NMR and mutagenesis evidence for an I domain allosteric site that regulates lymphocyte function-associated antigen 1 ligand binding

The leukocyte integrin, lymphocyte function-associated antigen 1 (LFA-1) (CD11a/CD18), mediates cell adhesion and signaling in inflammatory and immune responses. To support these functions, LFA-1 must convert from a resting to an activated state that avidly binds its ligands such as intercellular adhesion molecule 1 (ICAM-1). Biochemical and x-ray studies of the Mac-1 (CD11b/CD18) I domain suggest that integrin activation could involve a conformational change of the C-terminal α-helix. We report the use of NMR spectroscopy to identify CD11a I domain residues whose resonances are affected by binding to ICAM-1. We observed two distinct sites in the CD11a I domain that were affected. As expected from previous mutagenesis studies, a cluster of residues localized around the metal ion-dependent adhesion site (MIDAS) was severely perturbed on ICAM-1 binding. A second cluster of residues distal to the MIDAS that included the C-terminal α-helix of the CD11a I domain was also affected. Substitution of residues in the core of this second I domain site resulted in constitutively active LFA-1 binding to ICAM-1. Binding data indicates that none of the 20 substitution mutants we tested at this second site form an essential ICAM-1 binding interface. We also demonstrate that residues in the I domain linker sequences can regulate LFA-1 binding. These results indicate that LFA-1 binding to ICAM-1 is regulated by an I domain allosteric site (IDAS) and that this site is structurally linked to the MIDAS.

NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans

The solution structure of the three-heme electron transfer protein cytochrome c7 from Desulfuromonas acetoxidans is reported. The determination of the structure is obtained through NMR spectroscopy on the fully oxidized, paramagnetic form. The richness of structural motifs and the presence of three prosthetic groups in a protein of 68 residues is discussed in comparison with the four-heme cytochromes c3 already characterized through x-ray crystallography. In particular, the orientation of the three hemes present in cytochrome c7 is similar to that of three out of four hemes of cytochromes c3. The reduction potentials of the individual hemes, which have been obtained through the sequence-specific assignment of the heme resonances, are discussed with respect to the properties of the protein matrix. This information is relevant for any attempt to understand the electron transfer pathway.

Unusual 1H NMR chemical shifts support (His) Cɛ1—H⋅⋅⋅O⩵C H-bond: Proposal for reaction-driven ring flip mechanism in serine protease catalysis

13C-selective NMR, combined with inhibitor perturbation experiments, shows that the Cɛ1—H proton of the catalytic histidine in resting α-lytic protease and subtilisin BPN′ resonates, when protonated, at 9.22 ppm and 9.18 ppm, respectively, which is outside the normal range for such protons and ≈0.6 to 0.8 ppm further downfield than previously reported. They also show that the previous α-lytic protease assignments [Markley, J. L., Neves, D. E., Westler, W. M., Ibanez, I. B., Porubcan, M. A. & Baillargeon, M. W. (1980) Front. Protein Chem. 10, 31–61] were to signals from inactive or denatured protein. Simulations of linewidth vs. pH demonstrate that the true signal is more difficult to detect than corresponding signals from inactive derivatives, owing to higher imidazole pKa values and larger chemical shift differences between protonated and neutral forms. A compilation and analysis of available NMR data indicates that the true Cɛ1—H signals from other serine proteases are similarly displaced downfield, with past assignments to more upfield signals probably in error. The downfield displacement of these proton resonances is shown to be consistent with an H-bond involving the histidine Cɛ1—H as donor, confirming the original hypothesis of Derewenda et al. [Derewenda, Z. S., Derewenda, U. & Kobos, P. M. (1994) J. Mol. Biol. 241, 83–93], which was based on an analysis of literature x-ray crystal structures of serine hydrolases. The invariability of this H-bond among enzymes containing Asp-His-Ser triads indicates functional importance. Here, we propose that it enables a reaction-driven imidazole ring flip mechanism, overcoming a major dilemma inherent in all previous mechanisms, namely how these enzymes catalyze both the formation and productive breakdown of tetrahedral intermediates.

A nicked duplex decamer DNA with a PEG6 tether

A dumbbell double-stranded DNA decamer tethered with a hexaethylene glycol linker moiety (DDSDPEG), with a nick in the centre of one strand, has been synthesised. The standard NMR methods, E.COSY, TOCSY, NOESY and HMQC, were used to measure 1H, 31P and T1 spectral parameters. Molecular modelling using rMD-simulated annealing was used to compute the structure. Scalar couplings and dipolar contacts show that the molecule adopts a right-handed B-DNA helix in 38 mM phosphate buffer at pH 7. Its high melting temperature confirms the good base stacking and stability of the duplex. This is partly attributed to the presence of the PEG6 linker at both ends of the duplex that restricts the dynamics of the stem pentamers and thus stabilises the oligonucleotide. The inspection of the global parameters shows that the linker does not distort the B-DNA geometry. The computed structure suggests that the presence of the nick is not disturbing the overall tertiary structure, base pair geometry or duplex base pairing to a substantial extent. The nick has, however, a noticeable impact on the local geometry at the nick site, indicated clearly by NMR analysis and reflected in the conformational parameters of the computed structure. The 1H spectra also show much sharper resonances in the presence of K+ indicating that conformational heterogeneity of DDSDPEG is reduced in the presence of potassium as compared to sodium or caesium ions. At the same time the 1H resonances have longer T1 times. This parameter is suggested as a sensitive gauge of stabilisation.

Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR

We have used 19F NMR to analyze the metal ion-induced folding of the hammerhead ribozyme by selective incorporation of 5fluorouridine. We have studied the chemical shift and linewidths of 19F resonances of 5-fluorouridine at the 4 and 7 positions in the ribozyme core as a function of added Mg2+. The data fit well to a simple two-state model whereby the formation of domain 1 is induced by the noncooperative binding of Mg2+ with an association constant in the range of 100 to 500 M−1, depending on the concentration of monovalent ions present. The results are in excellent agreement with data reporting on changes in the global shape of the ribozyme. However, the NMR experiments exploit reporters located in the center of the RNA sections undergoing the folding transitions, thereby allowing the assignment of specific nucleotides to the separate stages. The results define the folding pathway at high resolution and provide a time scale for the first transition in the millisecond range.

Observation via one-dimensional 13Calpha NMR of local conformational substates in thermal unfolding equilibria of a synthetic analog of the GCN4 leucine zipper.

Synthesis of a 33-residue, capped leucine zipper analogous to that in GCN4 is reported. Histidine and arginine residues are mutated to lysine to reduce the unfolding temperature. CD and ultracentrifugation studies indicate that the molecule is a two-stranded coiled coil under benign conditions. Versions of the same peptide are made with 99% 13Calpha at selected sites. One-dimensional 13C NMR spectra are assigned by inspection and used to study thermal unfolding equilibria over the entire transition from 8 to 73 degrees C. Spectra at the temperature extremes establish the approximate chemical shifts for folded and unfolded forms at each labeled site. Resonances for each amino acid appear at both locations at intermediate T, indicating that folded and unfolded forms interconvert slowly (> >2 ms) on the NMR time scale. Moreover, near room temperature, the structured form's resonance is double at several, but not all, sites, indicating at least two slowly interconverting, structured, local conformational substates. Analysis of the dynamics is possible. For example, near room temperature at the Val-9, Ala-24, and Gly-31 positions, the equilibrium constant for interconversion of the two structured forms is near unity and the time scale is > or= 10-20 ms.

Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.

The measurement of dipolar contributions to the splitting of 15N resonances of 1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported. The splittings appear as small field-dependent perturbations of normal scalar couplings. Assignment of more than 90 resonances to specific sequential sites in the protein allows correlation of the dipolar contributions with predictions based on the known susceptibility and known structure of the protein. Implications as an additional source of information for protein structure determination in solution are discussed.

Stopped-flow NMR spectroscopy: real-time unfolding studies of 6-19F-tryptophan-labeled Escherichia coli dihydrofolate reductase.

Escherichia coli dihydrofolate reductase (DHFR; EC 1.5.1.3) contains five tryptophan residues that have been replaced with 6-19F-tryptophan. The 19F NMR assignments are known in the native, unliganded form and the unfolded form. We have used these assignments with stopped-flow 19F NMR spectroscopy to investigate the behavior of specific regions of the protein in real time during urea-induced unfolding. The NMR data show that within 1.5 sec most of the intensities of the native 19F resonances of the protein are lost but only a fraction (approximately 20%) of the intensities of the unfolded resonances appears. We postulate that the early disappearance of the native resonances indicates that most of the protein rapidly forms an intermediate in which the side chains have considerable mobility. Stopped-flow far-UV circular dichroism measurements indicate that this intermediate retains native-like secondary structure. Eighty percent of the intensities of the NMR resonances assigned to the individual tryptophans in the unfolded state appear with similar rate constants (k approximately 0.14 sec-1), consistent with the major phase of unfolding observed by stopped-flow circular dichroism (representing 80% of total amplitude). These data imply that after formation of the intermediate, which appears to represent an expanded structural form, all regions of the protein unfold at the same rate. Stopped-flow measurements of the fluorescence and circular dichroism changes associated with the urea-induced unfolding show a fast phase (half-time of about 1 sec) representing 20% of the total amplitude in addition to the slow phase mentioned above. The NMR data show that approximately 20% of the total intensity for each of the unfolded tryptophan resonances is present at 1.5 sec, indicating that these two phases may represent the complete unfolding of the two different populations of the native protein.

Submillisecond folding of monomeric lambda repressor.

The folding kinetics of a truncated form of the N-terminal domain of phage lambda repressor [lambda 6-85] has been investigated by using the technique of dynamic NMR. lambda 6-85 has been shown previously to fold in a purely two-state fashion. This allows the determination of folding and unfolding rates from simulation of the exchange-broadened aromatic resonances of Tyr-22. The folding kinetics were determined over a range of 1.35 to 3.14 M urea. The urea dependence of both folding and unfolding rate constants is exponential, suggesting that the rate-determining step is invariant at the urea concentrations studied. The folding and unfolding rates extrapolated to 0 M urea at 37 degrees C are 3600 +/- 400 s-1 and 27 +/- 6 s-1, respectively. The observed lambda 6-85 folding rate constant exceeds that of other fast-folding globular proteins by a factor of 14-54. The urea dependence of the folding and unfolding rate constants suggests that the transition state of the rate-determining step is considerably more exposed to solvent than previously studied protein-folding transition states. The surprising rapidity of lambda 6-85 folding and unfolding may be the consequence of its all-helical secondary structure. These kinetic results clearly demonstrate that all of the fundamental events of protein folding can occur on the submillisecond time scale.

Junções moleculares e agregados de nanobastões de ouro: um estudo SERS

A Espectroscopia Raman Intensificada pela Superfície (SERS) é um efeito de intensificação da intensidade Raman de uma molécula adsorvida numa superfície metálica nanoestruturada. Esta característica permite a utilização do SERS na caracterização vibracional de sistemas como junções moleculares (JM) (JM são sistemas constituídos de fios moleculares sintetizados em junções do tipo metal|fiomolecular|metal) e, no entendimento de quais características morfológicas de agregados metálicos mais influenciariam no sinal SERS obtido. Portanto, esta tese apresenta os seguintes objetivos: (a) síntese e caracterização de substratos SERS ativos, nanoesferas (AuNE) e nanobastões (AuNB) de ouro e eletrodo de ouro ativado eletroquimicamente; (b) síntese e caracterização SERS de fios moleculares em JM; (c) estudo do acoplamento plasmônico entre as superfícies metálicas em JM; (d) correlação entre SERS - morfologia de agregados individuais de AuNB. Os fios moleculares estudados foram os da família das oligofeniliminas (OPI) e, no melhor do nosso entendimento, esta foi a primeira vez que fios moleculares desta família foram caracterizados por Raman e SERS. As JM apresentaram um comportamento SERS não esperado. Enquanto para o modo vibracional, v(CS), a intensidade da banda se apresentou constante com o aumento do espaçamento entre as nanoestruturas metálicas (para distâncias de até 5 nm), o modo vibracional, β(CH), teve a intensidade de sua banda aumentada. Este comportamento foi explicado considerando a diferente natureza da interação dos plasmons nas JM, sendo estas interações do tipo, ressonância de plasmon de superfície (LSPR) - dipolo imagem, para ambos os modos. No entanto, para o modo β(CH) existe também uma intensificação extra devido ao aumento da polarizabilidade dos fios moleculares com o aumento do número de unidades. A correlação SERS - morfologia dos agregados de AuNB indicam que, para agregados onde predominam interações ponta a ponta, os espectros SERS apresentavam uma maior intensidade quando comparados com aqueles em que interações lado a lado predominavam. No entanto, este comportamento não foi observado para agregados contendo mais do que cinco nanopartículas onde estes dois tipos de interações ocorrem indicando que deve existir um acoplamento dos plasmons destes dois tipos de interações contribuindo para maiores valores de intensidade SERS.

Avaliação da integridade estrutural de elementos de concreto armado a partir das propriedades modais obtidas por técnicas de excitações aleatórias e transientes

A análise dinâmica experimental tem sido amplamente pesquisada como uma ferramenta de avaliação de integridade de estruturas de concreto armado. Existem técnicas de identificação de danos baseadas em propriedades modais como frequências de ressonâncias, deformadas modais, curvaturas modais e amortecimento. Há também técnicas baseadas na não linearidade da resposta dinâmica, que apesar do grande potencial na detecção de danos, têm sido pouco exploradas nos últimos anos. Este trabalho tem por objetivo avaliar a integridade estrutural de vigas de concreto armado através do comportamento da resposta dinâmica. Foram realizados ensaios dinâmicos em duas vigas de concreto armado com 3,5 m de comprimento, 25 cm de largura, 35 cm de altura e idênticas taxas de armaduras, mas configuradas com barras de aço de diferentes diâmetros, 2 ϕ 16 mm e 8 ϕ 8 mm, respectivamente. Tais vigas, inicialmente íntegras, foram submetidas a ciclos de carregamento e descarregamento com intensidades crescentes até atingir a ruptura do elemento. Após cada ciclo, as propriedades dinâmicas foram avaliadas experimentalmente, com o emprego de técnicas de excitação por sinais do tipo aleatório e tipo transiente, respectivamente, visando determinar parâmetros que indiquem a deterioração gradativa do elemento. Nesses ensaios dinâmicos aplicaram-se diferentes amplitudes da força de excitação. Verificou-se que o aumento da amplitude da força dinâmica de excitação provocou reduções nos valores das frequências de ressonância de 1,1% e 2,4%, associadas, respectivamente, às excitações aleatórias e transientes; e um comportamento não linear dos índices de amortecimento, associados às excitações aleatórias, mantendo um crescimento linear com as excitações transientes. Constatou-se, ainda, que os valores das frequências de ressonância decrescem com a redução de rigidez mecânica, diminuída com o aumento do nível de fissuração induzido nos modelos. Já os valores dos índices de amortecimento, após cada ciclo, se comportaram de forma não linear e assumiram diferentes valores, conforme a técnica de excitação empregada. Acredita-se que esta não linearidade está relacionada aos danos provocados no elemento pela solicitação estrutural e, por consequência, ao processo de como a dissipação de energia é empregada no processo de instauração, configuração e propagação das fissuras nos elementos de concreto armado.

Erratum: Suppression of localization in kronig-penney models with correlated disorder (Vol. 49, PG 147, 1994)

We consider the electron dynamics and transport properties of one-dimensional continuous models with random, short-range correlated impurities. We develop a generalized Poincare map formalism to cast the Schrodinger equation for any potential into a discrete set of equations, illustrating its application by means of a specific example. We then concentrate on the case of a Kronig-Penney model with dimer impurities. The previous technique allows us to show that this model presents infinitely many resonances (zeroes of the reflection coefficient at a single dimer) that give rise to a band of extended states, in contradiction with the general viewpoint that all one-dimensional models with random potentials support only localized states. We report on exact transfer-matrix numerical calculations of the transmission coefFicient, density of states, and localization length for various strengths of disorder. The most important conclusion so obtained is that this kind of system has a very large number of extended states. Multifractal analysis of very long systems clearly demonstrates the extended character of such states in the thermodynamic limit. In closing, we brieBy discuss the relevance of these results in several physical contexts.

Estimated chronologic ages of benthic microfossil events in ODP Site 105-647 (Table 1)

Benthic foraminifers were examined from the Paleogene of Ocean Drilling Program (ODP) Site 647 and Deep Sea Drilling Program (DSDP) Site 112 in the southern Labrador Sea. The Paleogene sequence of the deep Labrador Sea can be subdivided into seven assemblages, based on the ranges and relative abundance of characteristic taxa. The first occurrences (FOs) and last occurrences (LOs) of important benthic taxa are calibrated to a standard biochronology, by interpolating from our age model for Site 647. The biostratigraphy of Site 647 is used to improve the age estimates of Site112 cores. Fifteen microfossil events in Site 647 also are found in the sedimentary wedge along the Labrador Margin. A comparison of the probabilistic microfossil sequence from the Labrador Margin with that at Site 647 yields four isochronous benthic foraminifer LOs. Two new species are described from Sites 647 and 112: Hyperammina kenmilleri, Kaminski n.sp., and Ammodiscus nagyi Kaminski n.sp. Significant faunal turnovers are observed at the Ypresian/Lutetian and Eocene/Oligocene boundaries. The Ypresian/Lutetian boundary is characterized by a Glomospira-facies and is attributed to a rise in the CCD (carbonate compensation depth) associated with the NP14 lowstand in sea level. The Eocene/Oligocene boundary is delimited by the LO of Spiroplectammina spectabilis and Reticulophragmium amplectens. The change from an Eocene agglutinated assemblageto a predominantly calcareous assemblage in the early Oligocene took place gradually, over a period of about 4 Ma, but the rate of change accelerated near the boundary. This faunal turnover is attributed to changes in the preservationof agglutinated foraminifers, as delicate species disappeared first. Increasingly poorer preservation of agglutinated foraminifers in the late Eocene to earliest Oligocene reflects the first appearance of cool, nutrient-poor deep water in the southern Labrador Sea. The approximately coeval disappearance of agglutinated assemblages along the Labrador Margin was caused by a regional trend from slope to shelf environments, accentuated by the 'mid'-Oligocene lowstand in sea level.

Chemical analyses of the clay fraction in selected samples of Sediment core KS09 (Table 2)

A deep-sea core over 16 m long from the crestal area of the Mediterranean Ridge has been investigated with different techniques, including quantitative micropaleontology, stable isotopes (measured on the epipelagic species Globigerinoides ruber and on the mesopelagic species Globorotalia inflata), and clay mineralogy. The resulting record of climatic fluctuations can be cross correlated to other Mediterranean cores by means of isochronous lithologies (tephra layers and sapropels). The climatic record of the Mediterranean is similar in character, phase, and chronology to the records investigated in the equatorial Pacific and in the Caribbean. Isotope stages 1 to 17 have been recognized. Cyclically repeated stagnant cycles resulting in sapropel deposition complicate both the isotopic and the faunal signal. The isotopic investigations reveal that the temperature change in the surface layers of the eastern Mediterranean was no greater than 8°C in the late "glacial" Pleistocene. The chronostratigraphic and biostratigraphic interpretation of Core KS09 indicate that the mean sedimentation rate was 2.4 cm/1000 years, a value very close to the 2.5 cm/1000 years calculated for the entire Quaternary section at DSDP Site 125, also located in the crestal area of the Mediterranean Ridge in the Ionian Basin. The base of KS09 is likely to be very close to the Brunhes/Matuyama boundary dated at 0.7 my.

Sr and Nd composition, stable oxygen isotope record and lithogenic flux in eastern Mediterranean sediments

Isotopic ratios of Sr and Nd from lithogenic components of three isochronous core sections recovered from an east-west transect in the Eastern Mediterranean Sea (EMS) have been analyzed. The data are used for a quantitative estimate of the temporal and spatial variation of detrital flux to the EMS, assuming Saharan dust and Aegean/Nile particulate matter as dominant end members. It was established that the carbonate-free Saharan dust flux during deposition of the nonsapropel layers of marine oxygen isotope stage 5.4 (MIS 5.4) was similar to the present flux. During the deposition of sapropels S5 and S6, however, the Saharan dust input was drastically reduced and was not balanced by a change in the riverine influx at this time. Denser vegetation cover during more humid conditions may have reduced physical erosion and sediment removal in the source area. During marine oxygen isotope stage 6.2 (MIS 6.2) a pronounced increase of Saharan dust and detrital influx from the Aegean region is evident and implies more arid conditions in the southern and northern catchment areas. During this period, intersite variations are interpreted in terms of their geographic location relative to the seaways connecting the Aegean Sea and EMS. The width of the straits and hence the amount of sediment entering the eastern basins may have been affected by a low sea level that impeded interbasin sediment dispersal.