868 research outputs found
Numerical estimation of entropy loss on dimerization: improved prediction of the quaternary structure of the GCN4 leucine zipper
A lattice based model of a protein is used to study the dimerization
equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to
determine the free energy of both the monomeric and dimeric forms as a function
of temperature. The method of coincidences is then introduced to explicitly
calculate the entropy loss associated with dimerization, and from it the free
energy difference between monomer and dimer, as well as the corresponding
equilibrium reaction constant. We find that the entropy loss of dimerization is
a strong function of energy (or temperature), and that it is much larger than
previously estimated, especially for high energy states. The results confirm
that it is possible to study the dimerization equilibrium of GCN4 at
physiological concentrations within the reduced representation of the protein
employed
Monte Carlo study of cooperativity in homopolypeptides
©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/9412/1DOI:10.1063/1.463317A discretized model of globular proteins is employed in a Monte Carlo study of the helix-coil transition of polyalanine and the collapse transition of polyvaline. The present lattice realization permits real protein crystal structures to be represented at the level of 1 A resolution. Furthermore, the Monte Carlo dynamic scheme is capable of moving elements of assembled secondary and supersecondary structure. The potentials of mean force for the interactions are constructed from the statistics of a set of high resolution x-ray structures of nonhomologous proteins. The cooperativity of formation of ordered structures is found to be larger when the major contributions to the conformational energy of the low temperature states come from hydrogen bonds and short range conformational propensities. The secondary structure seen in the folded state is the result of an interplay between the short and long range interactions. Compactness itself, driven by long range, nonspecific interactions, seems to be insufficient to generate any appreciable secondary structure. A detailed examination of the dynamics of highly helical model proteins demonstrates that all elements of secondary structure are mobile in the present algorithm, and thus the folding pathways do not depend on the use of a lattice approximation. Possible applications of the present model to the prediction of protein 3D structures are briefly discussed
CABS-flex predictions of protein flexibility compared with NMR ensembles
Motivation: Identification of flexible regions of protein structures is
important for understanding of their biological functions. Recently, we have
developed a fast approach for predicting protein structure fluctuations from a
single protein model: the CABS-flex. CABS-flex was shown to be an efficient
alternative to conventional all-atom molecular dynamics (MD). In this work, we
evaluate CABS-flex and MD predictions by comparison with protein structural
variations within NMR ensembles.
Results: Based on a benchmark set of 140 proteins, we show that the relative
fluctuations of protein residues obtained from CABS-flex are well correlated to
those of NMR ensembles. On average, this correlation is stronger than that
between MD and NMR ensembles. In conclusion, CABS-flex is useful and
complementary to MD in predicting of protein regions that undergo
conformational changes and the extent of such changes
Monte Carlo dynamics of diamond-lattice multichain systems
©1986 American Institute of Physics. The electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?APCPCS/137/241/1DOI:10.1063/1.35530Presented at the 1985 La Jolla Workshop on Polymer Flow Interaction.We present preliminary results of Monte Carlo studies on the dynamics of multichain diamond-lattice systems at considerably greater densities than those done previously. Chain dynamics were simulated by a random sequence of three or four bond kink motions. The single bead autocorrelation function exhibits "slow" mode relaxation behavior with a g(t)∝ tβ. There is a smooth crossover from Rouse-like dynamics, β=1/2, at low density to smaller values of β at higher density and β=0 at the glass transition density (φG≅0.92). The simulation provides a self-diffusion coefficient D ∝ n-2, with n the number of beads, in agreement with experiment. A phenomenological model, different from the widely accepted reptation picture, is proposed
Virtual Frame Technique: Ultrafast Imaging with Any Camera
Many phenomena of interest in nature and industry occur rapidly and are
difficult and cost-prohibitive to visualize properly without specialized
cameras. Here we describe in detail the Virtual Frame Technique (VFT), a
simple, useful, and accessible form of compressed sensing that increases the
frame acquisition rate of any camera by several orders of magnitude by
leveraging its dynamic range. VFT is a powerful tool for capturing rapid
phenomenon where the dynamics facilitate a transition between two states, and
are thus binary. The advantages of VFT are demonstrated by examining such
dynamics in five physical processes at unprecedented rates and spatial
resolution: fracture of an elastic solid, wetting of a solid surface, rapid
fingerprint reading, peeling of adhesive tape, and impact of an elastic
hemisphere on a hard surface. We show that the performance of the VFT exceeds
that of any commercial high speed camera not only in rate of imaging but also
in field of view, achieving a 65MHz frame rate at 4MPx resolution. Finally, we
discuss the performance of the VFT with several commercially available
conventional and high-speed cameras. In principle, modern cell phones can
achieve imaging rates of over a million frames per second using the VFT.Comment: 7 Pages, 4 Figures, 1 Supplementary Vide
Effect of double bonds on the dynamics of hydrocarbon chains
©1992 American Institute of PhysicsThe electronic version of this article is the complete one and can be found online at: http://link.aip.org/link/?JCPSA6/97/1240/1DOI:10.1063/1.463250Brownian dynamics simulations of isolated 18-carbon chains have been performed, both for
saturated and unsaturated hydrocarbons. The effect of one or several (nonconjugated)
double bonds on the properties of the chains is discussed in terms of both equilibrium and
dynamic properties. The introduction of a cis double bond increases the relaxation
rates of the unsaturated chain with respect to the saturated alkane. On the other hand,
coupling effects in the torsional transitions around a trans double bond make the dynamics of
this unsaturated chain very similar to the saturated one. Based on these results, the
parameters and moves of a dynamic Monte Carlo algorithm are tuned to reproduce the
observed behavior, providing an efficient method for the study of more complicated systems
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
We describe a combination of all-atom simulations with CABS, a
well-established coarse-grained protein modeling tool, into a single multiscale
protocol. The simulation method has been tested on the C-terminal beta hairpin
of protein G, a model system of protein folding. After reconstructing atomistic
details, conformations derived from the CABS simulation were subjected to
replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb
force fields in explicit solvent. Such a combination accelerates system
convergence several times in comparison with all-atom simulations starting from
the extended chain conformation, demonstrated by the analysis of melting
curves, the number of native-like conformations as a function of time and
secondary structure propagation. The results strongly suggest that the proposed
multiscale method could be an efficient and accurate tool for high-resolution
studies of protein folding dynamics in larger systems.Comment: 12 pages, 4 figure
A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants
First published in DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 23 (1996) published by the American Mathematical Society.Presented at DIMACS Workshop on Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, March 20-21, 1995.A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al
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