Ribosomes can slide over and beyond “hungry” codons, resuming protein chain elongation many nucleotides downstream

In cells subjected to moderate aminoacyl-tRNA limitation, the peptidyl-tRNA–ribosome complex stalled at the “hungry” codon can slide well beyond it on the messenger RNA and resume translation further downstream. This behavior is proved by unequivocal amino acid sequence data, showing a protein that lacks the bypassed sequence encoded between the hungry codon and specific landing sites. The landing sites are codons cognate to the anticodon of the peptidyl-tRNA. The efficiency of this behavior can be as high as 10–20% but declines with the length of the slide. Interposition of “trap” sites (nonproductive landing sites) in the bypassed region reduces the frequency of successful slides, confirming that the ribosome–peptidyl-tRNA complex passes through the untranslated region of the message. This behavior appears to be quite general: it can occur at the two kinds of hungry codons tested, AUA and AAG; the sliding peptidyl-tRNA can be any of three species tested, phenylalanine, tyrosine, or leucine tRNA; the peptidyl component can be either of two very different peptide sequences; and translation can resume at any of the three codons tested.

Free energy of burying hydrophobic residues in the interface between protein subunits

We have obtained an experimental estimate of the free energy change associated with variations at the interface between protein subunits, a subject that has raised considerable interest since the concept of accessible surface area was introduced by Lee and Richards [Lee, B. & Richards, F. M. (1971) J. Mol. Biol. 55, 379–400]. We determined by analytical ultracentrifugation the dimer–tetramer equilibrium constant of five single and three double mutants of human Hb. One mutation is at the stationary α1β1 interface, and all of the others are at the sliding α1β2 interface where cleavage of the tetramer into dimers and ligand-linked allosteric changes are known to occur. A surprisingly good linear correlation between the change in the free energy of association of the mutants and the change in buried hydrophobic surface area was obtained, after corrections for the energetic cost of losing steric complementarity at the αβ dimer interface. The slope yields an interface stabilization free energy of −15 ± 1.2 cal/mol upon burial of 1 Å2 of hydrophobic surface, in very good agreement with the theoretical estimate given by Eisenberg and McLachlan [Eisenberg, D. & McLachlan, A. D. (1986) Nature (London) 319, 199–203].

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli

DNA polymerase V, composed of a heterotrimer of the DNA damage-inducible UmuC and UmuD\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathrm{_{2}^{^{\prime}}}}\end{equation*}\end{document} proteins, working in conjunction with RecA, single-stranded DNA (ssDNA)-binding protein (SSB), β sliding clamp, and γ clamp loading complex, are responsible for most SOS lesion-targeted mutations in Escherichia coli, by catalyzing translesion synthesis (TLS). DNA polymerase II, the product of the damage-inducible polB (dinA ) gene plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Replication-restart takes place almost immediately after the DNA is damaged (≈2 min post-UV irradiation), whereas TLS occurs after pol V is induced ≈50 min later. We discuss recent data for pol V-catalyzed TLS and pol II-catalyzed replication-restart. Specific roles during TLS for pol V and each of its accessory factors have been recently determined. Although the precise molecular mechanism of pol II-dependent replication-restart remains to be elucidated, it has recently been shown to operate in conjunction with RecFOR and PriA proteins.

Detecting the conformational change of transmembrane signaling in a bacterial chemoreceptor by measuring effects on disulfide cross-linking in vivo.

Transmembrane signaling by bacterial chemoreceptors is thought to involve relative movement among the four transmembrane helices of the homodimer. We assayed that movement by measuring effects of ligand occupancy on rates of oxidative cross-linking between cysteines introduced into neighboring helices of the transmembrane domain of chemoreceptor Trg from Escherichia coli. Measurements were done on chemoreceptors in their native environment, intact cells that were motile and chemotactically responsive. Receptor occupancy did not appear to cause drastic rearrangement of the four-helix structure since, among 67 cysteine pairs tested, the same 19 exhibited oxidative cross-linking in the presence or absence of saturating chemoattractant. However, occupancy did cause subtle changes that were detected as effects on rates of cross-linking. Among the seven disulfides appropriate for measurements of initial rates of formation, ligand occupancy had significant and different effects on all three cross-links that connected the two helices within a subunit but had minimal effects on the four that spanned the packing interface between subunits. This constitutes direct evidence that the conformational change of transmembrane signaling involves significant movement within a subunit and minimal movement between subunits, a pattern deduced from several previous studies and now documented directly. Among possible modes of movement between the two helices of a subunit, axial sliding of one helix relative to the other was the conformational change that best accounted for the observed effects on cross-linking.

ATPase activity of Escherichia coli Rep helicase crosslinked to single-stranded DNA: implications for ATP driven helicase translocation.

To examine the coupling of ATP hydrolysis to helicase translocation along DNA, we have purified and characterized complexes of the Escherichia coli Rep protein, a dimeric DNA helicase, covalently crosslinked to a single-stranded hexadecameric oligodeoxynucleotide (S). Crosslinked Rep monomers (PS) as well as singly ligated (P2S) and doubly ligated (P2S2) Rep dimers were characterized. The equilibrium and kinetic constants for Rep dimerization as well as the steady-state ATPase activities of both PS and P2S crosslinked complexes were identical to the values determined for un-crosslinked Rep complexes formed with dT16. Therefore, ATP hydrolysis by both PS and P2S complexes are not coupled to DNA dissociation. This also rules out a strictly unidirectional sliding mechanism for ATP-driven translocation along single-stranded DNA by either PS or the P2S dimer. However, ATP hydrolysis by the doubly ligated P2S2 Rep dimer is coupled to single-stranded DNA dissociation from one subunit of the dimer, although loosely (low efficiency). These results suggest that ATP hydrolysis can drive translocation of the dimeric Rep helicase along DNA by a "rolling" mechanism where the two DNA binding sites of the dimer alternately bind and release DNA. Such a mechanism is biologically important when one subunit binds duplex DNA, followed by subsequent unwinding.

Implications of fault constitutive properties for earthquake prediction.

The rate- and state-dependent constitutive formulation for fault slip characterizes an exceptional variety of materials over a wide range of sliding conditions. This formulation provides a unified representation of diverse sliding phenomena including slip weakening over a characteristic sliding distance Dc, apparent fracture energy at a rupture front, time-dependent healing after rapid slip, and various other transient and slip rate effects. Laboratory observations and theoretical models both indicate that earthquake nucleation is accompanied by long intervals of accelerating slip. Strains from the nucleation process on buried faults generally could not be detected if laboratory values of Dc apply to faults in nature. However, scaling of Dc is presently an open question and the possibility exists that measurable premonitory creep may precede some earthquakes. Earthquake activity is modeled as a sequence of earthquake nucleation events. In this model, earthquake clustering arises from sensitivity of nucleation times to the stress changes induced by prior earthquakes. The model gives the characteristic Omori aftershock decay law and assigns physical interpretation to aftershock parameters. The seismicity formulation predicts large changes of earthquake probabilities result from stress changes. Two mechanisms for foreshocks are proposed that describe observed frequency of occurrence of foreshock-mainshock pairs by time and magnitude. With the first mechanism, foreshocks represent a manifestation of earthquake clustering in which the stress change at the time of the foreshock increases the probability of earthquakes at all magnitudes including the eventual mainshock. With the second model, accelerating fault slip on the mainshock nucleation zone triggers foreshocks.

Rock friction and its implications for earthquake prediction examined via models of Parkfield earthquakes.

The friction of rocks in the laboratory is a function of time, velocity of sliding, and displacement. Although the processes responsible for these dependencies are unknown, constitutive equations have been developed that do a reasonable job of describing the laboratory behavior. These constitutive laws have been used to create a model of earthquakes at Parkfield, CA, by using boundary conditions appropriate for the section of the fault that slips in magnitude 6 earthquakes every 20-30 years. The behavior of this model prior to the earthquakes is investigated to determine whether or not the model earthquakes could be predicted in the real world by using realistic instruments and instrument locations. Premonitory slip does occur in the model, but it is relatively restricted in time and space and detecting it from the surface may be difficult. The magnitude of the strain rate at the earth's surface due to this accelerating slip seems lower than the detectability limit of instruments in the presence of earth noise. Although not specifically modeled, microseismicity related to the accelerating creep and to creep events in the model should be detectable. In fact the logarithm of the moment rate on the hypocentral cell of the fault due to slip increases linearly with minus the logarithm of the time to the earthquake. This could conceivably be used to determine when the earthquake was going to occur. An unresolved question is whether this pattern of accelerating slip could be recognized from the microseismicity, given the discrete nature of seismic events. Nevertheless, the model results suggest that the most likely solution to earthquake prediction is to look for a pattern of acceleration in microseismicity and thereby identify the microearthquakes as foreshocks.

The neck region of the myosin motor domain acts as a lever arm to generate movement.

The myosin head consists of a globular catalytic domain that binds actin and hydrolyzes ATP and a neck domain that consists of essential and regulatory light chains bound to a long alpha-helical portion of the heavy chain. The swinging neck-level model assumes that a swinging motion of the neck relative to the catalytic domain is the origin of movement. This model predicts that the step size, and consequently the sliding velocity, are linearly related to the length of the neck. We have tested this point by characterizing a series of mutant Dictyostelium myosins that have different neck lengths. The 2xELCBS mutant has an extra binding site for essential light chain. The delta RLCBS mutant myosin has an internal deletion that removes the regulatory light chain binding site. The delta BLCBS mutant lacks both light chain binding sites. Wild-type myosin and these mutant myosins were subjected to the sliding filament in vitro motility assay. As expected, mutants with shorter necks move slower than wild-type myosin in vitro. Most significantly, a mutant with a longer neck moves faster than the wild type, and the sliding velocities of these myosins are linearly related to the neck length, as predicted by the swinging neck-lever model. A simple extrapolation to zero speed predicts that the fulcrum point is in the vicinity of the SH1-SH2 region in the catalytic domain.

The role of surface loops (residues 204-216 and 627-646) in the motor function of the myosin head.

A characteristic feature of all myosins is the presence of two sequences which despite considerable variations in length and composition can be aligned with loops 1 (residues 204-216) and 2 (residues 627-646) in the chicken myosin-head heavy chain sequence. Recently, an intriguing hypothesis has been put forth suggesting that diverse performances of myosin motors are achieved through variations in the sequences of loops 1 and 2 [Spudich, J. (1994) Nature (London) 372, 515-518]. Here, we report on the study of the effects of tryptic digestion of these loops on the motor and enzymatic functions of myosin. Tryptic digestions of myosin, which produced heavy meromyosin (HMM) with different percentages of molecules cleaved at both loop 1 and loop 2, resulted in the consistent decrease in the sliding velocity of actin filaments over HMM in the in vitro motility assays, did not affect the Vmax, and increased the Km values for actin-activated ATPase of HMM. Selective cleavage of loop 2 on HMM decreased its affinity for actin but did not change the sliding velocity of actin in the in vitro motility assays. The cleavage of loop 1 and HMM decreased the mean sliding velocity of actin in such assays by almost 50% but did not alter its affinity for HMM. To test for a possible kinetic determinant of the change in motility, 1-N6-ethenoadenosine diphosphate (epsilon-ADP) release from cleaved and uncleaved myosin subfragment 1 (S1) was examined. Tryptic digestion of loop 1 slightly accelerated the release of epsilon-ADP from S1 but did not affect the rate of epsilon-ADP release from acto-S1 complex. Overall, the results of this work support the hypothesis that loop 1 can modulate the motor function of myosin and suggest that such modulation involves a mechanism other than regulation of ADP release from myosin.

Cytoplasmic dynein is associated with slow axonal transport.

Neuronal function is dependent on the transport of materials from the cell body to the synapse via anterograde axonal transport. Anterograde axonal transport consists of several components that differ in both rate and protein composition. In fast transport, membranous organelles are moved along microtubules by the motor protein kinesin. The cytoskeleton and the cytomatrix proteins move in the two components of slow transport. While the mechanisms underlying slow transport are unknown, it has been hypothesized that the movement of microtubules in slow transport is generated by sliding. To determine whether dynein, a motor protein that causes microtubule sliding in flagella, may play a role in slow axonal transport, we identified the transport rate components with which cytoplasmic dynein is associated in rat optic nerve. Nearly 80% of the anterogradely moving dynein was associated with slow transport, whereas only approximately 15% of the dynein was associated with the membranous organelles of anterograde fast axonal transport. A segmental analysis of the transport of dynein through contiguous regions of the optic nerve and tract showed that dynein is associated with the microfilaments and other proteins of slow component b. Dynein from this transport component has the capacity to bind microtubules in vitro. These results are consistent with the hypothesis that cytoplasmic dynein generates the movement of microtubules in slow axonal transport. A model is presented to illustrate how dynein attached to the slow component b complex of proteins is appropriately positioned to generate force of the correct polarity to slide microtubules down the axon.

Do psicólogo no programa de residência multiprofissional em saúde: posição-sujeito, análise de discurso e psicanálise lacaniana

A residência multiprofissional em saúde é uma modalidade de ensino de pós graduação lato sensu, voltada para a educação em serviço. Emerge no contexto brasileiro como uma proposta complementar a fim de se atingir as metas e os princípios preconizados pelo sistema único de saúde (SUS), principalmente quanto à integralidade. Além de trazer implicações e lançar desafios ao exercício profissional do psicólogo, inserindo-o no entrelaçamento de campos densos e complexos (saúde, educação e políticas públicas), a modalidade propõe que profissionais com formações diferentes atuem num mesmo campo, com discussões e intervenções conjuntas. A questão que move a pesquisa é a posição-sujeito no programa de residência multiprofissional face ao modelo de educação-saúde vinculado. Assevera-se que a posição-sujeito é objeto discursivo deslizante (de tessitura simbólica) que toma em consideração o sujeito constituído no claudicar da linguagem e interpelado pelo inconsciente e que se manifesta como efeito de significantes em direção ao grande Outro. Para tal, vale-se da interface dos aportes teóricos da análise de discurso pêchetiana e da psicanálise lacaniana. A análise de discurso sustenta o discurso como efeito de sentidos mediados pela ideologia e ocupa-se, especialmente, da incursão da alteridade do discurso-outro sobre o mesmo. A psicanálise lacaniana, por sua vez, reitera a primazia do inconsciente estruturado como linguagem diante de um eu imaginário e versa para o sujeito marcado como falta que, dividido, faz do discurso o estatuto do significado. Assim, é proeminente na análise do objeto a metodologia indiciária dada ao caráter simbólico e cambiante da posição-sujeito no discurso. A análise se realizou mediante o dispositivo da interpretação como gesto analítico, que acompanha as elações próprias do objeto. O corpora é constituído por uma materialidade escrita e por uma oral. A escrita compõe-se de recortes de leis, portarias e resoluções que fundam a modalidade de residência multiprofissional e reforçam os ideias do sistema único de saúde; a materialidade oral compõe-se de recortes e fragmentos discursivos advindos da transcrição de supervisões realizadas mediante a prática clínica do psicólogo-residente na cena hospitalar. Da análise, conclui-se que a materialidade escrita se posta como campo-Outro que ordena a estrutura política da residência multiprofissional e direciona a manutenção da ordem e reprodução das relações hierárquicas mediante ideologia assujeitante. Essa materialidade, por sua vez, age como intradiscurso e reverbera-se na memória discursiva e na prática clínica. A posição-sujeito, no plano da articulação significante, faz deslizar e produzir sentidos que denotam ora a manutenção e reprodução de uma posição fusionada ao discurso médico, científico-positivista; ora a posição-sujeito é marcada pelo saber condicionado ao fetiche da mercadoria, deflagrando a ordem do capital nas insígnias da multiprofissionalidade e da educação permanente. O trabalho propiciou, enfim, acompanhar as transmutações da posição-sujeito, independentemente do indivíduo ou da naturalização de sentidos provenientes da função que exerce. O objeto posição-sujeito reiterou a construção da realidade a partir da condição faltante. É essa condição faltante e incompleta que outorga ao desejo o modo de o sujeito se posicionar desta e outra maneira - na formação, no trabalho, na vida.

Forças, momentos e coeficiente de atrito em teste de três pontos e em teste de resistência ao deslizamento com braquetes autoligáveis e fios 0.014\" utilizando um novo dispositivo

O objetivo principal do estudo é comparar o teste em 3 pontos com braquetes com o teste de resistência ao deslizamento utilizando um novo dispositivo que realiza a mensuração simultânea do coeficiente de atrito, das forças e dos momentos nos braquetes de ancoragem e da força de desativação no braquete desalinhado, exercidos por fios ortodônticos. Os objetivos secundários foram desenvolver o dispositivo e comparar, no teste em 3 pontos: (i) a influência, nas grandezas e no coeficiente de atrito cinético, da variação da simetria nas distâncias inter-braquetes, do tipo de braquete de ancoragem (canino ou 2º pré-molar), do deslocamento (3 ou 5mm) do braquete central, do sentido do desalinhamento (vestibular ou lingual) do braquete central e da marca de fio-braquete; (ii) as 3 formas de cálculo do coeficiente de atrito cinético; (iii) os 10 ciclos, para vestibular ou lingual, para verificar se eles são semelhantes ou não entre si. Foram utilizados braquetes autoligáveis (dentes 13, 14 e 15) e fios 0.014\'\' NiTi e CuNiTi das marcas Aditek e Ormco. O teste de resistência ao deslizamento foi realizado no desalinhamento lingual, nos dois deslocamentos e na configuração simétrica. O teste em 3 pontos com braquetes foi realizado no desalinhamento lingual e vestibular, nos dois deslocamentos e na configuração simétrica e assimétrica. Por meio da ANOVA, foram comparados, entre os dois tipos de teste: (A) as grandezas e o coeficiente de atrito e (B) o coeficiente de atrito gerado apenas no braquete de 2º pré-molar. Utilizando-se do mesmo teste estatístico foram comparados, no teste em 3 pontos com braquetes: (A) na configuração simétrica, algumas grandezas e o coeficiente de atrito advindos da variação da marca de fio-braquete, do deslocamento, do desalinhamento e do tipo de braquete; (B) algumas grandezas e o coeficiente de atrito gerados na configuração simétrica e assimétrica; (C) os valores das 3 formas de cálculo do coeficiente de atrito na configuração simétrica; e (D) algumas grandezas e o coeficiente de atrito encontrados nos 10 ciclos. Resultados: (A) a maioria dos valores das grandezas e do coeficiente de atrito gerados pelos dois tipos de teste foram diferentes estatisticamente; (B) o braquete de 2º pré-molar apresentou valores de coeficiente de atrito diferentes entre os dois tipos de teste; (C) na configuração simétrica, as variáveis foram estatisticamente significantes na maioria dos casos para as grandezas analisadas e para o coeficiente de atrito; (D) houve diferença entre a configuração simétrica e assimétrica; (E) o coeficiente de atrito baseado nas duas normais e na força de atrito se aproximou mais da realidade clínica e foi sensível à variação da geometria da relação fio-braquete; e (F) os 10 ciclos para lingual foram semelhantes entre si em 70% dos casos e os 10 ciclos para vestibular foram diferentes em 57% dos casos. Conclusões: o teste em 3 pontos com braquetes é diferente do teste de resistência ao deslizamento; a variação das configurações geométricas e da marca de fio-braquete pode influenciar nos valores das grandezas e do coeficiente de atrito cinético; os 10 ciclos para lingual foram mais semelhantes entre si que os 10 ciclos para vestibular.

Efeito do cobre como adição interfacial no sistema tribológico pino X disco.

O presente trabalho de mestrado teve como meta realizar um estudo do comportamento do cobre particulado em ensaios tribológicos do tipo pino contra disco. O cobre é atualmente utilizado em até 15% em massa das pastilhas de freios automotivos e tal utilização é responsável pela emissão de até 70% do cobre particulado presente no ar. Devido ao caráter carcinogênico do cobre, se faz necessária sua substituição. Foram realizados ensaios tribológicos pino disco com adição de diferentes meios interfaciais. Foram utilizados pares tribológicos aço/aço, em ensaios a seco de pino contra disco com adição de meio interfacial nanoparticulado de óxido de ferro, grafite e de cobre metálico em diferentes granulometrias (400 m, 20 m e 50 nm). Após os ensaios, amostras das superfícies de pinos e discos para cada uma das adições de cobre, bem como para a condição sem adição de meio interfacial, foram caracterizadas utilizando técnicas de microscopia eletrônica de varredura, de forma a entender o comportamento das partículas de cobre e sua contribuição para o coeficiente de atrito. As adições de cobre obtiveram os maiores coeficientes de atrito, e entre elas os coeficientes de atrito foram mais altos durante todos os ensaios para a adição de 50 nm, seguido de 20 m e 400 m. A análise das superfícies tribológicas em MEV mostrou heterogeneidade das superfícies ensaiadas em relação à presença de debris oxidados e camadas compactas. Observou-se a presença de cobre apenas nas superfícies ensaiadas com adição dos cobres de 50 nm e 20 m. A presença de um filme óxido compacto e contínuo foi observada apenas nas superfícies tribológicas ensaiadas sem adição de meio interfacial e com adição de cobre a 400 m.

Testing a new Free Core Nutation empirical model

The Free Core Nutation (FCN) is a free mode of the Earth's rotation caused by the different material characteristics of the Earth's core and mantle. This causes the rotational axes of those layers to slightly diverge from each other, resulting in a wobble of the Earth's rotation axis comparable to nutations. In this paper we focus on estimating empirical FCN models using the observed nutations derived from the VLBI sessions between 1993 and 2013. Assuming a fixed value for the oscillation period, the time-variable amplitudes and phases are estimated by means of multiple sliding window analyses. The effects of using different a priori Earth Rotation Parameters (ERP) in the derivation of models are also addressed. The optimal choice of the fundamental parameters of the model, namely the window width and step-size of its shift, is searched by performing a thorough experimental analysis using real data. The former analyses lead to the derivation of a model with a temporal resolution higher than the one used in the models currently available, with a sliding window reduced to 400 days and a day-by-day shift. It is shown that this new model increases the accuracy of the modeling of the observed Earth's rotation. Besides, empirical models determined from USNO Finals as a priori ERP present a slightly lower Weighted Root Mean Square (WRMS) of residuals than IERS 08 C04 along the whole period of VLBI observations, according to our computations. The model is also validated through comparisons with other recognized models. The level of agreement among them is satisfactory. Let us remark that our estimates give rise to the lowest residuals and seem to reproduce the FCN signal in more detail.

Turkey votes: Part II - Erdoğan reloaded. EPC Commentary, 3 April 2014

On 30 March, Turkey’s ruling Justice and Development Party (AKP) scooped a significant victory in local elections, taking almost 44 percent of the vote despite accusations of corruption, undermining the rule of law, fundamental rights and freedoms. While there have been claims of election fraud and the main opposition party, the Republican People’s Party (CHP), has demanded recounts in several cities including Istanbul and Ankara, it is clear that even allowing for some level of fraud the win was substantial and more than most people expected. Prime Minister Recep Tayyip Erdoğan has reached a juncture. He has two choices: return to the path of democracy after a period of democratic back-sliding which included passing several controversial reforms such as a new internet law which led to the recent banning of Twitter and Youtube; or alternatively he can forge ahead with his much talked of revenge campaign against those he has accused of creating a “parallel state” and conspiring to remove him from power. Given that Erdoğan viewed this election as a referendum on his popularity and leadership there is a serious risk that he will do the latter; using the significant mandate given to him to do whatever he wants, including further cracking down on democracy.