138 research outputs found
Hybrid Monte Carlo simulation of polymer chains
We develop the hybrid Monte Carlo method for simulations of single
off-lattice polymer chains. We discuss implementation and choice of simulation
parameters in some detail. The performance of the algorithm is tested on models
for homopolymers with short- or long-range self-repulsion, using chains with
monomers. Without excessive fine tuning, we find that the
computational cost grows as with . In
addition, we report results for the scaling of the end-to-end distance,
.Comment: 13 pages, single postscript file, uuencoded form, Lund Preprint LU-TP
93-2
Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model
Folding properties of a two-dimensional toy protein model containing only two
amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An
efficient Monte Carlo procedure is employed to ensure that the ground states
are found. The thermodynamic properties are found to be strongly sequence
dependent in contrast to the kinetic ones. Hence, criteria for good folders are
defined entirely in terms of thermodynamic fluctuations. With these criteria
sequence patterns that fold well are isolated. For 300 chains with 20 randomly
chosen binary residues approximately 10% meet these criteria. Also, an analysis
is performed by means of statistical and artificial neural network methods from
which it is concluded that the folding properties can be predicted to a certain
degree given the binary numbers characterizing the sequences.Comment: 15 pages, 8 Postscript figures. Minor change
Monte Carlo Procedure for Protein Design
A new method for sequence optimization in protein models is presented. The
approach, which has inherited its basic philosophy from recent work by Deutsch
and Kurosky [Phys. Rev. Lett. 76, 323 (1996)] by maximizing conditional
probabilities rather than minimizing energy functions, is based upon a novel
and very efficient multisequence Monte Carlo scheme. By construction, the
method ensures that the designed sequences represent good folders
thermodynamically. A bootstrap procedure for the sequence space search is
devised making very large chains feasible. The algorithm is successfully
explored on the two-dimensional HP model with chain lengths N=16, 18 and 32.Comment: 7 pages LaTeX, 4 Postscript figures; minor change
Monte Carlo Update for Chain Molecules: Biased Gaussian Steps in Torsional Space
We develop a new elementary move for simulations of polymer chains in torsion
angle space. The method is flexible and easy to implement. Tentative updates
are drawn from a (conformation-dependent) Gaussian distribution that favors
approximately local deformations of the chain. The degree of bias is controlled
by a parameter b. The method is tested on a reduced model protein with 54 amino
acids and the Ramachandran torsion angles as its only degrees of freedom, for
different b. Without excessive fine tuning, we find that the effective step
size can be increased by a factor of three compared to the unbiased b=0 case.
The method may be useful for kinetic studies, too.Comment: 14 pages, 4 figure
Finite-Size Scaling on the Ising Coexistence Line
We study the finite-size scaling of moments of the magnetization in the
low-temperature phase of the two-dimensional Ising model.Comment: talk at Lattice '92, 4 pages, Latex, needs espcrc2.sty, figures not
included, CERN-TH.6724/9
Mechanical resistance in unstructured proteins
Single-molecule pulling experiments on unstructured proteins linked to
neurodegenerative diseases have measured rupture forces comparable to those for
stable folded proteins. To investigate the structural mechanisms of this
unexpected force resistance, we perform pulling simulations of the amyloid
{\beta}-peptide (A{\beta}) and {\alpha}-synuclein ({\alpha}S), starting from
simulated conformational ensembles for the free monomers. For both proteins,
the simulations yield a set of rupture events that agree well with the
experimental data. By analyzing the conformations right before rupture in each
event, we find that the mechanically resistant structures share a common
architecture, with similarities to the folds adopted by A{\beta} and {\alpha}S
in amyloid fibrils. The disease-linked Arctic mutation of A{\beta} is found to
increase the occurrence of highly force-resistant structures. Our study
suggests that the high rupture forces observed in A{\beta} and {\alpha}S
pulling experiments are caused by structures that might have a key role in
amyloid formation.Comment: v3: Added correct journal reference plus minor correction
Structure optimization in an off-lattice protein model
We study an off-lattice protein toy model with two species of monomers
interacting through modified Lennard-Jones interactions. Low energy
configurations are optimized using the pruned-enriched-Rosenbluth method
(PERM), hitherto employed to native state searches only for off lattice models.
For 2 dimensions we found states with lower energy than previously proposed
putative ground states, for all chain lengths . This indicates that
PERM has the potential to produce native states also for more realistic protein
models. For , where no published ground states exist, we present some
putative lowest energy states for future comparison with other methods.Comment: 4 pages, 2 figure
An effective all-atom potential for proteins
We describe and test an implicit solvent all-atom potential for simulations
of protein folding and aggregation. The potential is developed through studies
of structural and thermodynamic properties of 17 peptides with diverse
secondary structure. Results obtained using the final form of the potential are
presented for all these peptides. The same model, with unchanged parameters, is
furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta
protein and a three-helix-bundle protein, with very good results. The
computational efficiency of the potential makes it possible to investigate the
free-energy landscape of these 49--67-residue systems with high statistical
accuracy, using only modest computational resources by today's standards
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