247 research outputs found
An Analytical Approach to the Protein Designability Problem
We present an analytical method for determining the designability of protein
structures. We apply our method to the case of two-dimensional lattice
structures, and give a systematic solution for the spectrum of any structure.
Using this spectrum, the designability of a structure can be estimated. We
outline a heirarchy of structures, from most to least designable, and show that
this heirarchy depends on the potential that is used.Comment: 16 pages 4 figure
Protein and DNA sequence determinants of thermophilic adaptation
Prokaryotes living at extreme environmental temperatures exhibit pronounced
signatures in the amino acid composition of their proteins and nucleotide
compositions of their genomes reflective of adaptation to their thermal
environments. However, despite significant efforts, the definitive answer of
what are the genomic and proteomic compositional determinants of Optimal Growth
Temperature of prokaryotic organisms remained elusive. Here the authors
performed a comprehensive analysis of amino acid and nucleotide compositional
signatures of thermophylic adaptation by exhaustively evaluating all
combinations of amino acids and nucleotides as possible determinants of Optimal
Growth Temperature for all prokaryotic organisms with fully sequences genomes..
The authors discovered that total concentration of seven amino acids in
proteomes, IVYWREL, serves as a universal proteomic predictor of Optimal Growth
Temperature in prokaryotes. Resolving the old-standing controversy the authors
determined that the variation in nucleotide composition (increase of purine
load, or A+G content with temperature) is largely a consequence of thermal
adaptation of proteins. However, the frequency with which A and G nucleotides
appear as nearest neighbors in genome sequences is strongly and independently
correlated with Optimal Growth Temperature. as a result of codon bias in
corresponding genomes. Together these results provide a complete picture of
proteomic and genomic determinants of thermophilic adaptation.Comment: in press PLoS Computational Biology; revised versio
Mapping of mutation-sensitive sites in protein-like chains
In this work we have studied, with the help of a simple on-lattice model, the
distribution pattern of sites sensitive to point mutations ('hot' sites) in
protein-like chains. It has been found that this pattern depends on the
regularity of the matrix that rules the interaction between different kinds of
residues. If the interaction matrix is dominated by the hydrophobic effect
(Miyazawa Jernigan like matrix), this distribution is very simple - all the
'hot' sites can be found at the positions with maximum number of closest
nearest neighbors (bulk).
If random or nonlinear corrections are added to such an interaction matrix
the distribution pattern changes. The rising of collective effects allows the
'hot' sites to be found in places with smaller number of nearest neighbors
(surface) while the general trend of the 'hot' sites to fall into a bulk part
of a conformation still holds.Comment: 15 pages, 6 figure
Reply to Comment on "Criterion that Determines the Foldability of Proteins"
We point out that the correlation between folding times and in protein-like heteropolymer models where
and are the collapse and folding transition temperatures
was already established in 1993 before the other presumed equivalent criterion
(folding times correlating with alone) was suggested. We argue that the
folding times for these models show no useful correlation with the energy gap
even if restricted to the ensemble of compact structures as suggested by
Karplus and Shakhnovich (cond-mat/9606037).Comment: 6 pages, Latex, 2 Postscript figures. Plots explicitly showing the
lack of correlation between folding time and energy gap are adde
Is Heteropolymer Freezing Well Described by the Random Energy Model?
It is widely held that the Random Energy Model (REM) describes the freezing
transition of a variety of types of heteropolymers. We demonstrate that the
hallmark property of REM, statistical independence of the energies of states
over disorder, is violated in different ways for models commonly employed in
heteropolymer freezing studies. The implications for proteins are also
discussed.Comment: 4 pages, 3 eps figures To appear in Physical Review Letters, May 199
Two-Dimensional Polymers with Random Short-Range Interactions
We use complete enumeration and Monte Carlo techniques to study
two-dimensional self-avoiding polymer chains with quenched ``charges'' .
The interaction of charges at neighboring lattice sites is described by . We find that a polymer undergoes a collapse transition at a temperature
, which decreases with increasing imbalance between charges. At the
transition point, the dependence of the radius of gyration of the polymer on
the number of monomers is characterized by an exponent , which is slightly larger than the similar exponent for homopolymers. We
find no evidence of freezing at low temperatures.Comment: 4 two-column pages, 6 eps figures, RevTex, Submitted to Phys. Rev.
Localization in simple multiparticle catalytic absorption model
We consider the phase transition in the system of n simultaneously developing
random walks on the halfline x>=0. All walks are independent on each others in
all points except the origin x=0, where the point well is located. The well
depth depends on the number of particles simultaneously staying at x=0. We
consider the limit n>>1 and show that if the depth growth faster than 3/2 n
ln(n) with n, then all random walks become localized simultaneously at the
origin. In conclusion we discuss the connection of that problem with the phase
transition in the copolymer chain with quenched random sequence of monomers
considered in the frameworks of replica approach.Comment: 17 pages in LaTeX, 5 PostScript figures; submitted to J.Phys.(A):
Math. Ge
- …