2,474 research outputs found
Theoretical prediction of spectral and optical properties of bacteriochlorophylls in thermally disordered LH2 antenna complexes
A general approach for calculating spectral and optical properties of
pigment-protein complexes of known atomic structure is presented. The method,
that combines molecular dynamics simulations, quantum chemistry calculations
and statistical mechanical modeling, is demonstrated by calculating the
absorption and circular dichroism spectra of the B800-B850 BChls of the LH2
antenna complex from Rs. molischianum at room temperature. The calculated
spectra are found to be in good agreement with the available experimental
results. The calculations reveal that the broadening of the B800 band is mainly
caused by the interactions with the polar protein environment, while the
broadening of the B850 band is due to the excitonic interactions. Since it
contains no fitting parameters, in principle, the proposed method can be used
to predict optical spectra of arbitrary pigment-protein complexes of known
structure.Comment: ReVTeX4, 11 pages, 9 figures, submitted to J. Chem. Phy
Ab initio study of alanine polypeptide chains twisting
We have investigated the potential energy surfaces for alanine chains
consisting of three and six amino acids. For these molecules we have calculated
potential energy surfaces as a function of the Ramachandran angles Phi and Psi,
which are widely used for the characterization of the polypeptide chains. These
particular degrees of freedom are essential for the characterization of
proteins folding process. Calculations have been carried out within ab initio
theoretical framework based on the density functional theory and accounting for
all the electrons in the system. We have determined stable conformations and
calculated the energy barriers for transitions between them. Using a
thermodynamic approach, we have estimated the times of characteristic
transitions between these conformations. The results of our calculations have
been compared with those obtained by other theoretical methods and with the
available experimental data extracted from the Protein Data Base. This
comparison demonstrates a reasonable correspondence of the most prominent
minima on the calculated potential energy surfaces to the experimentally
measured angles Phi and Psi for alanine chains appearing in native proteins. We
have also investigated the influence of the secondary structure of polypeptide
chains on the formation of the potential energy landscape. This analysis has
been performed for the sheet and the helix conformations of chains of six amino
acids.Comment: 24 pages, 10 figure
A Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System
In the first work of this series [physics/0204035] it was shown that the
conformational space of a molecule could be described to a fair degree of
accuracy by means of a central hyperplane arrangement. The hyperplanes divide
the espace into a hierarchical set of cells that can be encoded by the face
lattice poset of the arrangement. The model however, lacked explicit rotational
symmetry which made impossible to distinguish rotated structures in
conformational space. This problem was solved in a second work
[physics/0404052] by sorting the elementary 3D components of the molecular
system into a set of morphological classes that can be properly oriented in a
standard 3D reference frame. This also made possible to find a solution to the
problem that is being adressed in the present work: for a molecular system
immersed in a heat bath we want to enumerate the subset of cells in
conformational space that are visited by the molecule in its thermal wandering.
If each visited cell is a vertex on a graph with edges to the adjacent cells,
here it is explained how such graph can be built
Dynamics of ions in the selectivity filter of the KcsA channel
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications
CHARMM36m: An improved force field for folded and intrinsically disordered proteins.
The all-atom additive CHARMM36 protein force field is widely used in molecular modeling and simulations. We present its refinement, CHARMM36m (http://mackerell.umaryland.edu/charmm_ff.shtml), with improved accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins
Radiative Damping and Functional Differential Equations
We propose a general technique to solve the classical many-body problem with
radiative damping. We modify the short-distance structure of Maxwell
electrodynamics. This allows us to avoid runaway solutions as if we had a
covariant model of extended particles. The resulting equations of motion are
functional differential equations (FDEs) rather than ordinary differential
equations. Using recently developed numerical techniques for stiff FDEs, we
solve these equations for the one-body central force problem with radiative
damping with a view to benchmark our new approach. Our results indicate that
locally the magnitude of radiation damping may be well approximated by the
standard third-order expression but the global properties of our solutions are
dramatically different. We comment on the two body problem and applications to
quantum field theory and quantum mechanics.Comment: (v1) 6 pages, version of Nov 22, 2007 (v2) 24 pages double-spaced.
calculations and results unchanged, explanations elaborate
Maximum Flux Transition Paths of Conformational Change
Given two metastable states A and B of a biomolecular system, the problem is
to calculate the likely paths of the transition from A to B. Such a calculation
is more informative and more manageable if done for a reduced set of collective
variables chosen so that paths cluster in collective variable space. The
computational task becomes that of computing the "center" of such a cluster. A
good way to define the center employs the concept of a committor, whose value
at a point in collective variable space is the probability that a trajectory at
that point will reach B before A. The committor "foliates" the transition
region into a set of isocommittors. The maximum flux transition path is defined
as a path that crosses each isocommittor at a point which (locally) has the
highest crossing rate of distinct reactive trajectories. (This path is
different from that of the MaxFlux method of Huo and Straub.) It is argued that
such a path is nearer to an ideal path than others that have been proposed with
the possible exception of the finite-temperature string method path. To make
the calculation tractable, three approximations are introduced, yielding a path
that is the solution of a nonsingular two-point boundary-value problem. For
such a problem, one can construct a simple and robust algorithm. One such
algorithm and its performance is discussed.Comment: 7 figure
Structure, dynamics, and function of the monooxygenase P450 BM-3: insights from computer simulations studies
The monooxygenase P450 BM-3 is a NADPH-dependent fatty acid hydroxylase enzyme isolated from soil bacterium Bacillus megaterium. As a pivotal member of cytochrome P450 superfamily, it has been intensely studied for the comprehension of structure-dynamics-function relationships in this class of enzymes. In addition, due to its peculiar properties, it is also a promising enzyme for biochemical and biomedical applications. However, despite the efforts, the full understanding of the enzyme structure and dynamics is not yet achieved. Computational studies, particularly molecular dynamics (MD) simulations, have importantly contributed to this endeavor by providing new insights at an atomic level regarding the correlations between structure, dynamics, and function of the protein. This topical review summarizes computational studies based on MD simulations of the cytochrome P450 BM-3 and gives an outlook on future directions
Predicting Transcription Factor Specificity with All-Atom Models
The binding of a transcription factor (TF) to a DNA operator site can
initiate or repress the expression of a gene. Computational prediction of sites
recognized by a TF has traditionally relied upon knowledge of several cognate
sites, rather than an ab initio approach. Here, we examine the possibility of
using structure-based energy calculations that require no knowledge of bound
sites but rather start with the structure of a protein-DNA complex. We study
the PurR E. coli TF, and explore to which extent atomistic models of
protein-DNA complexes can be used to distinguish between cognate and
non-cognate DNA sites. Particular emphasis is placed on systematic evaluation
of this approach by comparing its performance with bioinformatic methods, by
testing it against random decoys and sites of homologous TFs. We also examine a
set of experimental mutations in both DNA and the protein. Using our explicit
estimates of energy, we show that the specificity for PurR is dominated by
direct protein-DNA interactions, and weakly influenced by bending of DNA.Comment: 26 pages, 3 figure
Secondary-Structure Design of Proteins by a Backbone Torsion Energy
We propose a new backbone-torsion-energy term in the force field for protein
systems. This torsion-energy term is represented by a double Fourier series in
two variables, the backbone dihedral angles phi and psi. It gives a natural
representation of the torsion energy in the Ramachandran space in the sense
that any two-dimensional energy surface periodic in both phi and psi can be
expanded by the double Fourier series. We can then easily control
secondary-structure-forming tendencies by modifying the torsion-energy surface.
For instance, we can increase/decrease the alpha-helix-forming-tendencies by
lowering/raising the torsion-energy surface in the alpha-helix region and
likewise increase/decrease the beta-sheet-forming tendencies by
lowering/raising the surface in the beta-sheet region in the Ramachandran
space. We applied our approach to AMBER parm94 and AMBER parm96 force fields
and demonstrated that our modifications of the torsion-energy terms resulted in
the expected changes of secondary-structure-forming-tendencies by performing
folding simulations of alpha-helical and beta-hairpin peptides.Comment: 13 pages, (Revtex4), 5 figure
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