Related papers: Beta sheet propensity and the genetic code
This article introduces a novel binary representation of the canonical genetic code based on both the structural similarities of the nucleotides, as well as the physicochemical properties of the encoded amino acids. Each of the four mRNA…
Lymphocyte selection is a fundamental operation of adaptive immunity. In order to produce B-lymphocytes with a desired antigenic profile, a process of mutation-selection occurs in the germinal center, which is part of the lymph nodes. We…
In a letter published in Molecular Biology Evolution [10], Chen and Zhang argue that the variation of the mutation rate along the Escherichia coli genome that we recently reported [3] cannot be evolutionarily optimised. To support this…
A simple explanation for the symmetry of the genetic code has been suggested. An alternative to the wobble hypothesis has been proposed. The facts revealed in this study offer a new insight into physical mechanisms of the functioning of the…
The intrinsic property of proteins to form structural motifs such as alpha-helices and beta-sheets leads to a complex phase behavior in which proteins can assemble into various types of aggregates including crystals, liquidlike phases of…
A biological transition from a state N to a state T is characterized by a rearrangement of the gene expression profile in the system, quantitatively measured through the differential expression of genes. In contrast, changes in genetic…
It is widely recognized nowadays that complex diseases are caused by, amongst the others, multiple genetic factors. The recent advent of genome-wide association study (GWA) has triggered a wave of research aimed at discovering genetic…
Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prevision for the not yet measured thermodynamical…
{\bf Background}: Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to…
The biological process of gene assembly has been modeled based on three types of string rewriting rules, called string pointer rules, defined on so-called legal strings. It has been shown that reduction graphs, graphs that are based on the…
We consider a single genetic locus with two alleles $A_1$ and $A_2$ in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and…
Elizalde (2011) characterized which permutations can be obtained by ordering consecutive elements in the trajectories of (positive) beta-transformations and beta-shifts. We prove similar results for negative bases beta.
We will study the relationship between two well-known theories, genetic evolution and random matrix theory in the context of many-body systems. It is suggested that genetic evolution can be described by a random matrix theory with…
A transformation group approach to the prior for the parameters of the beta distribution is suggested which accounts for finite sets of data by imposing a limit to the range of parameter values under consideration. The relationship between…
Proteins have evolved through mutations, amino acid substitutions, since life appeared on Earth, some 109 years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function,…
GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the…
Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid…
We consider the Moran model of population genetics with two types, mutation, and selection, and investigate the line of descent of a randomly-sampled individual from a contemporary population. We trace this ancestral line back into the…
The evolution in coding DNA sequences brings new flexibility and freedom to the codon words, even as the underlying nucleotides get significantly ordered. These curious contra-rules of gene organisation are observed from the distribution of…
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific…