Dynamic properties of the Ras switch I region and its importance for binding to effectors

We have investigated the dynamic properties of the switch I region of the GTP-binding protein Ras by using mutants of Thr-35, an invariant residue necessary for the switch function. Here we show that these mutants, previously used as partial loss-of-function mutations in cell-based assays, have a reduced affinity to Ras effector proteins without Thr-35 being involved in any interaction. The structure of Ras(T35S)⋅GppNHp was determined by x-ray crystallography. Whereas the overall structure is very similar to wildtype, residues from switch I are completely invisible, indicating that the effector loop region is highly mobile. 31P-NMR data had indicated an equilibrium between two rapidly interconverting conformations, one of which (state 2) corresponds to the structure found in the complex with the effectors. 31P-NMR spectra of Ras mutants (T35S) and (T35A) in the GppNHp form show that the equilibrium is shifted such that they occur predominantly in the nonbinding conformation (state 1). On addition of Ras effectors, Ras(T35S) but not Ras(T35A) shift to positions corresponding to the binding conformation. The structural data were correlated with kinetic experiments that show two-step binding reaction of wild-type and (T35S)Ras with effectors requires the existence of a rate-limiting isomerization step, which is not observed with T35A. The results indicate that minor changes in the switch region, such as removing the side chain methyl group of Thr-35, drastically affect dynamic behavior and, in turn, interaction with effectors. The dynamics of the switch I region appear to be responsible for the conservation of this threonine residue in GTP-binding proteins.

Nitric oxide inhibits creatine kinase and regulates rat heart contractile reserve.

Cardiac myocytes express both constitutive and cytokine-inducible nitric oxide syntheses (NOS). NO and its congeners have been implicated in the regulation of cardiac contractile function. To determine whether NO could affect myocardial energetics, 31P NMR spectroscopy was used to evaluate high-energy phosphate metabolism in isolated rat hearts perfused with the NO donor S-nitrosoacetylcysteine (SNAC). All hearts were exposed to an initial high Ca2+ (3.5 mM) challenge followed by a recovery period, and then, either in the presence or absence of SNAC, to a second high Ca2+ challenge. This protocol allowed us to monitor simultaneously the effect of SNAC infusion on both contractile reserve (i.e., baseline versus high workload contractile function) and high-energy phosphate metabolism. The initial high Ca2+ challenge caused the rate-pressure product to increase by 74 +/- 5% in all hearts. As expected, ATP was maintained as phosphocreatine (PCr) content briefly dropped and then returned to baseline during the subsequent recovery period. Control hearts responded similarLy to the second high Ca2+ challenge, but SNAC-treated hearts did not demonstrate the expected increase in rate-pressure product. In these hearts, ATP declined significantly during the second high Ca2+ challenge, whereas phosphocreatine did not differ from controls, suggesting that phosphoryl transfer by creatine kinase (CK) was inhibited. CK activity, measured biochemically, was decreased by 61 +/- 13% in SNAC-treated hearts compared to controls. Purified CK in solution was also inhibited by SNAC, and reversal could be accomplished with DTT, a sulfhydryl reducing agent. Thus, NO can regulate contractile reserve, possibly by reversible nitrosothiol modification of CK.

Bond orientational order, molecular motion, and free energy of high-density DNA mesophases.

By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change between two distinct regions on the liquid-crystalline phase diagram: (i) a higher density hexagonally packed region with long-range bond orientational order in the plane perpendicular to the average molecular direction and (ii) a lower density cholesteric region with fluid-like positional order. X-ray scattering on highly ordered DNA arrays at high density and with the helical axis oriented parallel to the incoming beam showed a sixfold azimuthal modulation of the first-order diffraction peak that reflects the macroscopic bond-orientational order. Transition to the less-dense cholesteric phase through osmotically controlled swelling shows the loss of this bond orientational order, which had been expected from the change in optical birefringence patterns and which is consistent with a rapid onset of molecular positional disorder. This change in order was previously inferred from intermolecular force measurements and is now confirmed by 31P NMR. Controlled reversible swelling and compaction under osmotic stress, spanning a range of densities between approximately 120 mg/ml to approximately 600 mg/ml, allow measurement of the free-energy changes throughout each phase and at the phase transition, essential information for theories of liquid-crystalline states.

Visualization of intermediate and transition-state structures in protein-tyrosine phosphatase catalysis.

Engineering site-specific amino acid substitutions into the protein-tyrosine phosphatase (PTPase) PTP1 and the dual-specific vaccinia H1-related phosphatase (VHR), has kinetically isolated the two chemical steps of the reaction and provided a rare opportunity for examining transition states and directly observing the phosphoenzyme intermediate. Changing serine to alanine in the active-site sequence motif HCXXGXXRS shifted the rate-limiting step from intermediate formation to intermediate hydrolysis. Using phosphorus 31P NMR, the covalent thiol-phosphate intermediate was directly observed during catalytic turnover. The importance of the conserved aspartic acid (D92 in VHR and D181 in PTP1) in both chemical steps was established. Kinetic analysis of D92N and D181N mutants indicated that aspartic acid acts as a general acid by protonating the leaving-group phenolic oxygen. Structure-reactivity experiments with native and aspartate mutant enzymes established that proton transfer is concomitant with P-O cleavage, such that no charge develops on the phenolic oxygen. Steady- and presteady-state kinetics, as well as NMR analysis of the double mutant D92N/S131A (VHR), suggested that the conserved aspartic acid functions as a general base during intermediate hydrolysis. As a general base, aspartate would activate a water molecule to facilitate nucleophilic attack. The amino acids involved in transition-state stabilization for cysteinylphosphate hydrolysis were confirmed by the x-ray structure of the Yersinia PTPase complexed with vanadate, a transition-state mimic that binds covalently to the active-site cysteine. Consistent with the NMR, x-ray, biochemical, and kinetic data, a unifying mechanism for catalysis is proposed.

Evidence for DNA phosphate backbone alkylation and cleavage by pyrrolo[1,2-a]benzimidazoles: small molecules capable of causing base-pair-specific phosphodiester bond hydrolysis.

This report presents evidence that a reduced pyrrolo[1,2-a]benzimidazole (PBI) cleaves DNA as a result of phosphate alkylation followed by hydrolysis of the resulting phosphate triester. The base-pair specificity of the phosphate alkylation results from Hoogsteen-type hydrogen bonding of the reduced PBI in the major groove at only A.T and G.C base pairs. Alkylated phosphates were detected by 31P NMR and the cleavage products were detected by 1H NMR and HPLC. Evidence is also presented that a reduced PBI interacts with DNA in the major groove rather than in the minor groove or by intercalation.

Synthetic analogues of protein-lipid complexes

Hypercoiling poly(styrene-alt-maleic anhydride) (PSMA) is known to undergo conformational transition in response to environmental stimuli. The association of PSMA with lipid 2-dilauryl-sn-glycero-3-phosphocholine (DLPC) produces polymer-lipid complex analogues to lipoprotein assemblies found in lung surfactant. These complexes represent a new bio-mimetic delivery vehicle with applications in the cosmetic and pharmaceutical industries. The primary aim of this study was to develop a better understanding of PSMA-DLPC association by using physical and spectroscopic techniques. Ternary phase diagrams were constructed to examine the effects of various factors, such as molecular weight, pH and temperature on PSMA-DLPC association. 31P-NMR spectroscopy was used to investigate the polymorphic changes of DLPC upon associating with PSMA. The Langmuir Trough technique and surface tension measurement were used to explore the association behaviour of PSMA both at the interface and in the bulk of solution, as well as its interaction with DLPC membranes. The ultimate aim of this study was to investigate the potential use of PSMA-DLPC complexes to improve the bioavailability and therapeutic efficacy of a range of drugs. Typical compounds of ophthalmic interest range from new drugs such as Pirenzepine, which has attracted clinical interest for the control of myopia progression, to the well-established family of non-steroid anti-inflammatory drugs. These drugs have widely differing structures, sizes, solubility profiles and pH-sensitivities. In order to understand the ways in which these characteristics influence incorporation and release behaviour, the marker molecules Rhodamine B and Oil Red O were chosen. PSMA-DLPC complexes, incorporated with marker molecules and Pirenzepine, were encapsulated in hydrogels of the types used for soft contact lenses. Release studies were conducted to examine if this smart drug delivery system can retain such compounds and deliver them at a slow rate over a prolonged period of time.

Delivery of phosphonoformate prodrugs

AIDS dementia complex is a common neurological syndrome thought to result from the invasion of the CNS by HIV. Phosphonoformate has anti-HIV activity but due to its charged nature is excluded from the CNS by the blood-brain barrier. Lipophilic triesters of phosphonoformate designed to improve transport properties are unsuitable prodrugs due to their rapid and complicated hydrolysis, involving competitive P-O and P-C bond cleavage. Diesters, though hydrolytically stable, are considered too polar to passively diffuse into the CNS. Hydrophilic drugs mimicking endogenous nutrients are known to be actively transported across the blood-brain barrier. In this thesis the possibility that diesters of phosphonoformate may be actively transported is investigated. Triesters of phosphonoformate with labile aryl carboxyl esterrs were synthesised and their hydrolysis followed by 31P NMR spectroscopy. The triesters were found to undergo rapid hydrolysis via P-C bond cleavage to the phosphite. Phosphonoformate diesters designed to be analogues of actively transported -keto acids have been synthesised and fully characterised. Tyrosine-phosphonoformate and lipid-phosphonoformate conjugates have also been synthesised and characterised. An in vitro model of the blood-brain barrier utilising confluent monolayers of porcine brain microvessel endothelial cells grown on a permeable support has been established. The presence of enzyme and antigen markers specific to the blood-brain barrier has been demonstrated for the endothelial cells and the diffusional properties of the model investigated with hydrophilic and lipophilic compounds. Active transport systems for -keto acids and large amino acids have been identified in the endothelial cell monolayers using 14C-pyruvate and 3H-L-tyrosine respectively. Temperature and concentration dependence of the two systems have been demonstrated and transport constants calculated. Competition with 14C-pyruvate transport was shown with other monocarboxylic acids including the anti-epileptic drug valproate. Stereospecificity was shown in that L-lactate inhibited pyruvate transport while D-lactate did not. Sodium methyl methoxycarbonylphosphonate, a phosphonoformate diester was shown not to compete for 14C-pyruvate transport indicating that this compound has no affinity for the carrier. Competition with 3H-L-tyrosine transport was shown with other large amino acids, including the anti-Parkinsonian agent L-dopa. Stereospecificity was shown using L- and D-tyrosine and L- and D-dopa. The tyrosine-phosphonoformate conjugate, which was stable under the experimental conditions, was shown to compete with 3H-Ltyrosine transport indicating that it may be actively transported at the blood-brain barrier. Thirty two triesters, diesters and monoesters of phosphonoformate, showed no activity in an anti-HIV screen above that attributable to hydrolysis to the parent compound.

New strategy to overcome the intrinsic difficulty of phospholipids solubilisation and delivery to the eye

Purpose: Lipids play a vital role at interfaces such as the tear film in the protection of the anterior eye. Their role is to act as lubricants and reduce surface and interfacial tension. Although there is a lack of appropriate methods to solubilize and dilute phospholipids to the tear film. Here, we report that styrene-maleic acid copolymers (PSMA), can form polymer–lipid complexes in the form of monodisperse nanometric particles, which can easily solubilise these phospholipid molecules by avoiding for example, the use of any kind of surfactant. Method: The interactions of PSMA with phospholipids have been studied by its adsorption from aqueous solutions into monolayers of dimyristoyl-phosphorylcholine (DMPC). The Langmuir trough (LT) technique is used to study this pH-dependant complex formation. The formed nanoparticles have been also analysed by 31P NMR, particle size distribution by light scattering (DLS) and morphology by electron microscopy (SEM). Results: The LT has been found to be a useful technique for in vitro simulation of in vivo lipid layer behaviour: The limiting surface pressure of unstable tear films ranges between 20 and 30 mN/m. More stable tear films show an increase in surface pressure, within the range of 35–45 mN/m. The DMPC monolayers have a limiting surface pressure of 38 mN/m (water), and 45 mN/m (pH 4 buffer), and the PSMA-DMPC complexes formed at pH 4 have a value of 42 mN/m, which resembles that of the stable tear film. The average particle size distribution is 53 ± 10 nm with a low polydispersity index (PDI) of 0.24 ± 0.03. Conclusions: New biocompatible and cheap lipid solubilising agents such as PSMA can be used for the study of the tear film composition and properties. These polymer–lipid complexes in the form of nanoparticles can be used to solubilise and release in a controlled way other hydrophobic molecules such as some drugs or proteins.

Novel sol–gel preparation of (P2O5)0.4–(CaO)0.25–(Na2O)X–(TiO2)(0.35−X) bioresorbable glasses (X = 0.05, 0.1, and 0.15)

Quaternary phosphate-based glasses in the P2O5–CaO–Na2O–TiO2 system with a fixed P2O5 and CaO content of 40 and 25 mol% respectively have been successfully synthesised via sol–gel method and bulk, transparent samples were obtained. The structure, elemental proportion, and thermal properties of stabilised sol–gel glasses have been characterised using X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDX), 31P nuclear magnetic resonance (31P NMR), titanium K-edge X-ray absorption near-edge structure (XANES), fourier transform infrared (FTIR) spectroscopy, and differential thermal analysis (DTA). The XRD results confirmed the amorphous nature for all stabilized sol–gel derived glasses. The EDX result shows the relatively low loss of phosphorus during the sol–gel process and Ti K-edge XANES confirmed titanium in the glass structure is in mainly six-fold coordination environment. The 31P NMR and FTIR results revealed that the glass structure consist of mainly Q1 and Q2 phosphate units and the Ti4+ cation was acting as a cross-linking between phosphate units. In addition DTA results confirmed a decrease in the glass transition and crystallisation temperature with increasing Na2O content. Ion release studies also demonstrated a decrease in degradation rates with increasing TiO2 content therefore supporting the use of these glasses for biomedical applications that require a degree of control over glass degradation. These sol–gel glasses also offer the potential to incorporate proactive molecules for drug delivery application due to the low synthesis temperature employed.

Polymer-lipid interactions:biomimetic self-assembly behaviour and surface properties of poly(styrene-alt-maleic acid) with diacylphosphatidylcholines

Abstract Various lubricating body fluids at tissue interfaces are composed mainly of combinations of phospholipids and amphipathic apoproteins. The challenge in producing synthetic replacements for them is not replacing the phospholipid, which is readily available in synthetic form, but replacing the apoprotein component, more specifically, its unique biophysical properties rather than its chemistry. The potential of amphiphilic reactive hypercoiling behaviour of poly(styrene-alt-maleic acid) (PSMA) was studied in combination with two diacylphosphatidylcholines (PC) of different chain lengths in aqueous solution. The surface properties of the mixtures were characterized by conventional Langmuir-Wilhelmy balance (surface pressure under compression) and the du Noüy tensiometer (surface tension of the non-compressed mixtures). Surface tension values and 31P NMR demonstrated that self-assembly of polymer-phospholipid mixtures were pH and concentration-dependent. Finally, the particle size and zeta potential measurements of this self-assembly showed that it can form negatively charged nanosized structures that might find use as drug or lipids release systems on interfaces such as the tear film or lung interfacial layers. The structural reorganization was sensitive to the alkyl chain length of the PC.

Seawater carbonate chemistry and biological processes of Sepia officinalis during experiments, 2010

Acidification of ocean surface waters by anthropogenic carbon dioxide (CO2) emissions is a currently developing scenario that warrants a broadening of research foci in the study of acid-base physiology. Recent studies working with environmentally relevant CO2 levels, indicate that some echinoderms and molluscs reduce metabolic rates, soft tissue growth and calcification during hypercapnic exposure. In contrast to all prior invertebrate species studied so far, growth trials with the cuttlefish Sepia officinalis found no indication of reduced growth or calcification performance during long-term exposure to 0.6 kPa CO2. It is hypothesized that the differing sensitivities to elevated seawater pCO2 could be explained by taxa specific differences in acid-base regulatory capacity. In this study, we examined the acid-base regulatory ability of S. officinalis in vivo, using a specially modified cannulation technique as well as 31P NMR spectroscopy. During acute exposure to 0.6 kPa CO2, S. officinalis rapidly increased its blood [HCO3] to 10.4 mM through active ion-transport processes, and partially compensated the hypercapnia induced respiratory acidosis. A minor decrease in intracellular pH (pHi) and stable intracellular phosphagen levels indicated efficient pHi regulation. We conclude that S. officinalis is not only an efficient acid-base regulator, but is also able to do so without disturbing metabolic equilibria in characteristic tissues or compromising aerobic capacities. The cuttlefish did not exhibit acute intolerance to hypercapnia that has been hypothesized for more active cephalopod species (squid). Even though blood pH (pHe) remained 0.18 pH units below control values, arterial O2 saturation was not compromised in S. officinalis because of the comparatively lower pH sensitivity of oxygen binding to its blood pigment. This raises questions concerning the potentially broad range of sensitivity to changes in acid-base status amongst invertebrates, as well as to the underlying mechanistic origins. Further studies are needed to better characterize the connection between acid-base status and animal fitness in various marine species.

Síntese e estudo de polioxotungstatos do tipo Keggin com interesse catalítico

O objectivo principal deste trabalho foi estudar as propriedades e comportamento de polioxotungstatos (POM) do tipo Keggin com interesse em catálise oxidativa. Os estudos efectuados centraram-se no comportamento electroquímico dos aniões em meio não aquoso, na estabilidade das suas estruturas em diferentes meios, na sua capacidade de catalisar a oxidação de diferentes substratos orgânicos e na sua eficácia em oxidar, de forma selectiva, um modelo não fenólico da lenhina. Efectuou-se, igualmente, o estudo estrutural de diversos aniões pela técnica de EXAFS. Neste trabalho, prepararam-se e caracterizaram-se alguns dos sais de tetra-n-butilamónio (TBA) dos polioxotungstatos estudados: compostos de Keggin, TBAx[XW12O40], lacunares, TBAxHy[XW11O39], mono-substituídos, TBAxHy[XW11M(H2O)O39]·nH2O, com X= P e Si e M = CoII, NiII, ZnII, CuIl, RuIII, MnIII e FeIII e os compostos com mistura de átomos adenda TBAx[XW11VO40]·nH2O (X = P e Si). Seleccionou-se este conjunto de polioxotungstatos de forma a efectuar-se um estudo comparativo da influência da natureza do heteroátomo central (P e Si) e dos metais de transição M nas propriedades estudadas. O conjunto de sais de TBA dos silicotungstatos estudados mostraram ser isoestruturais, apresentando a mesma estrutura dos fosfotungstatos análogos. O comportamento electroquímico dos polioxotungstatos foi estudado em soluções de acetonitrilo por voltametria cíclica e electrólise a potencial controlado. Verificou-se a ocorrência de vários processos mono-electrónicos de oxi-redução, reversíveis ou quasi-reversíveis, associados aos átomos de WVI/V e a alguns dos metais de transição. Os metais em estado de oxidação +3 reduziram-se mais facilmente do que os átomos de WVI. O metal CuII apresentou um comportamento diferente dos outros metais de transição. Este metal, na estrutura do POM, reduziu-se a CuI, proporcionando a observação do anião [PW11CuIO39]6- pela primeira vez. A redução posterior do CuI conduziu à formação de Cu0, que se depositou na superfície do eléctrodo. A re-oxidação do cobre a CuII conduziu à reconstituição da estrutura do POM, nas condições estudadas. Constatou-se que a ocorrência de protões na fórmula molecular dos POMs influenciou o seu comportamento electroquímico. Para os compostos que apresentam protões, a redução dos átomos de tungsténio ocorreu a potenciais menos negativos do que para aqueles que não apresentam protões na sua fórmula. Para os primeiros observou-se a transferência global de um maior número de electrões no mesmo intervalo de potencial, originando soluções fortemente azuladas. Quando os catiões tetra-n-butilamónio foram substituídos por catiões de menor dimensão, como Li+ e Na+, ocorreu a formação de pares iónicos com os polianiões [PW12O40]3- e [SiW11VO40]5-, originando um aumento do potencial de redução. Não houve evidência da formação de pares iónicos com os catiões TBA+. Este foi o primeiro estudo sistemático do comportamento electroquímico dos aniões lacunares e mono-substituídos em meio não aquoso. Estudou-se a estrutura dos polioxotungstatos em sais de TBA e em soluções de acetonitrilo. A aplicação da técnica de EXAFS ao estudo deste tipo de compostos em solução foi realizada pela primeira vez. Pela análise estrutural nos sólidos verificou-se que, a natureza do metal de transição M e do átomo central X, na estrutura do POM, influenciam o tamanho dos vários octaedros que o constituem. Não se observaram diferenças significativas nas estruturas dos polianiões em solução. A estabilidade da estrutura dos polioxometalatos na presença de um excesso de H2O2, em soluções de acetonitrilo/H2O foi analisada por espectroscopia de absorção de EXAFS, RMN de 31P, IV e espectrofotometria de absorção no UV-Vis. De uma forma geral, os POMs em que o átomo central da estrutura é o Si apresentaram maior estabilidade do que os POMs correspondentes com átomo de P no centro. Em solução de acetonitrilo, na ausência de H2O2, todos os aniões mostraram ser estáveis durante vários dias. Em solução, na presença de H2O2 em excesso (H2O2/POM = 1300), o anião lacunar [PW11O39]7- não é estável, transformando-se no anião de Venturello, {PO4[W(O)(O2)2]4}3-, após a formação de [PW12O40]3-, como produto intermediário. Em relação aos aniões substituídos [PW11M(H2O)O39]p-, M = MnIII, RuIII, FeIII, CoII e ZnII, verificou-se o seguinte na presença de H2O2: os aniões com MnIII e CoII transformaram-se no anião de Keggin, [PW12O40]3-. Os aniões de RuIII e FeIII mantiveram as suas estruturas e o anião de ZnII decompôs-se em {HPO4[W(O)(O2)2]2}2- e fosfato. Para estes casos de não estabilidade estrutural, o processo de decomposição foi mais rápido na presença de maiores conteúdos de água. Pela análise de EXAFS, na presença de um menor excesso de H2O2 (H2O2/POM = 70) e apenas 8% de parte aquosa, verificou-se que os aniões substituídos por MnIII mantiveram a sua estrutura, embora o ligando H2O, coordenado ao Mn, tivesse sido substituído por um grupo oxo no polianião [SiW11Mn(H2O)O39]5-, e por um grupo peroxo no polianião [PW11Mn(H2O)O39]4-. O anião com RuIII, nestas condições, também mostrou substituir o seu ligando H2O por um grupo peroxo ou hidrogenoperoxo. Os polioxotungstatos mono-substituídos e lacunares mostraram ser catalisadores eficientes para a oxidação de cis-cicloocteno, geraniol e ciclooctano com H2O2. A maior novidade deste trabalho residiu na actividade catalítica apresentada pelos silicotungstatos estudados, contrariando o que é referido na literatura. Outro aspecto inovador foi o elevado valor de conversão obtido para a oxidação de ciclooctano. Este substrato foi oxidado com 74% de conversão, após 2h de reacção e com 80% de selectividade para o hidroperóxido de ciclooctilo, na presença do anião [PW11Fe(H2O)O39]4-. Os restantes produtos de reacção foram o ciclooctanol e a ciclooctanona. Os silicotungstatos apresentaram maior selectividade para o hidroperóxido de ciclooctilo do que os fosfotungstatos. O geraniol foi completamente oxidado após 3h de reacção, com 82% de selectividade para o 2,3-epoxigeraniol, na presença do anião [PW11Mn(H2O)O39]4-. O cis-cicloocteno foi oxidado ao seu epóxido, com 92% de conversão ao fim de 5h de reacção, na presença do anião lacunar [PW11O39]7-. O estudo da capacidade oxidativa do anião [SiW11VO40]5- foi analisada utilizando-se um modelo não fenólico da lenhina, a anisoína. Estudaram-se as condições favoráveis à obtenção de uma reacção selectiva para o anisilo, de forma a poder estudar-se a cinética da reacção. A estequiometria da reacção mostrou ser de 1:2 anisoína/POM. As ordens de reacção foram determinadas pelo método das velocidades iniciais e, a partir destes resultados, conheceu-se que o POM não estava envolvido no passo que limita a velocidade da reacção, sendo esta limitada pela transformação da anisoína. O estudo realizado sobre o efeito isotópico sugeriu que o passo que limitou a velocidade de reacção correspondeu à enolação da anisoína. Desta forma, observou-se pela primeira vez, que o POM oxida um modelo não fenólico da lenhina por via de enolação.