1,669 research outputs found
Low-energy expansion formula for one-dimensional Fokker-Planck and Schr\"odinger equations with periodic potentials
We study the low-energy behavior of the Green function for one-dimensional
Fokker-Planck and Schr\"odinger equations with periodic potentials. We derive a
formula for the power series expansion of reflection coefficients in terms of
the wave number, and apply it to the low-energy expansion of the Green
function
The Emergence of Scaling in Sequence-based Physical Models of Protein Evolution
It has recently been discovered that many biological systems, when
represented as graphs, exhibit a scale-free topology. One such system is the
set of structural relationships among protein domains. The scale-free nature of
this and other systems has previously been explained using network growth
models that, while motivated by biological processes, do not explicitly
consider the underlying physics or biology. In the present work we explore a
sequence-based model for the evolution protein structures and demonstrate that
this model is able to recapitulate the scale-free nature observed in graphs of
real protein structures. We find that this model also reproduces other
statistical feature of the protein domain graph. This represents, to our
knowledge, the first such microscopic, physics-based evolutionary model for a
scale-free network of biological importance and as such has strong implications
for our understanding of the evolution of protein structures and of other
biological networks.Comment: 20 pages (including figures), 4 figures, to be submitted to PNA
Origin of Native Driving Force in Protein Folding
We derive an expression with four adjustable parameters that reproduces well
the 20x20 Miyazawa-Jernigan potential matrix extracted from known protein
structures. The numerical values of the parameters can be approximately
computed from the surface tension of water, water-screened dipole interactions
between residues and water and among residues, and average exposures of
residues in folded proteins.Comment: LaTeX file, Postscript file; 4 pages, 1 figure (mij.eps), 2 table
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
Oral pathobiont induces systemic inflammation and metabolic changes associated with alteration of gut microbiota.
Periodontitis has been implicated as a risk factor for metabolic disorders such as type 2 diabetes, atherosclerotic vascular diseases, and non-alcoholic fatty liver disease. Although bacteremias from dental plaque and/or elevated circulating inflammatory cytokines emanating from the inflamed gingiva are suspected mechanisms linking periodontitis and these diseases, direct evidence is lacking. We hypothesize that disturbances of the gut microbiota by swallowed bacteria induce a metabolic endotoxemia leading metabolic disorders. To investigate this hypothesis, changes in the gut microbiota, insulin and glucose intolerance, and levels of tissue inflammation were analysed in mice after oral administration of Porphyromonas gingivalis, a representative periodontopathogens. Pyrosequencing revealed that the population belonging to Bacteroidales was significantly elevated in P. gingivalis-administered mice which coincided with increases in insulin resistance and systemic inflammation. In P. gingivalis-administered mice blood endotoxin levels tended to be higher, whereas gene expression of tight junction proteins in the ileum was significantly decreased. These results provide a new paradigm for the interrelationship between periodontitis and systemic diseases
Design of Force Fields from Data at Finite Temperature
We investigate the problem of how to obtain the force field between atoms of
an experimentally determined structure. We show how this problem can be
efficiently solved, even at finite temperature, where the position of the atoms
differs substantially from the ground state. We apply our method to systems
modeling proteins and demonstrate that the correct potentials can be recovered
even in the presence of thermal noise.Comment: 10 pages, 1 postcript figure, Late
Deriving amino acid contact potentials from their frequencies of occurence in proteins: a lattice model study
The possibility of deriving the contact potentials between amino acids from
their frequencies of occurence in proteins is discussed in evolutionary terms.
This approach allows the use of traditional thermodynamics to describe such
frequencies and, consequently, to develop a strategy to include in the
calculations correlations due to the spatial proximity of the amino acids and
to their overall tendency of being conserved in proteins. Making use of a
lattice model to describe protein chains and defining a "true" potential, we
test these strategies by selecting a database of folding model sequences,
deriving the contact potentials from such sequences and comparing them with the
"true" potential. Taking into account correlations allows for a markedly better
prediction of the interaction potentials
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