Chromatography and mass spectrometry in the study of structure and dynamics of chiral molecules

Part A Dynamic high performance liquid chromatography on chiral stationary phases is a consolidated technique that allows the investigation of chiral molecules with labile stereogenic elements that interconvert very quickly at room temperature and result in stereoinversion processes occurring on the time scale of the separation process. Kinetic parameters for on-column interconversions can be extracted from exchange-deformed experimental peak profiles by computer simulation. The technique has been used in a wide range of temperatures and is complementary in scope to dynamic nuclear magnetic resonance spectroscopy. Here we report, in the first part, the separation of the enantiomers of benzodiazepines, a class of molecules whose conformational enantiomers interconvert not only through a single bond rotation but also via “ring-flip” inversion. The second part concerns the first HPLC resolution of the conformational enantiomers of tri-O-thymotide (TOT) a macrocyclic trilactone existing in fast-exchanging multiple chiral conformations. Variable chromatography on brush type stationary phases showed dynamic features due to on-column interconversions of TOT. Part B Chiral recognition is a branch of chemistry aimed at understanding the reactivity as well as the size- and shape-specificity of non-covalent interactions between molecular aggregates formed by chiral species. Mass spectrometry (MS) is a powerful tool for investigating chiral recognition in the gas phase in the absence of perturbing environmental phenomena and discriminating and even quantifying chiral species by interaction with chiral reference molecules. A small library of synthetic receptors was prepared by macrocyclization of complementary A and B fragments to yield A2B2 macrocycles, where A are activated forms of isophthalic acid derivatives and B are chiral, C2 symmetric 1,2-diamines derived from 1,2-diphenylethylendiamine. Their enantioselectivity was investigated by ESI-MS and revealed large enantioselectivities towards the enantiomers of aminoacids and peptide guests. The stability of the complexes increases with the size of guests and with large aromatic portions on the guest. Part C This part of my academic program was developed at the University of California, Davis, under the supervision of prof. Carlito Lebrilla, during the last period of my Ph.D. activity. An important goal in proteomic is to quantify the profile changes of protein abundances in biological systems. Quantifying these changes is a key to understand changes in cell state at a molecular level. In the last years label-free quantitation using MRM (multiple reaction monitoring), which correlates the mass spectrometric signal of intact proteolytic peptides with the relative or absolute protein quantity, is become a powerful tool for accurate quantitation. Here we report a label-free method to quantify proteins and their glycoforms in biologic fluids (milk, feces and urine) by MRM, including the selection of proteotryptic peptides and the optimization and validation of transitions

The effect of prime-site occupancy on the hepatitis C virus NS3 protease structure.

We recently reported a new class of inhibitors of the chymotrypsin-like serine protease NS3 of the hepatitis C virus. These inhibitors exploit the binding potential of the S′ site of the protease, which is not generally used by the natural substrates. The effect of prime-site occupancy was analyzed by circular dichroism spectroscopy and limited proteolysis-mass spectrometry. Generally, nonprime inhibitors cause a structural change in NS3. Binding in the S′ site produces additional conformational changes with different binding modes, even in the case of the NS3/4A cofactor complex. Notably, inhibitor binding either in the S or S′ site also has profound effects on the stabilization of the protease. In addition, the stabilization propagates to regions not in direct contact with the inhibitor. In particular, the N-terminal region, which according to structural studies is endowed with low structural stability and is not stabilized by nonprime inhibitors, was now fully protected from proteolytic degradation. From the perspective of drug design, P-P′ inhibitors take advantage of binding pockets, which are not exploited by the natural HCV substrates; hence, they are an entry point for a novel class of NS3/4A inhibitors. Here we show that binding of each inhibitor is associated with a specific structural rearrangement. The development of a range of inhibitors belonging to different classes and an understanding of their interactions with the protease are required to address the issue of the most likely outcome of viral protease inhibitor therapy, that is, viral resistanc

Transport phenomena in electrolyte solutions: Non-equilibrium thermodynamics and statistical mechanics

The theory of transport phenomena in multicomponent electrolyte solutions is presented here through the integration of continuum mechanics, electromagnetism, and non-equilibrium thermodynamics. The governing equations of irreversible thermodynamics, including balance laws, Maxwell's equations, internal entropy production, and linear laws relating the thermodynamic forces and fluxes, are derived. Green-Kubo relations for the transport coefficients connecting electrochemical potential gradients and diffusive fluxes are obtained in terms of the flux-flux time correlations. The relationship between the derived transport coefficients and those of the Stefan-Maxwell and infinitely dilute frameworks are presented, and the connection between the transport matrix and experimentally measurable quantities is described. To exemplify application of the derived Green-Kubo relations in molecular simulations, the matrix of transport coefficients for lithium and chloride ions in dimethyl sulfoxide is computed using classical molecular dynamics and compared with experimental measurements.Comment: fixed typos, added references, addressed comment

Amino acid sequences and active site function in yeast hexokinase B

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Membrane Association of the PTEN Tumor Suppressor: Molecular Details of the Protein-Membrane Complex from SPR Binding Studies and Neutron Reflection

The structure and function of the PTEN phosphatase is investigated by studying its membrane affinity and localization on in-plane fluid, thermally disordered synthetic membrane models. The membrane association of the protein depends strongly on membrane composition, where phosphatidylserine (PS) and phosphatidylinositol diphosphate (PI(4,5)P2) act pronouncedly synergistic in pulling the enzyme to the membrane surface. The equilibrium dissociation constants for the binding of wild type (wt) PTEN to PS and PI(4,5)P2 were determined to be Kd∼12 µM and 0.4 µM, respectively, and Kd∼50 nM if both lipids are present. Membrane affinities depend critically on membrane fluidity, which suggests multiple binding sites on the protein for PI(4,5)P2. The PTEN mutations C124S and H93R show binding affinities that deviate strongly from those measured for the wt protein. Both mutants bind PS more strongly than wt PTEN. While C124S PTEN has at least the same affinity to PI(4,5)P2 and an increased apparent affinity to PI(3,4,5)P3, due to its lack of catalytic activity, H93R PTEN shows a decreased affinity to PI(4,5)P2 and no synergy in its binding with PS and PI(4,5)P2. Neutron reflection measurements show that the PTEN phosphatase “scoots" along the membrane surface (penetration <5 Å) but binds the membrane tightly with its two major domains, the C2 and phosphatase domains, as suggested by the crystal structure. The regulatory C-terminal tail is most likely displaced from the membrane and organized on the far side of the protein, ∼60 Å away from the bilayer surface, in a rather compact structure. The combination of binding studies and neutron reflection allows us to distinguish between PTEN mutant proteins and ultimately may identify the structural features required for membrane binding and activation of PTEN

Assembly and Regulation of WW-PPXY Complexes in Hippo Signaling

The Hippo signaling pathway is an evolutionarily conserved regulator of cell growth, proliferation, and apoptosis. A key function of the pathway is to regulate the subcellular distribution and activity of Yorkie in Drosophila or Yes-associated protein (YAP) and transcription co-activator with PDZ-binding motif (TAZ) in mammals. The dysregulation of the Hippo signaling pathway has been linked to a variety of diseases, including cancer, making it a highly valuable target for therapeutic development. A unique property of the pathway is the prevalence of proteins containing WW domains, small globular domains that mediate protein-protein interactions through recognition of PPXY motifs. Many of these proteins are multivalent, containing multiple WW domains or PPXY motifs, but the function of this multivalency in complex formation is not well understood. Additionally, several of these WW domain-containing proteins interact with the same PPXY motif-containing proteins and vice versa, and it is not well understood how partner selectivity is accomplished. Understanding the contribution of multivalency to complex assembly and how partner selectivity is achieved may help guide the development of drugs or therapeutics to treat diseases such as cancer. This thesis reports on work focused on analyzing the interactions of a multivalent Drosophila PPXY motif-containing protein to a WW domain binding partner, as well as the mammalian orthologs of these proteins. Chapter 1 provides an introduction to the Hippo signaling pathway, WW domains, and the role of WW domain-PPXY motif interactions in the pathway. Chapter 2 presents studies on the solution properties of the PPXY motif-containing region of Warts, a serine/threonine kinase that regulates Yorkie activity, and its interactions with the tandem WW domains of Yorkie. We show that this region of Warts, which contains five PPXY motifs, is monomeric and primarily disordered, except for some helicity present in the C-terminal region of the protein. We also demonstrate that Warts and Yorkie form an ensemble of interconverting complexes of varying Yorkie stoichiometries, with Yorkie binding to specific PPXY motif combinations with varying stabilities. Chapter 3 is an investigation into the molecular features that contribute to complex stability in Yorkie-Warts interactions. We show that physical features of the linkers connecting PPXY sites contribute to complex stability. Short or structured linkers result in stronger binding, while both positively and negatively charged residues near the PPXY motifs weaken binding. Chapter 4 investigates the mammalian orthologs of Yorkie and Warts, YAP and LATS1 respectively, and an additional WW domain containing protein, KIBRA. We demonstrate that KIBRA and YAP bind to specific motifs on LATS1 to form a ternary complex. Finally, chapter 5 discusses the impacts and highlights of the reported work and outlines future projects. These results expand our understanding of how these proteins interact with another. In particular, this work provides novel insight into how multivalency contributes to complex assembly in these interactions and emphasizes the need to use multivalent constructs to capture all of the contributors to binding affinity

The effect of blending on selected physical properties of crude oils and their products

A study was made of the effect of blending practice upon selected physical properties of crude oils, and of various base oils and petroleum products, using a range of binary mixtures. The crudes comprised light, medium and heavy Kuwait crude oils. The properties included kinematic viscosity, pour point, boiling point and Reid vapour pressure. The literature related to the prediction of these properties, and the changes reported to occur on blending, was critically reviewed as a preliminary to the study. The kinematic viscosity of petroleum oils in general exhibited non-ideal behaviour upon blending. A mechanism was proposed for this behaviour which took into account the effect of asphaltenes content. A correlation was developed, as a modification of Grunberg's equation, to predict the viscosities of binary mixtures of petroleum oils. A correlation was also developed to predict the viscosities of ternary mixtures. This correlation showed better agreement with experimental data (< 6% deviation for crude oils and 2.0% for base oils) than currently-used methods, i.e. ASTM and Refutas methods. An investigation was made of the effect of temperature on the viscosities of crude oils and petroleum products at atmospheric pressure. The effect of pressure on the viscosity of crude oil was also studied. A correlation was developed to predict the viscosity at high pressures (up to 8000 psi), which gave significantly better agreement with the experimental data than the current method due to Kouzel (5.2% and 6.0% deviation for the binary and ternary mixtures respectively). Eyring's theory of viscous flow was critically investigated, and a modification was proposed which extends its application to petroleum oils. The effect of blending on the pour points of selected petroleum oils was studied together with the effect of wax formation and asphaltenes content. Depression of the pour point was always obtained with crude oil binary mixtures. A mechanism was proposed to explain the pour point behaviour of the different binary mixtures. The effects of blending on the boiling point ranges and Reid vapour pressures of binary mixtures of petroleum oils were investigated. The boiling point range exhibited ideal behaviour but the R.V.P. showed negative deviations from it in all cases. Molecular weights of these mixtures were ideal, but the densities and molar volumes were not. The stability of the various crude oil binary mixtures, in terms of viscosity, was studied over a temperature range of 1oC - 30oC for up to 12 weeks. Good stability was found in most cases