2,059 research outputs found
Casting Polymer Nets to Optimize Noisy Molecular Codes
Life relies on the efficient performance of molecular codes, which relate
symbols and meanings via error-prone molecular recognition. We describe how
optimizing a code to withstand the impact of molecular recognition noise may be
approximated by the statistics of a two-dimensional network made of polymers.
The noisy code is defined by partitioning the space of symbols into regions
according to their meanings. The "polymers" are the boundaries between these
regions and their statistics defines the cost and the quality of the noisy
code. When the parameters that control the cost-quality balance are varied, the
polymer network undergoes a first-order transition, where the number of encoded
meanings rises discontinuously. Effects of population dynamics on the evolution
of molecular codes are discussed.Comment: PNAS 200
A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost
Molecular codes translate information written in one type of molecules into
another molecular language. We introduce a simple model that treats molecular
codes as noisy information channels. An optimal code is a channel that conveys
information accurately and efficiently while keeping down the impact of errors.
The equipoise of the three conflicting needs, for minimal error-load, minimal
cost of resources and maximal diversity of vocabulary, defines the fitness of
the code. The model suggests a mechanism for the emergence of a code when
evolution varies the parameters that control this equipoise and the mapping
between the two molecular languages becomes non-random. This mechanism is
demonstrated by a simple toy model that is formally equivalent to a mean-field
Ising magnet.Comment: Keywords: molecular codes, rate-distortion theory, biological
information channels, stochastic maps, genetic code, genetic network
A rate-distortion scenario for the emergence and evolution of noisy molecular codes
We discuss, in terms of rate-distortion theory, the fitness of molecular
codes as the problem of designing an optimal information channel. The fitness
is governed by an interplay between the cost and quality of the channel, which
induces smoothness in the code. By incorporating this code fitness into
population dynamics models, we suggest that the emergence and evolution of
molecular codes may be explained by simple channel design considerations.Comment: PACS numbers: 87.10.+e, 87.14.Gg, 87.14.E
Molecular Recognition as an Information Channel: The Role of Conformational Changes
Molecular recognition, which is essential in processing information in
biological systems, takes place in a crowded noisy biochemical environment and
requires the recognition of a specific target within a background of various
similar competing molecules. We consider molecular recognition as a
transmission of information via a noisy channel and use this analogy to gain
insights on the optimal, or fittest, molecular recognizer. We focus on the
optimal structural properties of the molecules such as flexibility and
conformation. We show that conformational changes upon binding, which often
occur during molecular recognition, may optimize the detection performance of
the recognizer. We thus suggest a generic design principle termed
'conformational proofreading' in which deformation enhances detection. We
evaluate the optimal flexibility of the molecular recognizer, which is
analogous to the stochasticity in a decision unit. In some scenarios, a
flexible recognizer, i.e., a stochastic decision unit, performs better than a
rigid, deterministic one. As a biological example, we discuss conformational
changes during homologous recombination, the process of genetic exchange
between two DNA strands.Comment: Keywords--Molecular information channels, molecular recognition,
conformational proofreading.
http://www.weizmann.ac.il/complex/tlusty/papers/IEEE2009b.pd
High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity
Homologous recombination plays a key role in generating genetic diversity,
while maintaining protein functionality. The mechanisms by which RecA enables a
single-stranded segment of DNA to recognize a homologous tract within a whole
genome are poorly understood. The scale by which homology recognition takes
place is of a few tens of base pairs, after which the quest for homology is
over. To study the mechanism of homology recognition, RecA-promoted homologous
recombination between short DNA oligomers with different degrees of heterology
was studied in vitro, using fluorescence resonant energy transfer. RecA can
detect single mismatches at the initial stages of recombination, and the
efficiency of recombination is strongly dependent on the location and
distribution of mismatches. Mismatches near the 5' end of the incoming strand
have a minute effect, whereas mismatches near the 3' end hinder strand exchange
dramatically. There is a characteristic DNA length above which the sensitivity
to heterology decreases sharply. Experiments with competitor sequences with
varying degrees of homology yield information about the process of homology
search and synapse lifetime. The exquisite sensitivity to mismatches and the
directionality in the exchange process support a mechanism for homology
recognition that can be modeled as a kinetic proofreading cascade.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/NuclAcidRes2006.pdf
http://nar.oxfordjournals.org/cgi/content/short/34/18/502
Coding limits on the number of transcription factors
Transcription factor proteins bind specific DNA sequences to control the
expression of genes. They contain DNA binding domains which belong to several
super-families, each with a specific mechanism of DNA binding. The total number
of transcription factors encoded in a genome increases with the number of genes
in the genome. Here, we examined the number of transcription factors from each
super-family in diverse organisms.
We find that the number of transcription factors from most super-families
appears to be bounded. For example, the number of winged helix factors does not
generally exceed 300, even in very large genomes. The magnitude of the maximal
number of transcription factors from each super-family seems to correlate with
the number of DNA bases effectively recognized by the binding mechanism of that
super-family. Coding theory predicts that such upper bounds on the number of
transcription factors should exist, in order to minimize cross-binding errors
between transcription factors. This theory further predicts that factors with
similar binding sequences should tend to have similar biological effect, so
that errors based on mis-recognition are minimal. We present evidence that
transcription factors with similar binding sequences tend to regulate genes
with similar biological functions, supporting this prediction.
The present study suggests limits on the transcription factor repertoire of
cells, and suggests coding constraints that might apply more generally to the
mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/
http://www.biomedcentral.com/1471-2164/7/23
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