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PubMed2002

A unique fold of phospholipase C-beta mediates dimerization and interaction with G alpha q.

GTP-bound subunits of the Gq family of G alpha subunits directly activate phospholipase C-beta (PLC-beta) isozymes to produce the second messengers inositol 1,4,5-trisphosphate and diacylglycerol. PLC-betas are GTPase activating proteins (GAPs) that also promote the formation of GDP-bound, inactive G beta subunits. Both phospholipase activation by G alpha-GTP subunits and GAP activity require a C-terminal region unique to PLC-beta isozymes. The crystal structure of the C-terminal region from an avian PLC-beta, determined at 2.4 A resolution, reveals a novel fold composed almost entirely of three long helices forming a coiled-coil that dimerizes along its long axis in an antiparallel orientation. The dimer interface is extensive ( approximately 3,200 A(2)), and, based on gel exclusion chromatography, full length PLC-betas are dimeric, indicating that PLC-betas likely function as dimers. Sequence conservation, mutational data and molecular modeling show that an electrostatically positive surface of the dimer contains the major determinants for binding G beta q. Effector dimerization, as highlighted by PLC-betas, provides a viable mechanism for regulating signaling cascades linked to heterotrimeric G proteins.

Amino Acid Sequence↗

PubMed2006

Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation.

The structural characterization of amyloid fibers is one of the most investigated areas in structural biology. The structural motif, denoted as steric zipper, recently discovered for the peptide GNNQQNY [Nelson, R., Sawaya, M. R., Balbirnie, M., Madsen, A. O., Riekel, C., Grothe, R. & Eisenberg, D. (2005) Nature 435, 773-778], is expected to exert strong influence in this field. To obtain further insights into the features of this unique structural motif, we report several molecular dynamics simulations of various GNNQQNY aggregates. Our analyses show that even pairs of beta-sheets composed of a limited number of beta-strands are stable in the 20-ns time interval considered, which suggests that steric zipper interactions at a beta-sheet-beta-sheet interface strongly contribute to the stability of these aggregates. Moreover, although the basic features of side chain-side chain interactions are preserved in the simulation, the backbone structure undergoes significant variations. Upon equilibration, a significant twist of the beta-strands that compose the beta-sheets is observed. These results demonstrate that the occurrence of steric zipper interactions is compatible with flat and twisted beta-sheets. Molecular dynamics simulations carried out on two pairs of beta-sheets, separated in the crystal state by a hydrated interface, lead to interesting results. The two pairs of sheets, while twisting, associate through stable peptide-peptide interactions. These findings provide insight into the mechanism that leads to the formation of higher aggregates. On these bases, it is possible to reconcile the crystallographic and the EM data on the size of the basic GNNQQNY fiber unit.

Amino Acid Sequence↗

PubMed2003

A structural basis for half-of-the-sites metal binding revealed in Drosophila melanogaster porphobilinogen synthase.

Porphobilinogen synthase (PBGS) proteins fall into several distinct groups with different metal ion requirements. Drosophila melanogaster porphobilinogen synthase (DmPBGS) is the first non-mammalian metazoan PBGS to be characterized. The sequence shows the determinants for two zinc binding sites known to be present in both mammalian and yeast PBGS, proteins that differ in the exhibition of half-of-the-sites metal binding. The pH-dependent activity of DmPBGS is uniquely affected by zinc. A tight binding catalytic zinc binds at 0.5/subunit with a Kd well below microm. A second inhibitory zinc exhibits a Kd of approximately 5 microm and appears to bind at a stoichiometry of 1/subunit. A molecular model of DmPBGS suggests that the inhibitory zinc is located at a subunit interface using Cys-219 and His-10 as ligands. Zinc binding to this previously unknown inhibitory site is proposed to inhibit opening of the active site lid. As predicted, the DmPBGS mutant H10F is active but is not inhibited by zinc. H10F binds a catalytic zinc at 0.5/subunit and binds a second nonessential and noninhibitory zinc at 0.5/subunit. This result reveals a structural basis for half-of-the-sites metal binding that is consistent with a reciprocating motion model for function of oligomeric PBGS.

Animals↗

PubMed1995

The equine endometrial cup reaction: a review.

The function of eCG in equine pregnancy is far from clear but it has become evident that eCG has little or no FSH activity in the horse and is therefore probably not responsible for the secondary ovulations. eCG does have luteotrophic activity and it could play a role in the resurgence of the primary corpus luteum (1,7,44). Some evidence exists that the receptor population on the equine gonads is heterogenous in a way that makes it possible to distinguish eCG from eLH, resulting in different post-receptor effects (7). There is also evidence that eCG itself is heterogenous, both in glycosylation and in primary structure, not only between different individual animals but also within one animal during different stages of gestation. The differences could simply reflect the difference between stored and secreted hormone, but on the other hand the release of different eCG forms could be under endocrine control, allowing the mare to produce forms appropriate to specific biological needs (74). Thus some forms of eCG could play a role in immunological events taking place at the foeto-maternal interface. The role of cytotoxic antibodies in the equine pregnancy is not understood. The fact that they are not harmful to the pregnancy can be explained by the fact that their target, the paternal MHC molecules, are withdrawn from the endometrial cup tissue by the time the antibodies start appearing in the circulation. This unique way of regulation of MHC expression is also poorly understood.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed2006

The HUGO Gene Nomenclature Database, 2006 updates.

The HUGO Gene Nomenclature Committee (HGNC) aims to give every human gene a unique and ideally meaningful name and symbol. The HGNC database, previously known as Genew, contains over 22,000 public records with approved human gene nomenclature and associated information. The database has undergone major improvements throughout the last year, is publicly available for online searching at http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl and has a new custom downloads interface at http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/gdlw.pl.

Databases, Genetic↗

PubMed1991

Role of the Z band in the mechanical properties of the heart.

In striated muscle the mechanism of contraction involves the cooperative movement of contractile and elastic components. This review emphasizes a structural approach that describes the cellular and extracellular components with known anatomical, biochemical, and physical properties that make them candidates for these contractile and elastic components. Classical models of contractile and elastic elements and their underlying assumptions are presented. Mechanical properties of cardiac and skeletal muscle are compared and contrasted and then related to ultrastructure. Information from these approaches leads to the conclusion that the Z band is essential for muscle contraction. Our review of Z band structure shows the Z band at the interface where extracellular components meet the cell surface. The Z band is also the interface from cell surface to myofibril, from extra-myofibrillar to myofibril, and finally from sarcomere to sarcomere. Our studies of Z band in defined physiologic states show that this lattice is an integral part of the contractile elements and can function as an elastic component. The Z band is a complex dynamic lattice uniquely suited to play several roles in muscle contraction.

Animals↗

PubMed1997

Towards a novel augmented-reality tool to visualize dynamic 3-D anatomy.

Using augmented reality (AR) to teach dynamic 3-D anatomy may impart better understanding of bone dynamics during body movement. We are currently developing an AR tool that will allow superimposition and registration of bone structures on real anatomical counterparts of a human subject. This article describes the application, the problems to be solved, and reports on preliminary developmental studies of a first prototype of the tool. Specifically, studies test approaches to simulating real-time dynamic anatomy, and the feasibility in achieving registration of 3-D anatomical bones on their real counterparts. Such a tool will offer several unique advantages over traditional teaching methods and overcome many of their current limitations.

Anatomy↗

PubMedDate not supplied

Nursing informatics as a support function for oncology nursing research.

PURPOSE/OBJECTIVES: To provide an overview of nursing informatics and examples of informatics research highlighting the potential for intersecting such research with oncology nursing research. DATA SOURCES: Literature and online sources. DATA SYNTHESIS: Nursing informatics may be discussed from technical, theoretical, or clinical perspectives. The interface between nursing practice and nursing informatics provides an opportunity to create new science and research to expand the boundaries of nursing knowledge. CONCLUSIONS: It is time to evaluate the potential for intersecting informatics research with oncology nursing research. In an era of continuous healthcare change, nursing informatics has the potential to provide a unique contribution to oncology clinical practice and nursing research. IMPLICATIONS FOR NURSING PRACTICE: By creatively applying nursing informatics, oncology nurse researchers may better capture the phenomena relevant to oncology nursing practice and further the discipline.

Clinical Nursing Research↗

PubMedDate not supplied

VIR.II: a new interface with the antibody sequences in the Kabat database.

The Kabat database is the source of information par excellence on antibody sequences. In 1995, we developed an interface with the Kabat database, called VIR. VIR has been very useful in conducting studies aiming to find structure-function relationships in antibodies. Here we report a new version adapted to the World Wide Web, called VIR.II. VIR.II allows searches by type of chain (V(H) or V(L)), by species, and by specificity. The species are selected using a pulldown menu, whereas the specificities can be selected from a list containing the unique specificities reported in the Kabat database. These facilities avoid mistakes and redundancies in the searches. Another feature, and probably the most important one, is that VIR.II introduces a classification of specificities in terms of the chemical and biochemical nature of the antigen, like anti-protein, anti-peptide, anti-hapten, etc. This classification has been useful in discovering patterns in the antigen-binding site of antibodies that correlate with the type of antigen the antibody interacts with. To illustrate this, while showing the capabilities of VIR.II, we analyze all the murine anti-peptide and anti-protein antibody sequences compiled as of July, 2000 in the Kabat database.

Amino Acid Sequence↗

PubMed2004

Modelling extracellular domains of GABA-A receptors: subtypes 1, 2, 3, and 5.

GABA is the main inhibitory neurotransmitter in the mammalian central nervous system. When GABA binds to the ubiquitous GABA-A receptors on neurons, chloride channels are activated leading to a rapid increase in chloride conductance that depresses excitatory depolarization. The GABA-A receptors are targets for many clinically important drugs, such as the benzodiazepines, general anaesthetics, and barbiturates. All of these drugs enhance the chloride current activated by GABA. Of the GABA-A receptor family, the subtype 2 is critical for the treatment of anxiety spectrum disorders. To avoid unwanted side effects, it is necessary to find highly selective drugs that interact only with subtype 2 but not with the related receptors such as subtypes 1, 3, and 5. To realize such a goal, it is important to have not only the 3D (dimensional) structure of subtype 2 but also the 3D structures of subtypes 1, 3, and 5. In this study, the 3D structures of all the four subtypes of GABA-A receptors have been derived. The computer-modeled heteropentameric structures bear the following features: (1) each of the five subunits in the pentamer has an intrachain disulfide bond, a hallmark of ligand-gated pentameric channels; (2) those residues which are sensitive to the binding of the benzodiazepine site ligands are grouped around the alpha1,2,3,5/gamma2 interfaces; and (3) those residues which are sensitive to the binding of GABA molecules are grouped around the alpha1,2,3,5/beta2 interfaces. All these findings are fully consistent with experimental observations. Meanwhile, for those sensitive or key residues, a close look at their subtle difference among the four subtypes has been provided through a highlighted superposition picture. In addition to providing the atomic coordinates, the predicted structures have further clarified some ambiguities that could not been uniquely determined by the existing experimental data, such as the directionality of the subunit arrangement in the heteropentamers. The 3D models may provide a reasonable structural frame or footing for designing highly selective drugs. The present models might be also useful in understanding the basic mechanism of operation of the GABA-A receptors, stimulating novel strategies for developing more specific drugs and better treatments.

Amino Acid Sequence↗

PubMed1991

Langmuir-Blodgett monolayer films of bacterial photosynthetic membranes and isolated reaction centers: preparation, spectrophotometric and electrochemical characterization.

The Langmuir-Blodgett (LB) film technique has been successfully applied to the construction of stable and photo-active films of chromatophore membranes and isolated reaction centers from two species of photosynthetic bacteria, Rhodobacter sphaeroides and Rhodopseudomonas viridis. LB films of these preparations were characterized at the air/water interface through compression isotherms and film stabilities. Films deposited on glass slides were analyzed by spectrophotometric and redox potentiometric techniques. The results obtained indicate that the in vivo properties of the photosynthetic apparatus in the deposited films are essentially unchanged. Furthermore, the pigments and redox cofactors in the films are highly oriented and offer a unique opportunity for structural and functional studies of the kind described in the accompanying paper (Biochim. Biophys. Acta 1057 (1991) 258-272).

Cytochrome c Group↗

PubMed2001

Prevention of T cell-driven complement activation and inflammation by tryptophan catabolism during pregnancy.

Indoleamine 2,3 dioxygenase (IDO) activity during pregnancy protects developing fetuses from maternal immune responses in CBA mice. We show here that fetal allografts were rejected only in mating combinations where paternally inherited tissue antigens elicited potent maternal T cell responses after exposure to IDO inhibitor. IDO inhibitor treatment triggered extensive inflammation at the maternal-fetal interface in susceptible mating combinations, which was characterized by complement deposition and hemorrhagic necrosis. Identical inflammatory responses occurred in B cell-deficient (RAG-I-/-) mothers that carried a monoclonal cohort of CD8+ T cells specific for a single paternally inherited fetal major histocompatibility complex antigen. Thus, fetal allograft rejection was accompanied by a unique form of inflammation that was characterized by T cell-dependent, antibody-independent activation of complement. In contrast, no inflammation, complement deposition or T cell infiltration was elicited when mice carrying syngeneic fetuses were exposed to IDO inhibitor. These data show that IDO activity protects the fetus by suppressing T cell-driven local inflammatory responses to fetal alloantigens.

Animals↗

PubMed2003

The airway epithelium: structural and functional properties in health and disease.

The major function of the respiratory epithelium was once thought to be that of a physical barrier. However, it constitutes the interface between the internal milieu and the external environment as well as being a primary target for inhaled respiratory drugs. It also responds to changes in the external environment by secreting a large number of molecules and mediators that signal to cells of the immune system and underlying mesenchyme. Thus, the epithelium is in a unique position to translate gene-environment interactions. Normally, the epithelium has a tremendous capacity to repair itself following injury. However, evidence is rapidly accumulating to show that the airway epithelium of asthmatics is abnormal and has increased susceptibility to injury compared to normal epithelium. Areas of detachment and fragility are a characteristic feature not observed in other inflammatory diseases such as COPD. In addition to being more susceptible to damage, normal repair processes are also compromised. Failure of appropriate growth and differentiation of airway epithelial cells will cause persistent mucosal injury. The response to traditional therapy such as glucocorticoids may also be compromised. However, whether the differences observed in asthmatic epithelium are a cause of or secondary to the development of the disease remains unanswered. Strategies to address this question include careful examination of the ontogeny of the disease in children and use of gene array technology should provide some important answers, as well as allow a better understanding of the critical role that the epithelium plays under normal conditions and in diseases such as asthma.

Asthma↗

PubMed2006

Structural determinants that target the hepatitis C virus core protein to lipid droplets.

Hepatitis C virus core protein is targeted to lipid droplets, which serve as intracellular storage organelles, by its C-terminal domain, termed D2. From circular dichroism and nuclear magnetic resonance analyses, we demonstrate that the major structural elements within D2 consist of two amphipathic alpha-helices (Helix I and Helix II) separated by a hydrophobic loop. Both helices require a hydrophobic environment for folding, indicating that lipid interactions contribute to their structural integrity. Mutational studies revealed that a combination of Helix I, the hydrophobic loop, and Helix II is essential for efficient lipid droplet association and pointed to an in-plane membrane interaction of the two helices at the phospholipid layer interface. Aside from lipid droplet association, membrane interaction of D2 is necessary for folding and stability of core following maturation at the endoplasmic reticulum membrane by signal peptide peptidase. These studies identify critical determinants within a targeting domain that enable trafficking and attachment of a viral protein to lipid droplets. They also serve as a unique model for elucidating the specificity of protein-lipid interactions between two membrane-bound organelles.

Amino Acid Sequence↗

PubMed2003

Purification of avian circulating primordial germ cells by nycodenz density gradient centrifugation.

1. Primordial germ cells (PGCs) are the progenitor cells for gametes. In aves, PGCs show a unique migration pathway, that is, they circulate temporarily through the bloodstream during early development. 2. In this study we developed a method to purify circulating primordial germ cells (cPGCs) in quail and chicks by Nycodenz density gradient centrifugation. 3. The process consisted of primary and secondary purification. In primary purification, cPGCs were enriched at the interface of 8 and 12% Nycodenz fractions. In secondary purification, cPGCs were harvested from 8% Nycodenz fraction at a purity of 90% and from 10% Nycodenz fraction at a purity of 70%. The recovery rate of cPGCs was over 70%. 4. This method would facilitate research on cPGCs' culture and the production of transgenic birds using cPGCs.

Animals↗

PubMed2006

Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data.

BACKGROUND: Over the past decade our laboratory has focused on understanding how soluble cytoskeleton-associated proteins interact with membranes and other lipid aggregates. Many protein domains mediating specific cell membrane interactions appear by fluorescence microscopy and other precision techniques to be partially inserted into the lipid bilayer. It is unclear whether these protein-lipid-interactions are dependent on shared protein motifs or unique regional physiochemistry, or are due to more global characteristics of the protein. RESULTS: We have developed a novel computational program that predicts a protein's lipid-binding site(s) from primary sequence data. Hydrophobic labeling, Fourier transform infrared spectroscopy (FTIR), film balance, T-jump, CD spectroscopy and calorimetry experiments confirm that the interfaces predicted for several key cytoskeletal proteins (alpha-actinin, Arp2, CapZ, talin and vinculin) partially insert into lipid aggregates. The validity of these predictions is supported by an analysis of the available three-dimensional structural data. The lipid interfaces predicted by our algorithm generally contain energetically favorable secondary structures (e.g., an amphipathic alpha-helix flanked by a flexible hinge or loop region), are solvent-exposed in the intact protein, and possess favorable local or global electrostatic properties. CONCLUSION: At present, there are few reliable methods to determine the region of a protein that mediates biologically important interactions with lipids or lipid aggregates. Our matrix-based algorithm predicts lipid interaction sites that are consistent with the available biochemical and structural data. To determine whether these sites are indeed correctly identified, and whether use of the algorithm can be safely extended to other classes of proteins, will require further mapping of these sites, including genetic manipulation and/or targeted crystallography.

Algorithms↗

PubMed2002

Exploring the interface between metallo-proteinase activity and growth factor and cytokine bioavailability.

Metallo-proteinases are implicated in many processes involved in tissue remodeling, cell motility, morphogenesis, and cell and organ growth and differentiation. Recent data suggest that several members of the metzincin family including the matrix metallo-proteinases (MMPs), adamalysin-related proteinases, and the newly described pappalysins, are intimately involved in the activation and/or release of cytokines and growth factors. We review how metzincins, working through unique mechanisms, influence the extracellular milieu of several important cytokines and growth factors including transforming growth factor-beta (TGF-beta), TNF-alpha, IGFs and HB-epidermal growth factor (EGF). Because metzincins can modulate the bioavailability of these peptides, they may serve as unique target molecules to control cytokine and growth factor action in the extracellular environment.

ADAM Proteins↗

PubMed2006

Dynamics and internal stress at the nanoscale related to unique thermomechanical behavior in polymer nanocomposites.

A small amount of alumina nanoparticles in polymethylmethacrylate causes a sharp depression of the glass transition temperature (Tg) accompanied by a toughening of the composite. We investigated this phenomenon using multispeckle x-ray photon correlation spectroscopy. Measurements reveal a dynamic structure factor that has the form exp[-(t/taua)beta], with beta greater than 1. We show for the first time that beta(T) tracks the internal stress at the polymer-particle interface. The internal stress, which we propose arises due to the entropic penalty that the polymer faces in the presence of the nanoparticles, engenders temporally heterogeneous dynamics. In the jammed glassy state, we show that the dominant fast relaxation mode--taumax--aided by a weak dewetting interface relieves the stress and follows the variations in Tg.

Journal Article↗