4,381 research outputs found
Population genetics of translational robustness
Recent work has shown that expression level is the main predictor of a
gene’s evolutionary rate, and that more highly expressed genes evolve
slower. A possible explanation for this observation is selection for proteins
which fold properly despite mistranslation, in short selection for
translational robustness. Translational robustness leads to the somewhat
paradoxical prediction that highly expressed genes are extremely tolerant to
missense substitutions but nevertheless evolve very slowly. Here, we study a
simple theoretical model of translational robustness that allows us to gain
analytic insight into how this paradoxical behavior arises.Comment: 32 pages, 4 figures, Genetics in pres
Visual adaptation to convexity in macaque area V4
Aftereffects are perceptual illusions caused by visual adaptation to one or more stimulus attribute, such as orientation, motion, or shape. Neurophysiological studies seeking to understand the basis of visual adaptation have observed firing rate reduction and changes in tuning of stimulus-selective neurons following periods of prolonged visual stimulation. In the domain of shape, recent psychophysical work has shown that adaptation to a convex pattern induces a subsequently seen rectangle to appear slightly concave. In the present study, we investigate the possible contribution of V4 neurons of rhesus monkeys, which are thought to be involved in the coding of convexity, to shape-specific adaptation. Visually responsive neurons were monitored during the brief presentation of simple shapes varying in their convexity level. Each test presentation was preceded by either a blank period or several seconds of adaptation to a convex or concave stimulus, presented in two different sizes. Adaptation consistently shifted the tuning of neurons away from the convex or concave adapter, including shifting response to the neutral rectangle in the direction of the opposite convexity. This repulsive shift resembled the known perceptual distortion associated with adaptation to such stimuli. In addition, adaptation caused a nonspecific response decrease, as well as a specific decrease for repeated stimuli. The latter effects were observed whether or not the adapting and test stimuli matched closely in their size. Taken together, these results provide evidence for shape-specific adaptation of neurons in area V4, which may contribute to the perception of the convexity aftereffect
Thermodynamics of Neutral Protein Evolution
Naturally evolving proteins gradually accumulate mutations while continuing
to fold to thermodynamically stable native structures. This process of neutral
protein evolution is an important mode of genetic change, and forms the basis
for the molecular clock. Here we present a mathematical theory that predicts
the number of accumulated mutations, the index of dispersion, and the
distribution of stabilities in an evolving protein population from knowledge of
the stability effects (ddG values) for single mutations. Our theory
quantitatively describes how neutral evolution leads to marginally stable
proteins, and provides formulae for calculating how fluctuations in stability
cause an overdispersion of the molecular clock. It also shows that the
structural influences on the rate of sequence evolution that have been observed
in earlier simulations can be calculated using only the single-mutation ddG
values. We consider both the case when the product of the population size and
mutation rate is small and the case when this product is large, and show that
in the latter case proteins evolve excess mutational robustness that is
manifested by extra stability and increases the rate of sequence evolution. Our
basic method is to treat protein evolution as a Markov process constrained by a
minimal requirement for stable folding, enabling an evolutionary description of
the proteins solely in terms of the experimentally measureable ddG values. All
of our theoretical predictions are confirmed by simulations with model lattice
proteins. Our work provides a mathematical foundation for understanding how
protein biophysics helps shape the process of evolution
Strong magnetoresistance induced by long-range disorder
We calculate the semiclassical magnetoresistivity of
non-interacting fermions in two dimensions moving in a weak and smoothly
varying random potential or random magnetic field. We demonstrate that in a
broad range of magnetic fields the non-Markovian character of the transport
leads to a strong positive magnetoresistance. The effect is especially
pronounced in the case of a random magnetic field where becomes
parametrically much larger than its B=0 value.Comment: REVTEX, 4 pages, 2 eps figure
Zero-frequency anomaly in quasiclassical ac transport: Memory effects in a two-dimensional metal with a long-range random potential or random magnetic field
We study the low-frequency behavior of the {\it ac} conductivity
of a two-dimensional fermion gas subject to a smooth random
potential (RP) or random magnetic field (RMF). We find a non-analytic
correction to , which corresponds to a
long-time tail in the velocity correlation function. This contribution
is induced by return processes neglected in Boltzmann transport theory. The
prefactor of this -term is positive and proportional to for
RP, while it is of opposite sign and proportional to in the weak RMF
case, where is the mean free path and the disorder correlation length.
This non-analytic correction also exists in the strong RMF regime, when the
transport is of a percolating nature. The analytical results are supported and
complemented by numerical simulations.Comment: 12 pages, RevTeX, 7 figure
Analyzing Machupo virus-receptor binding by molecular dynamics simulations
In many biological applications, we would like to be able to computationally
predict mutational effects on affinity in protein-protein interactions.
However, many commonly used methods to predict these effects perform poorly in
important test cases. In particular, the effects of multiple mutations,
non-alanine substitutions, and flexible loops are difficult to predict with
available tools and protocols. We present here an existing method applied in a
novel way to a new test case; we interrogate affinity differences resulting
from mutations in a host-virus protein-protein interface. We use steered
molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike
glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then
approximate affinity using the maximum applied force of separation and the area
under the force-versus-distance curve. We find, even without the rigor and
planning required for free energy calculations, that these quantities can
provide novel biophysical insight into the GP1/hTfR1 interaction. First, with
no prior knowledge of the system we can differentiate among wild type and
mutant complexes. Moreover, we show that this simple SMD scheme correlates well
with relative free energy differences computed via free energy perturbation.
Second, although the static co-crystal structure shows two large
hydrogen-bonding networks in the GP1/hTfR1 interface, our simulations indicate
that one of them may not be important for tight binding. Third, one viral site
known to be critical for infection may mark an important evolutionary
suppressor site for infection-resistant hTfR1 mutants. Finally, our approach
provides a framework to compare the effects of multiple mutations, individually
and jointly, on protein-protein interactions.Comment: 33 pages, 8 figures, 5 table
Solution of the Quasispecies Model for an Arbitrary Gene Network
In this paper, we study the equilibrium behavior of Eigen's quasispecies
equations for an arbitrary gene network. We consider a genome consisting of genes, so that each gene sequence may be written as . We assume a single fitness peak (SFP) model
for each gene, so that gene has some ``master'' sequence for which it is functioning. The fitness landscape is then determined by
which genes in the genome are functioning, and which are not. The equilibrium
behavior of this model may be solved in the limit of infinite sequence length.
The central result is that, instead of a single error catastrophe, the model
exhibits a series of localization to delocalization transitions, which we term
an ``error cascade.'' As the mutation rate is increased, the selective
advantage for maintaining functional copies of certain genes in the network
disappears, and the population distribution delocalizes over the corresponding
sequence spaces. The network goes through a series of such transitions, as more
and more genes become inactivated, until eventually delocalization occurs over
the entire genome space, resulting in a final error catastrophe. This model
provides a criterion for determining the conditions under which certain genes
in a genome will lose functionality due to genetic drift. It also provides
insight into the response of gene networks to mutagens. In particular, it
suggests an approach for determining the relative importance of various genes
to the fitness of an organism, in a more accurate manner than the standard
``deletion set'' method. The results in this paper also have implications for
mutational robustness and what C.O. Wilke termed ``survival of the flattest.''Comment: 29 pages, 5 figures, to be submitted to Physical Review
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