Structural basis and prediction of substrate specificity in protein serine/threonine kinases

The large number of protein kinases makes it impractical to determine their specificities and substrates experimentally. Using the available crystal structures, molecular modeling, and sequence analyses of kinases and substrates, we developed a set of rules governing the binding of a heptapeptide substrate motif (surrounding the phosphorylation site) to the kinase and implemented these rules in a web-interfaced program for automated prediction of optimal substrate peptides, taking only the amino acid sequence of a protein kinase as input. We show the utility of the method by analyzing yeast cell cycle control and DNA damage checkpoint pathways. Our method is the only available predictive method generally applicable for identifying possible substrate proteins for protein serine/threonine kinases and helps in silico construction of signaling pathways. The accuracy of prediction is comparable to the accuracy of data from systematic large-scale experimental approaches.

Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-α

Importin-alpha is the nuclear import receptor that recognizes cargo proteins carrying conventional basic monopartite and bipartite nuclear localization sequences (NLSs) and facilitates their transport into the nucleus. Bipartite NLSs contain two clusters of basic residues, connected by linkers of variable lengths. To determine the structural basis of the recognition of diverse bipartite NLSs by mammalian importin-alpha, we co-crystallized a non-autoinhibited mouse receptor protein with peptides corresponding to the NLSs from human retinoblastoma protein and Xenopus laevis phosphoprotein N1N2, containing diverse sequences and lengths of the linker. We show that the basic clusters interact analogously in both NLSs, but the linker sequences adopt different conformations, whereas both make specific contacts with the receptor. The available data allow us to draw general conclusions about the specificity of NLS binding by importin-alpha and facilitate an improved definition of the consensus sequence of a conventional basic/bipartite NLS (KRX10-12KRRK) that can be used to identify novel nuclear proteins.

The LFA-1-associated molecule PTA-1 (CD226) on T cells forms a dynamic molecular complex with protein 4.1G and human discs large

Clustering of the T cell integrin, LFA-1, at specialized regions of intercellular contact initiates integrin-mediated adhesion and downstream signaling, events that are necessary for a successful immunological response. But how clustering is achieved and sustained is not known. Here we establish that an LFA-1-associated molecule, PTA-1, is localized to membrane rafts and binds the carboxyl-terminal domain of isoforms of the actin-binding protein 4.1G. Protein 4.1 is known to associate with the membrane-associated guanylate kinase homologue, human discs large. We show that the carboxyl-terminal peptide of PTA-1 also can bind human discs large and that the presence or absence of this peptide greatly influences binding between PTA-1 and different isoforms of 4.1G. T cell stimulation with phorbol ester or PTA-1 cross-linking induces PTA-1 and 4.1G to associate tightly with the cytoskeleton, and the PTA-1 from such activated cells now can bind to the amino-terminal region of 4.1G. We propose that these dynamic associations provide the structural basis for a regulated molecular adhesive complex that serves to cluster and transport LFA-1 and associated molecules.

Molecular analysis reveals tighter social regulation of immigration in patrilocal populations than in matrilocal populations

Human social organization can deeply affect levels of genetic diversity. This fact implies that genetic information can be used to study social structures, which is the basis of ethnogenetics. Recently, methods have been developed to extract this information from genetic data gathered from subdivided populations that have gone through recent spatial expansions, which is typical of most human populations. Here, we perform a Bayesian analysis of mitochondrial and Y chromosome diversity in three matrilocal and three patrilocal groups from northern Thailand to infer the number of males and females arriving in these populations each generation and to estimate the age of their range expansion. We find that the number of male immigrants is 8 times smaller in patrilocal populations than in matrilocal populations, whereas women move 2.5 times more in patrilocal populations than in matrilocal populations. In addition to providing genetic quantification of sex-specific dispersal rates in human populations, we show that although men and women are exchanged at a similar rate between matrilocal populations, there are far fewer men than women moving into patrilocal populations. This finding is compatible with the hypothesis that men are strictly controlling male immigration and promoting female immigration in patrilocal populations and that immigration is much less regulated in matrilocal populations.

Coherent-state quantum key distribution without random basis switching

The random switching of measurement bases is commonly assumed to be a necessary step of quantum key distribution protocols. In this paper we present a no-switching protocol and show that switching is not required for coherent-state continuous-variable quantum key distribution. Further, this protocol achieves higher information rates and a simpler experimental setup compared to previous protocols that rely on switching. We propose an optimal eavesdropping attack against this protocol, assuming individual Gaussian attacks. Finally, we investigate and compare the no-switching protocol applied to the original Bennett-Brassard 1984 scheme.

Molecular characterization of Thelastomatoidea (Nematoda : Oxyurida) from cockroaches in Australia

A molecular approach was used to genetically characterize 5 species (Aoruroides queenslandensis. Blattophila sphaerolaima, Cordonicola gibsoni, Desmicola ornato and Leidynemella fusiformis) belonging to the superfamily. Thelastomatoidea fi (Nematoda: Oxyurida), a group of pinworms that parasitizes terrestrial arthropods. The D3 domain of the large subunit Of nuclear ribosomal RNA (LSU) was sequenced for individual specimens, and the analysis of the sequence data allowed the genetic relationships of the 5 species to be studied dagger. The sequence variation in the D3 domain within individual species (0-1-8%) was significantly less than the differences among species (4(.)3-12(.)4%). Phylogenetic analyses, Using maximum parsimony, maximum likelihood, and neighbour-joining, tree-building methods, established relationships among the 5 species of Thelastomatoidea and Oxyuris equi (a species of the order Oxyurida). The molecular approach employed provides the prospect for developing DNA tools for the specific identification of the Thelastomatoidea, irrespective of developmental stage and sex, as a basis for systematic, ecological and/or population genetic investigations of members within this superfamily.

Molecular investigations into vaginal immunization with HIV gp41 antigenic construct H4A in a quick release solid dosage form

A robust vaginal immune response is considered essential for an effective prophylactic vaccine that prevents transmission of HIV and other sexually acquired diseases. Considerable attention has recently focused on the potential of vaginally administered vaccines as a means to induce such local immunity. However, the potential for vaccination at this site remains in doubt as the vaginal mucosa is generally considered to have low immune inductive potential. In the current study, we explored for the first time the use of a quick release, freeze-dried, solid dosage system for practical vaginal administration of a protein antigen. These solid dosage forms overcome the common problem associated with leakage and poor retention of vaginally administered antigen solutions. Mice were immunized vaginally with H4A, an HIV gp41 envelope based recombinant protein, using quick release, freeze-dried solid rods, and the immune responses compared to a control group immunized via subcutaneous H4A injection. Vaginally immunized mice failed to elicit robust immune responses. Our detailed investigations, involving cytokine analysis, the stability of H4A in mouse cervicovaginal lavage, and elucidation of the state of H4A protein in the immediate-release dosage form, revealed that antigen instability in vaginal fluid, the state of the antigen in the dosage form, and the cytokine profile induced are all likely to have contributed to the observed lack of immunogenicity. These are important factors affecting vaginal immunization and provide a rational basis for explaining the typically poor and variable elicitation of immunity at this site, despite the presence of immune responsive cells within the vaginal mucosae. In future mucosal vaccine studies, a more explicit focus on antigen stability in the dosage form and the immune potential of available antigen-responsive cells is recommended.

Elements of molecular neurobiology

The 1980s have seen spectacular advances in our understanding of the molecular bases of neurobiology. Biological membranes, channel proteins, cytoskeletal elements, and neuroactive peptides have all been illuminated by the molecular approach. The operation of synapses can be seen to be far more subtle and complex than has previously been imagined, and the development of the brain and physical basis of memory have both been illuminated by this new understanding. In addition, some of the ways in which the brain may go wrong can be traced to malfunction at the molecular level. This study attemps a synthesis of this new knowledge, to provide an indication of how an understanding at the molecular level can help towards a theory of the brain in health and disease. The text will be of benefit to undergraduate students of biochemistry, medical science, pharmacy, pharmacology and general biology.

Liquid-phase adsorption of n-paraffins on type 5A molecular sieves

As a basis for the commercial separation of normal paraffins a detailed study has been made of factors affecting the adsorption of binary liquid mixtures of high molecular weight normal paraffins (C12, C16, and C20) from isooctane on type 5A molecular sieves. The literature relating to molecular sieve properties and applications, and to liquid-phase adsorption of high molecular weight normal paraffin compounds by zeolites, was reviewed. Equilibrium isotherms were determined experimentally for the normal paraffins under investigation at temperatures of 303oK, 323oK and 343oK and showed a non-linear, favourable- type of isotherm. A higher equilibrium amount was adsorbed with lower molecular weight normal paraffins. An increase in adsorption temperature resulted in a decrease in the adsorption value. Kinetics of adsorption were investigated for the three normal paraffins at different temperatures. The effective diffusivity and the rate of adsorption of each normal paraffin increased with an increase in temperature in the range 303 to 343oK. The value of activation energy was between 2 and 4 kcal/mole. The dynamic properties of the three systems were investigated over a range of operating conditions (i.e. temperature, flow rate, feed concentration, and molecular sieve size in the range 0.032 x 10-3 to 2 x 10-3m) with a packed column. The heights of adsorption zones calculated by two independent equations (one based on a constant width, constant velocity and adsorption zone and the second on a solute material balance within the adsorption zone) agreed within 3% which confirmed the validity of using the mass transfer zone concept to provide a simple design procedure for the systems under study. The dynamic capacity of type 5A sieves for n-eicosane was lower than for n-hexadecane and n-dodecane corresponding to a lower equilibrium loading capacity and lower overall mass transfer coefficient. The values of individual external, internal, theoretical and experimental overall mass transfer coefficient were determined. The internal resistance was in all cases rate-controlling. A mathematical model for the prediction of dynamic breakthrough curves was developed analytically and solved from the equilibrium isotherm and the mass transfer rate equation. The experimental breakthrough curves were tested against both the proposed model and a graphical method developed by Treybal. The model produced the best fit with mean relative percent deviations of 26, 22, and 13% for the n-dodecane, n-hexadecane, and n-eicosane systems respectively.

A comparative molecular similarity indices (CoMSIA) study of peptide binding to the HLA-A3 superfamily

Epitope identification is the basis of modern vaccine design. The present paper studied the supermotif of the HLA-A3 superfamily, using comparative molecular similarity indices analysis (CoMSIA). Four alleles with high phenotype frequencies were used: A*1101, A*0301, A*3101 and A*6801. Five physicochemical properties—steric bulk, electrostatic potential, local hydro-phobicity, hydrogen-bond donor and acceptor abilities—were considered and ‘all fields’ models were produced for each of the alleles. The models have a moderate level of predictivity and there is a good correlation between the data. A revised HLA-A3 supermotif was defined based on the comparison of favoured and disfavoured properties for each position of the MHC bound peptide. The present study demonstrated that CoMSIA is an effective tool for studying peptide–MHC interactions.

Structural basis for receptor activity-modifying protein-dependent selective peptide recognition by a G protein-coupled receptor

Association of receptor activity-modifying proteins (RAMP1-3) with the G protein-coupled receptor (GPCR) calcitonin receptor-like receptor (CLR) enables selective recognition of the peptides calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) that have diverse functions in the cardiovascular and lymphatic systems. How peptides selectively bind GPCR:RAMP complexes is unknown. We report crystal structures of CGRP analog-bound CLR:RAMP1 and AM-bound CLR:RAMP2 extracellular domain heterodimers at 2.5 and 1.8 Å resolutions, respectively. The peptides similarly occupy a shared binding site on CLR with conformations characterized by a β-turn structure near their C termini rather than the α-helical structure common to peptides that bind related GPCRs. The RAMPs augment the binding site with distinct contacts to the variable C-terminal peptide residues and elicit subtly different CLR conformations. The structures and accompanying pharmacology data reveal how a class of accessory membrane proteins modulate ligand binding of a GPCR and may inform drug development targeting CLR:RAMP complexes.

The extracellular surface of the GLP-1 receptor is a molecular trigger for biased agonism

Ligand-directed signal bias offers opportunities for sculpting molecular events, with the promise of better, safer therapeutics. Critical to the exploitation of signal bias is an understanding of the molecular events coupling ligand binding to intracellular signaling. Activation of class B G protein-coupled receptors is driven by interaction of the peptide N terminus with the receptor core. To understand how this drives signaling, we have used advanced analytical methods that enable separation of effects on pathway-specific signaling from those that modify agonist affinity and mapped the functional consequence of receptor modification onto three-dimensional models of a receptor-ligand complex. This yields molecular insights into the initiation of receptor activation and the mechanistic basis for biased agonism. Our data reveal that peptide agonists can engage different elements of the receptor extracellular face to achieve effector coupling and biased signaling providing a foundation for rational design of biased agonists.

Epigenetic Basis of Centromere Maintenance and Inheritance

Centromeres are essential chromosomal loci at which kinetochore formation occurs for spindle fiber attachment during mitosis and meiosis, guiding proper segregation of chromosomes. In humans, centromeres are located at large arrays of alpha satellite DNA, contributing to but not defining centromere function. The histone variant CENP-A assembles at alpha satellite DNA, epigenetically defining the centromere. CENP-A containing chromatin exists as an essential domain composed of blocks of CENP-A nucleosomes interspersed with blocks of H3 nucleosomes, and is surrounded by pericentromeric heterochromatin. In order to maintain genomic stability, the CENP-A domain is propagated epigenetically over each cell division; disruption of propagation is associated with chromosome instabilities such as aneuploidy, found in birth defects and in cancer.

The CENP-A chromatin domain occupies 30-45% of the alpha satellite array, varying in genomic distance according to the underlying array size. However, the molecular mechanisms that control assembly and organization of CENP-A chromatin within its genomic context remain unclear. The domain may shift, expand, or contract, as CENP-A is loaded and dispersed each cell cycle. We hypothesized that in order to maintain genome stability, the centromere is inherited as static chromatin domains, maintaining size and position within the pericentric heterochromatin. Utilizing stretched chromatin fibers, I found that CENP-A chromatin is limited to a sub-region of the alpha satellite array that is fixed in size and location through the cell cycle and across populations.

The average amount of CENP-A at human centromeres is largely consistent, implying that the variation in size of CENP-A domains reflects variations in the number of CENP-A subdomains and/or the density of CENP-A nucleosomes. Multi-color nascent protein labeling experiments were utilized to examine the distribution and incorporation of distinct pools of CENP-A over several cell cycles. I found that in each cell cycle there is independent CENP-A distribution, occurring equally between sister centromeres across all chromosomes, in similar quantities. Furthermore, centromere inheritance is achieved through specific placement of CENP-A, following an oscillating pattern that fixes the location and size of the CENP-A domain. These results suggest that spatial and temporal dynamics of CENP-A are important for maintaining centromere and genome stability.

Understanding the genetic basis of phenotype variability in individuals with neurocognitive disorders

Thesis (Ph.D.)--University of Washington, 2016-06

Symmetry properties of one- and two- electron molecular integrals

The maximum numbers of distinct one- and two-electron integrals that arise in calculating the electronic energy of a molecule are discussed. It is shown that these may be calculated easily using the character table of the symmetry group of the set of basis functions used to express the wave function. Complications arising from complex group representations and from a conflict of symmetry between the basis set and the nuclear configuration are considered and illustrated by examples.