WW domain-mediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: The proline glycine and methionine-rich motif

Pre-mRNA splicing requires the bridging of the 5′ and 3′ ends of the intron. In yeast, this bridging involves interactions between the WW domains in the splicing factor PRP40 and a proline-rich domain in the branchpoint binding protein, BBP. Using a proline-rich domain derived from formin (a product of the murine limb deformity locus), we have identified a family of murine formin binding proteins (FBP’s), each of which contains one or more of a special class of tyrosine-rich WW domains. Two of these WW domains, in the proteins FBP11 and FBP21, are strikingly similar to those found in the yeast splicing factor PRP40. We show that FBP21 is present in highly purified spliceosomal complex A, is associated with U2 snRNPs, and colocalizes with splicing factors in nuclear speckle domains. Moreover, FBP21 interacts directly with the U1 snRNP protein U1C, the core snRNP proteins SmB and SmB′, and the branchpoint binding protein SF1/mBBP. Thus, FBP21 may play a role in cross-intron bridging of U1 and U2 snRNPs in the mammalian A complex.

Comparing protein–ligand interactions in solution and single crystals by Raman spectroscopy

By using a Raman microscope, we show that it is possible to probe the conformational states in protein crystals and crystal fragments under growth conditions (in hanging drops). The flavin cofactor in the enzyme para-hydroxybenzoate hydroxylase can assume two conformations: buried in the protein matrix (“in”) or essentially solvent-exposed (“out”). By using Raman difference spectroscopy, we previously have identified characteristic flavin marker bands for the in and out conformers in the solution phase. Now we show that the flavin Raman bands can be used to probe these conformational states in crystals, permitting a comparison between solution and crystal environments. The in or out marker bands are similar for the respective conformers in the crystal and in solution; however, significant differences do exist, showing that the environments for the flavin's isoalloxazine ring are not identical in the two phases. Moreover, the Raman-band widths of the flavin modes are narrower for both in and out conformers in the crystals, indicating that the flavin exists in a more limited range of closely related conformational states in the crystal than in solution. In general, the ability to compare detailed Raman data for complexes in crystals and solution provides a means of bridging crystallographic and solution studies.

Peopling the past: New perspectives on the ancient Maya

The new direction in Maya archaeology is toward achieving a greater understanding of people and their roles and their relations in the past. To answer emerging humanistic questions about ancient people's lives Mayanists are increasingly making use of new and existing scientific methods from archaeology and other disciplines. Maya archaeology is bridging the divide between the humanities and sciences to answer questions about ancient people previously considered beyond the realm of archaeological knowledge.

Excited-state dynamics in photosystem II: Insights from the x-ray crystal structure

The heart of oxygenic photosynthesis is photosystem II (PSII), a multisubunit protein complex that uses solar energy to drive the splitting of water and production of molecular oxygen. The effectiveness of the photochemical reaction center of PSII depends on the efficient transfer of excitation energy from the surrounding antenna chlorophylls. A kinetic model for PSII, based on the x-ray crystal structure coordinates of 37 antenna and reaction center pigment molecules, allows us to map the major energy transfer routes from the antenna chlorophylls to the reaction center chromophores. The model shows that energy transfer to the reaction center is slow compared with the rate of primary electron transport and depends on a few bridging chlorophyll molecules. This unexpected energetic isolation of the reaction center in PSII is similar to that found in the bacterial photosystem, conflicts with the established view of the photophysics of PSII, and may be a functional requirement for primary photochemistry in photosynthesis. In addition, the model predicts a value for the intrinsic photochemical rate constant that is 4 times that found in bacterial reaction centers.

Direct measurement of salt-bridge solvation energies using a peptide model system: implications for protein stability.

The solvation energies of salt bridges formed between the terminal carboxyl of the host pentapeptide AcWL- X-LL and the side chains of Arg or Lys in the guest (X) position have been measured. The energies were derived from octanol-to-buffer transfer free energies determined between pH 1 and pH 9. 13C NMR measurements show that the salt bridges form in the octanol phase, but not in the buffer phase, when the side chains and the terminal carboxyl group are charged. The free energy of salt-bridge formation in octanol is approximately -4 kcal/mol (1 cal = 4.184 J), which is equal to or slightly larger than the sum of the solvation energies of noninteracting pairs of charged side chains. This is about one-half the free energy that would result from replacing a charge pair in octanol with a pair of hydrophobic residues of moderate size. Therefore, salt bridging in octanol can change the favorable aqueous solvation energy of a pair of oppositely charged residues to neutral or slightly unfavorable but cannot provide the same free energy decrease as hydrophobic residues. This is consistent with recent computational and experimental studies of protein stability.

Interactions of protein antigens with antibodies.

There are now several crystal structures of antibody Fab fragments complexed to their protein antigens. These include Fab complexes with lysozyme, two Fab complexes with influenza virus neuraminidase, and three Fab complexes with their anti-idiotype Fabs. The pattern of binding that emerges is similar to that found with other protein-protein interactions, with good shape complementarity between the interacting surfaces and reasonable juxtapositions of polar residues so as to permit hydrogen-bond formation. Water molecules have been observed in cavities within the interface and on the periphery, where they often form bridging hydrogen bonds between antibody and antigen. For the most part the antigen is bound in the middle of the antibody combining site with most of the six complementarity-determining residues involved in binding. For the most studied antigen, lysozyme, the epitopes for four antibodies occupy approximately 45% of the accessible surface area. Some conformational changes have been observed to accompany binding in both the antibody and the antigen, although most of the information on conformational change in the latter comes from studies of complexes with small antigens.

Crystal structure of the membrane-exposed domain from a respiratory quinol oxidase complex with an engineered dinuclear copper center.

Cytochrome oxidase is a membrane protein complex that catalyzes reduction of molecular oxygen to water and utilizes the free energy of this reaction to generate a transmembrane proton gradient during respiration. The electron entry site in subunit II is a mixed-valence dinuclear copper center in enzymes that oxidize cytochrome c. This center has been lost during the evolution of the quinoloxidizing branch of cytochrome oxidases but can be restored by engineering. Herein we describe the crystal structures of the periplasmic fragment from the wild-type subunit II (CyoA) of Escherichia coli quinol oxidase at 2.5-A resolution and of the mutant with the engineered dinuclear copper center (purple CyoA) at 2.3-A resolution. CyoA is folded as an 11-stranded mostly antiparallel beta-sandwich followed by three alpha-helices. The dinuclear copper center is located at the loops between strands beta 5-beta 6 and beta 9-beta 10. The two coppers are at a 2.5-A distance and symmetrically coordinated to the main ligands that are two bridging cysteines and two terminal histidines. The residues that are distinct in cytochrome c and quinol oxidases are around the dinuclear copper center. Structural comparison suggests a common ancestry for subunit II of cytochrome oxidase and blue copper-binding proteins.

The CuA center of cytochrome-c oxidase: electronic structure and spectra of models compared to the properties of CuA domains.

The electronic structure and spectrum of several models of the binuclear metal site in soluble CuA domains of cytochrome-c oxidase have been calculated by the use of an extended version of the complete neglect of differential overlap/spectroscopic method. The experimental spectra have two strong transitions of nearly equal intensity around 500 nm and a near-IR transition close to 800 nm. The model that best reproduces these features consists of a dimer of two blue (type 1) copper centers, in which each Cu atom replaces the missing imidazole on the other Cu atom. Thus, both Cu atoms have one cysteine sulfur atom and one imidazole nitrogen atom as ligands, and there are no bridging ligands but a direct Cu-Cu bond. According to the calculations, the two strong bands in the visible region originate from exciton coupling of the dipoles of the two copper monomers, and the near-IR band is a charge-transfer transition between the two Cu atoms. The known amino acid sequence has been used to construct a molecular model of the CuA site by the use of a template and energy minimization. In this model, the two ligand cysteine residues are in one turn of an alpha-helix, whereas one ligand histidine is in a loop following this helix and the other one is in a beta-strand.

Use of binding energy by an RNA enzyme for catalysis by positioning and substrate destabilization.

A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a series of oligonucleotide substrates and products of the Tetrahymena ribozyme, which catalyzes a site-specific phosphodiester cleavage reaction: CCCUCUpA+G<-->CCCUCU-OH+GpA. The results suggest that this RNA enzyme, like protein enzymes, can utilize binding interactions to achieve substantial catalysis via entropic fixation and substrate destabilization. The stronger binding of the all-ribose oligonucleotide product compared to an analog with a terminal 3' deoxyribose residue gives an effective concentration of 2200 M for the 3' hydroxyl group, a value approaching those obtained with protein enzymes and suggesting the presence of a structurally well defined active site capable of precise positioning. The stabilization from tertiary binding interactions is 40-fold less for the oligonucleotide substrate than the oligonucleotide product, despite the presence of the reactive phosphoryl group in the substrate. This destabilization is accounted for by a model in which tertiary interactions away from the site of bond cleavage position the electron-deficient 3' bridging phosphoryl oxygen of the oligonucleotide substrate next to an electropositive Mg ion. As the phosphodiester bond breaks and this 3' oxygen atom develops a negative charge in the transition state, the weak interaction of the substrate with Mg2+ becomes strong. These strategies of "substrate destabilization" and "transition state stabilization" provide estimated rate enhancements of approximately 280- and approximately 60-fold, respectively. Analogous substrate destabilization by a metal ion or hydrogen bond donor may be used more generally by RNA and protein enzymes catalyzing reactions of phosphate esters.

Supramolecular coordination complexes as building blocks for porous and magnetic materials

In this work, new coordination polymers based on two different classes of synthons are presented. In addition, manganese-based metallacrowns of magnetic interest are studied, both in the solid state and in solution. Firstly, functionalized bispyrazolylmethane derivatives are employed as bridging ligands for the establishment of silver-based coordination polymers; the influence of the substituent groups and of the counterions on the supramolecular packing is also investigated. Secondly, the use of metallacrown (MC) complexes as building blocks for porous coordination polymers is discussed. The design of a new metallacrown species is presented, which shows the tendency of aggregating in the solid state to form coordination polymers. Two new coordination polymers are indeed reported, of which one is the first MC-based permanently porous coordination network ever presented. The solid resists solvent evacuation and exhibits gas uptake ability. Furthermore, the isolation and characterization of a new metallacryptate species based on manganese ions is described. The metal-rich structure comprises nine Mn(II)/Mn(III) ions and presents an inverse metallacrown core subunit that binds a μ3-O2- ion. The metallacryptate is isolated in high yields and stable in solution. Lastly, a family of 3d-4f heterometallic metallacrowns is characterized in solution by means of UV-Vis spectrophotometry and of paramagnetically shifted 1H-NMR. The lanthanide-induced shifts observed in the spectra are employed to describe the molecules behaviour in solution and are qualitatively related to the magnetic properties of the compounds.

Complexos de dirutênio com os fármacos ibuprofeno, ácido acetilsalicílico, naproxeno, indometacina, e com ácido y-linolêncio: Síntese, caracterização, avaliação da ação antiproliferativa sobre células tumorais e estudo da interação da unidade dimetálica com adenina e adenosina

Este trabalho tem como principal objetivo contribuir para o desenvolvimento de novos potenciais metalofármacos de rutênio. Nele são descritas a síntese, a caracterização e a avaliação da ação antiproliferativa de alguns complexos de dirutênio (II,III) com os fármacos antiinflamatórios não-esteróides (AINEs): ibuprofeno (ibp), ácido acetilsalicílico (aas), naproxeno (npx) e indometacina (ind) e também com o ácido γ-linolênico (lin), sobre células cancerígenas. Os compostos obtidos foram caracterizados por análise elementar, espectroscopia de absorção eletrônica, medidas de susceptibilidade magnética, espectroscopia vibracional FTIR e Raman, difratometria de raios X de pó, medidas de condutividade molar e análise térmica (TG, OTAe OSC). Todos os complexos sintetizados apresentam estrutura em gaiola, com os carboxilatos derivados dos fármacos AINEs coordenados à unidade dimetálica Ru2( (II,III), em ponte equatorial, estabilizando assim a ligação direta rutênio-rutênio. As posições axiais são ocupadas por íons cloreto, no caso dos complexos [Ru2(O2(CR)4(Cl] (O2(CR = ibp, aas, npx ou ind), ou por moléculas de água, nas espécies do tipo [Ru2(O2(CR)4(H2O)2]PF6(O2CR =npx e ind). Ensaios biológicos demonstraram que os compostos [Ru2(ibp) 4Cl]•½H2O e [Ru2(npx)4(H2O)2]PF6 apresentam ação antiproliferativa sobre células de glioma de rato C6 in vitro, dependendo do tempo de exposição do meio celular ao complexo. O complexo [Ru2 (lin)4Cl] também apresenta efeito sobre a proliferação de células C6; entretanto, nesse caso, efeitos significativos são observaçlos já nas primeiras 24 h de exposição. Estudos mostraram que as bases adenina e adenosina reagem com o complexo [Ru2(OAc)4(H2O)2]PF6 sem que ocorra quebra da estrutura em gaiola. As bases nitrogenadas substituem axialmente as moléculas de água, formando pontes axiais entre duas unidades de dirutênio (II,III) no estado sólido.

Espécies polinucleares de cobre e ferro com catalisadores de oxidação e modelos de sítios ativos

Diferentes complexos de cobre(II), contendo ligantes do tipo base de Schiff e um grupamento imidazólico, com interesse bioinorgânico, catalítico e como novos materiais, foram preparados na forma de sais perclorato, nitrato ou cloreto e caracterizados através de diferentes técnicas espectroscópicas (UV/Vis, IR, EPR, Raman) e espectrometria de massa Tandem (ESI-MS/MS), além de análise elementar, condutividade molar e medidas de propriedades magnéticas. Alguns destes compostos, obtidos como cristais adequados, tiveram suas estruturas determinadas por cristalografia de raios-X. As espécies di- e polinucleares contendo pontes cloreto, mostraram desdobramentos das hiperfinas nos espectros de EPR, relacionados à presença do equilíbrio com a respectiva espécie mononuclear, devido à labilidade dos íons cloretos, dependendo do contra-íon e do tipo de solvente utilizado. Adicionalmente, em solução alcalina, estes compostos estão em equilíbrio com as correspondentes espécies polinucleares, onde os centros de cobre estão ligados através de um ligante imidazolato. Em meio alcalino, estes compostos polinucleares contendo ponte imidazolato foram também isolados e caracterizados por diferentes técnicas espectroscópicas e magnéticas. Através da variação estrutural e também do ligante-ponte foi possível modular o fenômeno da interação magnética entre os íons de cobre em estruturas correlatas di- e polinucleares. Os respectivos parâmetros magnéticos foram obtidos com ajuste das curvas experimentais de XM vs T, correlacionando-se muito bem com a geometria, ângulos e distâncias de ligação entre os íons, quando comparado com outros complexos similares descritos na literatura. Posteriormente, estudaram-se os fatores relacionados com a reatividade de todas essas espécies como catalisadores na oxidação de substratos de interesse (fenóis e aminas), através da variação do tamanho da cavidade nas estruturas cíclicas ou de variações no ligante coordenado ao redor do íon metálico. Vários deles se mostraram bons miméticos de tirosinases e catecol oxidases. Um novo complexo-modelo da citocromo c oxidase (CcO), utilizando a protoporfirina IX condensada ao quelato N,N,-bis[2-(1,2-metilbenzimidazolil)etil]amino e ao resíduo de glicil-L-histidina, foi sintetizado e caracterizado através de diferentes técnicas espectroscópicas, especialmente EPR. A adição de H2O2 ao sistema completamente oxidado, FeIII/CuII, a -55°C, ou o borbulhamento de oxigênio molecular a uma solução do complexo na sua forma reduzida, FeII/CuI, saturada de CO, resultou na formação de adutos com O2, de baixo spin, estáveis a baixas temperaturas.

Three Dichotomies in Lawyers’ Ethics (With Particular Attention to the Corporation as Client)

Three usually unexpressed, and too often unnoticed, conceptual dichotomies underlie our perception and understanding of lawyers’ ethics. First, the existence of a special body of professional ethics and professional regulation presupposes some special need or risk. Criminal and civil law are apparently insufficient. Ordinary day-to-day morality and ordinary ethics, likewise, are not considered to be enough. What is the risk entailed by the notion of a profession that is special; who needs protection, and from what? Two quite different possible answers to this question provide the first of the three dichotomies examined in this article: one can understand the risk as primarily to a vulnerable client from a powerful professional; or, to the contrary, from a powerful client-lawyer combination toward vulnerable others. Second, what is the foundational orientation of lawyers? Are lawyers serving primarily their particular clients, and those clients’ preferences, choices and autonomy? Or is the primary allegiance of lawyers to some community or collective goal or interest distinct from the particular goals or interests of the client? The third dichotomy concerns not the substance of the risk, or the primary orientation, but the appropriate means of responding to that risk or that fundamental obligation. Should professional ethics be implemented primarily through rules? Or, should we rely on character and the discretion of lawyers to make a thought out, all things considered, decision? Each of these three presents a fundamental difference in how we perceive and address issues of lawyers’ ethics. Each affects our understanding and analysis on multiple levels, from (1) determining the appropriate or requisite conduct in a particular situation, to (2) framing a specific rule or approach for a particular category of situations, to (3) more general or abstract theory or policy. A person’s inclinations in regard to the dichotomies affects the conclusions that person will reach on each of those levels of analysis, yet those inclinations and assumptions are frequently unexamined and unarticulated. One’s position on each of the dichotomies tends to structure the approach and outcome without the issues and choice having been explicitly addressed or possibly even noticed. This article is an effort to ameliorate that problem. Part I addresses the question of what is the risk in the work of lawyers, or the function of lawyers, for which professional ethics is the answer. The concluding section focuses on the particular problem of the corporation as client. Part II then asks the related and possibly consequent question of what is the foundational orientation or allegiance of the lawyer? Is it to the individual client? Or is it to some larger community interest? Again, the concluding section focuses on the corporation. Part III turns to the means or method for addressing the obligations and possible problems of the professional ethics of lawyers. Should lawyers’ ethics guide and confine the conduct of lawyers primarily through rules? Or should it function primarily through reliance on the knowledge, judgment and character of lawyers? If the latter were the guide, ethical decisions would be made on a situation by situation basis under the discretion of each lawyer. Toward the end of each discussion possibilities for bridging the dichotomy are considered (and with such bridges each dichotomy may come to look more like a spectrum or continuum.). At several points after its introduction in Parts I and II, the special problem of the corporation as client is revisited and possible solutions suggested. Illustrating the usefulness of keeping the dichotomies in view, Part IV applies them to several exemplary situations of ethical difficulty in actual lawyer practice. For readers finding it difficult to envision the consequences of these distinctions, turning ahead to Part IV may be useful in making the discussion more concrete. Some commonalities across the dichotomies and connections among them are then developed in the concluding section, Part V.

Three Dichotomies in Lawyers’ Ethics (With Particular Attention to the Corporation as Client)

Three usually unexpressed, and too often unnoticed, conceptual dichotomies underlie our perception and understanding of lawyers’ ethics. First, the existence of a special body of professional ethics and professional regulation presupposes some special need or risk. Criminal and civil law are apparently insufficient. Ordinary day-to-day morality and ordinary ethics, likewise, are not considered to be enough. What is the risk entailed by the notion of a profession that is special; who needs protection, and from what? Two quite different possible answers to this question provide the first of the three dichotomies examined in this article: one can understand the risk as primarily to a vulnerable client from a powerful professional; or, to the contrary, from a powerful client-lawyer combination toward vulnerable others. Second, what is the foundational orientation of lawyers? Are lawyers serving primarily their particular clients, and those clients’ preferences, choices and autonomy? Or is the primary allegiance of lawyers to some community or collective goal or interest distinct from the particular goals or interests of the client? The third dichotomy concerns not the substance of therisk, or the primary orientation, but the appropriate means of responding to that risk or that fundamental obligation. Should professional ethics be implemented primarily through rules? Or, should we rely on character and the discretion of lawyers to make a thought out, all things considered, decision? Each of these three presents a fundamental difference in how we perceive and address issues of lawyers’ ethics. Each affects our understanding and analysis on multiple levels, from (1) determining the appropriate or requisite conduct in aparticular situation, to (2) framing a specific rule or approach for a particular category of situations, to (3) more general or abstract theory or policy. A person’s inclinations in regard to the dichotomies affects the conclusions that person will reach on each of those levels of analysis, yet those inclinations and assumptions are frequently unexamined and unarticulated. One’s position on each of the dichotomies tends to structure the approach and outcome without the issues and choice having been explicitly addressed or possibly even noticed. This article is an effort to ameliorate that problem. Part I addresses the question of what is the risk in the work of lawyers, or the function of lawyers, for which professional ethics is the answer. The concluding section focuses on the particular problem of the corporation as client. Part II then asks the related and possibly consequent question of what is the foundational orientation or allegiance of the lawyer? Is it to the individual client? Or is it to some larger community interest? Again, the concluding section focuses on thecorporation. Part III turns to the means or method for addressing the obligations and possible problems of the professional ethics of lawyers. Should lawyers’ ethics guide and confine the conduct of lawyers primarily through rules? Or should it function primarily through reliance on the knowledge, judgment and character of lawyers? If the latter were the guide, ethical decisions would be made on a situation by situation basis under the discretion of each lawyer. Toward the end of each discussion possibilities for bridging the dichotomy are considered (and with such bridges each dichotomy may come to look more like a spectrum or continuum.). At several points after its introduction in Parts I and II, the special problem of the corporation as client is revisited and possible solutions suggested. Illustrating the usefulness of keeping the dichotomies in view, Part IV applies them to several exemplary situations of ethical difficulty in actual lawyer practice. For readers finding it difficult to envision the consequences of these distinctions, turning ahead to Part IV may be useful in making the discussion more concrete. Some commonalities across the dichotomies and connections among them are then developed in the concluding section, Part V.

Giant magnetoresistance in ultrasmall graphene based devices

By computing spin-polarized electronic transport across a finite zigzag graphene ribbon bridging two metallic graphene electrodes, we demonstrate, as a proof of principle, that devices featuring 100% magnetoresistance can be built entirely out of carbon. In the ground state a short zigzag ribbon is an antiferromagnetic insulator which, when connecting two metallic electrodes, acts as a tunnel barrier that suppresses the conductance. The application of a magnetic field makes the ribbon ferromagnetic and conductive, increasing dramatically the current between electrodes. We predict large magnetoresistance in this system at liquid nitrogen temperature and 10 T or at liquid helium temperature and 300 G.