Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

<p>Abstract</p> <p>Background</p> <p>Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate.</p> <p>Results</p> <p>This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in multidomain proteins or contained in distinct proteins. Substantial homogenization of evolutionary rates in multidomain proteins was, indeed, observed in both animals and plants, although highly significant differences between domain-specific rates remained. The contributions of the translation rate, as determined by the effect of the fusion of a pair of domains within a multidomain protein, and intrinsic, domain-specific structural-functional constraints appear to be comparable in magnitude.</p> <p>Conclusion</p> <p>Fusion of domains in a multidomain protein results in substantial homogenization of the domain-specific evolutionary rates but significant differences between domain-specific evolution rates remain. Thus, the rate of translation and intrinsic structural-functional constraints both exert sizable and comparable effects on sequence evolution.</p> <p>Reviewers</p> <p>This article was reviewed by Sergei Maslov, Dennis Vitkup, Claus Wilke (nominated by Orly Alter), and Allan Drummond (nominated by Joel Bader). For the full reviews, please go to the Reviewers' Reports section.</p

Spin-filter tunnel junction with matched Fermi surfaces

Efficient injection of spin-polarized current into a semiconductor is a basic prerequisite for building semiconductor-based spintronic devices. Here, we use inelastic electron tunneling spectroscopy to show that the efficiency of spin-filter-type spin injectors is limited by spin scattering of the tunneling electrons. By matching the Fermi-surface shapes of the current injection source and target electrode material, spin injection efficiency can be significantly increased in epitaxial ferromagnetic insulator tunnel junctions. Our results demonstrate that not only structural but also Fermi-surface matching is important to suppress scattering processes in spintronic devices.Comment: 5 pages, 4 figure

The origins of phagocytosis and eukaryogenesis

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Grain boundary energies and cohesive strength as a function of geometry

Cohesive laws are stress-strain curves used in finite element calculations to describe the debonding of interfaces such as grain boundaries. It would be convenient to describe grain boundary cohesive laws as a function of the parameters needed to describe the grain boundary geometry; two parameters in 2D and 5 parameters in 3D. However, we find that the cohesive law is not a smooth function of these parameters. In fact, it is discontinuous at geometries for which the two grains have repeat distances that are rational with respect to one another. Using atomistic simulations, we extract grain boundary energies and cohesive laws of grain boundary fracture in 2D with a Lennard-Jones potential for all possible geometries which can be simulated within periodic boundary conditions with a maximum box size. We introduce a model where grain boundaries are represented as high symmetry boundaries decorated by extra dislocations. Using it, we develop a functional form for the symmetric grain boundary energies, which have cusps at all high symmetry angles. We also find the asymptotic form of the fracture toughness near the discontinuities at high symmetry grain boundaries using our dislocation decoration model.Comment: 12 pages, 19 figures, changed titl

Bias Dependent 1/f Conductivity Fluctuations in Low-Doped La1−x_{1-x}Cax_{x}MnO3_3 Manganite Single Crystals

Low frequency noise in current biased La$_{0.82}$Ca$_{0.18}$MnO$_{3}$ single crystals has been investigated in a wide temperature range from 79 K to 290 K. Despite pronounced changes in magnetic properties and dissipation mechanisms of the sample with changing temperature, the noise spectra were found to be always of the 1/f type and their intensity (except the lowest temperature studied) scaled as a square of the bias. At liquid nitrogen temperatures and under bias exceeding some threshold value, the behavior of the noise deviates from the quasi-equilibrium modulation noise and starts to depend in a non monotonic way on bias. It has been verified that the observed noise obeys Dutta and Horn model of 1/f noise in solids. The appearance of nonequilibrium 1/f noise and its dependence on bias have been associated with changes in the distribution of activation energies in the underlying energy landscape. These changes have been correlated with bias induced changes in the intrinsic tunneling mechanism dominating dissipation in La$_{0.82}$Ca$_{0.18}$MnO$_{3}$ at low temperatures.Comment: Accepted for publication in the Journal of Applied Physic

Wavelets: mathematics and applications

The notion of wavelets is defined. It is briefly described {\it what} are wavelets, {\it how} to use them, {\it when} we do need them, {\it why} they are preferred and {\it where} they have been applied. Then one proceeds to the multiresolution analysis and fast wavelet transform as a standard procedure for dealing with discrete wavelets. It is shown which specific features of signals (functions) can be revealed by this analysis, but can not be found by other methods (e.g., by the Fourier expansion). Finally, some examples of practical application are given (in particular, to analysis of multiparticle production}. Rigorous proofs of mathematical statements are omitted, and the reader is referred to the corresponding literature.Comment: 16 pages, 5 figures, Latex, Phys. Atom. Nuc

Life at high Deborah number

In many biological systems, microorganisms swim through complex polymeric fluids, and usually deform the medium at a rate faster than the inverse fluid relaxation time. We address the basic properties of such life at high Deborah number analytically by considering the small-amplitude swimming of a body in an arbitrary complex fluid. Using asymptotic analysis and differential geometry, we show that for a given swimming gait, the time-averaged leading-order swimming kinematics of the body can be expressed as an integral equation on the solution to a series of simpler Newtonian problems. We then use our results to demonstrate that Purcell's scallop theorem, which states that time-reversible body motion cannot be used for locomotion in a Newtonian fluid, breaks down in polymeric fluid environments