1,412 research outputs found
Identification of Characteristic Protein Folding Channels in a Coarse-Grained Hydrophobic-Polar Peptide Model
Folding channels and free-energy landscapes of hydrophobic-polar
heteropolymers are discussed on the basis of a minimalistic off-lattice
coarse-grained model. We investigate how rearrangements of hydrophobic and
polar monomers in a heteropolymer sequence lead to completely different folding
behaviors. Studying three exemplified sequences with the same content of
hydrophobic and polar residues, we can reproduce within this simple model
two-state folding, folding through intermediates, as well as metastability.Comment: 26 pages, 6 figure
Advanced multicanonical Monte Carlo methods for efficient simulations of nucleation processes of polymers
The investigation of freezing transitions of single polymers is
computationally demanding, since surface effects dominate the nucleation
process. In recent studies we have systematically shown that the freezing
properties of flexible, elastic polymers depend on the precise chain length.
Performing multicanonical Monte Carlo simulations, we faced several
computational challenges in connection with liquid-solid and solid-solid
transitions. For this reason, we developed novel methods and update strategies
to overcome the arising problems. We introduce novel Monte Carlo moves and two
extensions to the multicanonical method.Comment: 10 pages, 11 figure
Different Kinds of Protein Folding Identified with a Coarse-Grained Heteropolymer Model
Applying multicanonical simulations we investigated folding properties of
off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We
study for various sequences folding channels in the free-energy landscape by
comparing the equilibrium conformations with the folded state in terms of an
angular overlap parameter. Although all investigated heteropolymer sequences
contain the same content of hydrophobic and polar monomers, our analysis of the
folding channels reveals a variety of characteristic folding behaviors known
from realistic peptides.Comment: 3 pages, 2 figure
Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins
Within the frame of an effective, coarse-grained hydrophobic-polar protein
model, we employ multicanonical Monte Carlo simulations to investigate
free-energy landscapes and folding channels of exemplified heteropolymer
sequences, which are permutations of each other. Despite the simplicity of the
model, the knowledge of the free-energy landscape in dependence of a suitable
system order parameter enables us to reveal complex folding characteristics
known from real bioproteins and synthetic peptides, such as two-state folding,
folding through weakly stable intermediates, and glassy metastability.Comment: 10 pages, 1 figur
Elastic Lennard-Jones Polymers Meet Clusters -- Differences and Similarities
We investigate solid-solid and solid-liquid transitions of elastic flexible
off-lattice polymers with Lennard-Jones monomer-monomer interaction and
anharmonic springs by means of sophisticated variants of multicanonical Monte
Carlo methods. We find that the low-temperature behavior depends strongly and
non-monotonically on the system size and exhibits broad similarities to unbound
atomic clusters. Particular emphasis is dedicated to the classification of
icosahedral and non-icosahedral low-energy polymer morphologies.Comment: 9 pages, 17 figure
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