459 research outputs found
Recovery of Protein Structure from Contact Maps
We present an efficient algorithm to recover the three dimensional structure
of a protein from its contact map representation. First we show that when a
physically realizable map is used as target, our method generates a structure
whose contact map is essentially similar to the target. Furthermore, the
reconstructed and original structures are similar up to the resolution of the
contact map representation. Next we use non-physical target maps, obtained by
corrupting a physical one; in this case our method essentially recovers the
underlying physical map and structure. Hence our algorithm will help to fold
proteins, using dynamics in the space of contact maps. Finally we investigate
the manner in which the quality of the recovered structure degrades when the
number of contacts is reduced.Comment: 27 pages, RevTex, 12 figures include
Evolutionary advantage of cell size control
We analyze the advantage of cell size control strategies in growing
populations under mortality constraints. We demonstrate a general advantage of
the adder control strategy in the presence of growth-dependent mortality, and
for different size-dependent mortality landscapes. Its advantage stems from
epigenetic heritability of cell size, which enables selection to act on the
distribution of cell sizes in a population to avoid mortality thresholds and
adapt to a mortality landscape
Importance of chirality and reduced flexibility of protein side chains: A study with square and tetrahedral lattice models
In simple models side chains are often represented implicitly (e.g., by
spin-states) or simplified as one atom. We study side chain effects using
square lattice and tetrahedral lattice models, with explicitly side chains of
two atoms. We distinguish effects due to chirality and effects due to side
chain flexibilities, since residues in proteins are L-residues, and their side
chains adopt different rotameric states. Short chains are enumerated
exhaustively. For long chains, we sample effectively rare events (eg, compact
conformations) and obtain complete pictures of ensemble properties of these
models at all compactness region. We find that both chirality and reduced side
chain flexibility lower the folding entropy significantly for globally compact
conformations, suggesting that they are important properties of residues to
ensure fast folding and stable native structure. This corresponds well with our
finding that natural amino acid residues have reduced effective flexibility, as
evidenced by analysis of rotamer libraries and side chain rotatable bonds. We
further develop a method calculating the exact side-chain entropy for a given
back bone structure. We show that simple rotamer counting often underestimates
side chain entropy significantly, and side chain entropy does not always
correlate well with main chain packing. Among compact backbones with maximum
side chain entropy, helical structures emerges as the dominating
configurations. Our results suggest that side chain entropy may be an important
factor contributing to the formation of alpha helices for compact
conformations.Comment: 16 pages, 15 figures, 2 tables. Accepted by J. Chem. Phy
Switching and growth for microbial populations in catastrophic responsive environments
Phase variation, or stochastic switching between alternative states of gene
expression, is common among microbes, and may be important in coping with
changing environments. We use a theoretical model to assess whether such
switching is a good strategy for growth in environments with occasional
catastrophic events. We find that switching can be advantageous, but only when
the environment is responsive to the microbial population. In our model,
microbes switch randomly between two phenotypic states, with different growth
rates. The environment undergoes sudden "catastrophes", the probability of
which depends on the composition of the population. We derive a simple
analytical result for the population growth rate. For a responsive environment,
two alternative strategies emerge. In the "no switching" strategy, the
population maximises its instantaneous growth rate, regardless of catastrophes.
In the "switching" strategy, the microbial switching rate is tuned to minimise
the environmental response. Which of these strategies is most favourable
depends on the parameters of the model. Previous studies have shown that
microbial switching can be favourable when the environment changes in an
unresponsive fashion between several states. Here, we demonstrate an
alternative role for phase variation in allowing microbes to maximise their
growth in catastrophic responsive environments.Comment: 9 pages, 10 figures; replaced with revised versio
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