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

The origins of phagocytosis and eukaryogenesis

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The perturbative partition function of supersymmetric 5D Yang-Mills theory with matter on the five-sphere

Based on the construction by Hosomichi, Seong and Terashima we consider N=1 supersymmetric 5D Yang-Mills theory with matter on a five-sphere with radius r. This theory can be thought of as a deformation of the theory in flat space with deformation parameter r and this deformation preserves 8 supercharges. We calculate the full perturbative partition function as a function of r/g^2, where g is the Yang-Mills coupling, and the answer is given in terms of a matrix model. We perform the calculation using localization techniques. We also argue that in the large N-limit of this deformed 5D Yang-Mills theory this matrix model provides the leading contribution to the partition function and the rest is exponentially suppressed.Comment: 34 pages; v2: typos fixed, matches published version; v3: factor correcte

Search for the standard model Higgs boson decaying to bottom quarks in pp collisions at √s = 7 TeV

A search for the standard model Higgs boson (H) decaying to b[bar over b] when produced in association with weak vector bosons (V) is reported for the following modes: W(μν)H, W(eν)H, Z(μμ)H, Z(ee)H and Z(νν)H. The search is performed in a data sample corresponding to an integrated luminosity of 4.7 fb[superscript −1], recorded by the CMS detector in proton–proton collisions at the LHC with a center-of-mass energy of 7 TeV. No significant excess of events above the expectation from background is observed. Upper limits on the VH production cross section times the H→b[bar over b] branching ratio, with respect to the expectations for a standard model Higgs boson, are derived for a Higgs boson in the mass range 110–135 GeV. In this range, the observed 95% confidence level upper limits vary from 3.4 to 7.5 times the standard model prediction; the corresponding expected limits vary from 2.7 to 6.7 times the standard model prediction.European Organization for Nuclear ResearchUnited States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Measurement of the production cross section for pairs of isolated photons in pp collisions at √s = 7 TeV

The integrated and differential cross sections for the production of pairs of isolated photons is measured in proton-proton collisions at a centre-of-mass energy of 7 TeV with the CMS detector at the LHC. A data sample corresponding to an integrated luminosity of 36 pb[superscript −1] is analysed. A next-to-leading-order perturbative QCD calculation is compared to the measurements. A discrepancy is observed for regions of the phase space where the two photons have an azimuthal angle difference Δφ ≲ 2.8 rad.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Measurement of the elliptic anisotropy of charged particles produced in PbPb collisions at √sNN=2.76 TeV

The anisotropy of the azimuthal distributions of charged particles produced in [√ over s[subscript NN]]=2.76 TeV PbPb collisions is studied with the CMS experiment at the LHC. The elliptic anisotropy parameter, v[subscript 2], defined as the second coefficient in a Fourier expansion of the particle invariant yields, is extracted using the event-plane method, two- and four-particle cumulants, and Lee-Yang zeros. The anisotropy is presented as a function of transverse momentum (p[subscript T]), pseudorapidity (η) over a broad kinematic range, 0.3<p[subscript T]<20 GeV/c, |η|<2.4, and in 12 classes of collision centrality from 0 to 80%. The results are compared to those obtained at lower center-of-mass energies, and various scaling behaviors are examined. When scaled by the geometric eccentricity of the collision zone, the elliptic anisotropy is found to obey a universal scaling with the transverse particle density for different collision systems and center-of-mass energies

Measurement of the charge asymmetry in top-quark pair production in proton–proton collisions at √s = 7 TeV

The difference in angular distributions between top quarks and antiquarks, commonly referred to as the charge asymmetry, is measured in pp collisions at the LHC with the CMS experiment. The data sample corresponds to an integrated luminosity of 1.09 fb[superscript −1] at a centre-of-mass energy of 7 TeV. Top-quark pairs are selected in the final state with an electron or muon and four or more jets. At least one jet is identified as originating from b-quark hadronization. The charge asymmetry is measured in two variables, one based on the pseudorapidities (η) of the top quarks and the other on their rapidities (y). The results A[η over C] = −0.017 ± 0.032 (stat.)[+0.025 over −0.036] (syst.) and A[y over C] = −0.013 ± 0.028 (stat.)[+0.029 over −0.031] (syst.) are consistent within uncertainties with the standard-model predictions.United States. Dept. of EnergyNational Science Foundation (U.S.)Alfred P. Sloan Foundatio

Search for the standard model Higgs boson decaying into two photons in pp collisions at √s = 7 TeV

A search for a Higgs boson decaying into two photons is described. The analysis is performed using a dataset recorded by the CMS experiment at the LHC from pp collisions at a center-of-mass energy of 7 TeV, which corresponds to an integrated luminosity of 4.8 fb[superscript −1]. Limits are set on the cross section of the standard model Higgs boson decaying to two photons. The expected exclusion limit at 95% confidence level is between 1.4 and 2.4 times the standard model cross section in the mass range between 110 and 150 GeV. The analysis of the data excludes, at 95% confidence level, the standard model Higgs boson decaying into two photons in the mass range 128 to 132 GeV. The largest excess of events above the expected standard model background is observed for a Higgs boson mass hypothesis of 124 GeV with a local significance of 3.1σ . The global significance of observing an excess with a local significance ⩾3.1σ anywhere in the search range 110–150 GeV is estimated to be 1.8σ. More data are required to ascertain the origin of this excess.United States. Dept. of EnergyNational Science Foundation (U.S.

Search for narrow resonances using the dijet mass spectrum in pp collisions at √s=8 TeV

Results are presented of a search for the production of new particles decaying to pairs of partons (quarks, antiquarks, or gluons), in the dijet mass spectrum in proton-proton collisions at √s=8  TeV. The data sample corresponds to an integrated luminosity of 4.0  fb[superscript -1], collected with the CMS detector at the LHC in 2012. No significant evidence for narrow resonance production is observed. Upper limits are set at the 95% confidence level on the production cross section of hypothetical new particles decaying to quark-quark, quark-gluon, or gluon-gluon final states. These limits are then translated into lower limits on the masses of new resonances in specific scenarios of physics beyond the standard model. The limits reach up to 4.8 TeV, depending on the model, and extend previous exclusions from similar searches performed at lower collision energies. For the first time mass limits are set for the Randall–Sundrum graviton model in the dijet channel.United States. Dept. of EnergyNational Science Foundation (U.S.

Search for exotic resonances decaying into WZ/ZZ in pp collisions at √s=7 TeV

Journal of High Energy Physics 2013.2 (2013): 036 reproduced by permission of Scuola Internazionale Superiore di Studi Avanzati (SISSA)Artículo escrito por un elevado número de autores, solo se referencian el que aparece en primer lugar, el nombre del grupo de colaboración, si le hubiere, y los autores pertenecientes a la UAMA search for new exotic particles decaying to the VZ final state is performed, where V is either a W or a Z boson decaying into two overlapping jets and the Z decays into a pair of electrons, muons or neutrinos. The analysis uses a data sample of pp collisions corresponding to an integrated luminosity of 5 fb-1 collected by the CMS experiment at the LHC at √s=7 TeV in 2011. No significant excess is observed in the mass distribution of the VZ candidates compared with the background expectation from standard model processes. Model-dependent upper limits at the 95% confidence level are set on the product of the cross section times the branching fraction of hypothetical particles decaying to the VZ final state as a function of mass. Sequential standard model W′ bosons with masses between 700 and 940 GeV are excluded. In the Randall-Sundrum model for graviton resonances with a coupling parameter of 0.05, masses between 750 and 880 GeV are also exclude