
to the protein folding problem. At present, the energy function is based on the Landau
Hamiltonian, the minima of which are stable conformations of protein fragments; these
minima are obtained as kink solutions of the Discrete Nonlinear Schrödinger Equation. The
parameters of the Hamiltonian have been obtained by statistical analysis of known protein
structures. The unique feature of this approach is that the curvature description is sufficient
for protein folding without any long-distance interactions other than the excluded-volume
interactions. The combination of those two methodologies - molecular dynamics with the
use of physics-base UNRES force field and the kink approach have been applied to study
the flexibility and movement of the kinks as well as their formation and disappearance in
the folding process.
UNRES, force-field, Davydov soliton, dark soliton, molecular
dynamics, energy landscape, Landau Hamiltonian, gauge inverse, physics-based,
cumulant-cluster expansion, mean-force potentials, loop structures, wave-analysis
physics, protein flexibility, kink formation, kink disappearance, kink movement,
folding pathways, local interactions.
Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland.