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At least 703 records · Page 39Linked to original sources
PubMed2007

Does tetracycline bind helix 2 of prion? An integrated spectroscopical and computational study of the interaction between the antibiotic and alpha helix 2 human prion protein fragments.

We demonstrate here that tetracycline (TC) can strongly interact (KD' = 189 +/- 7 nM) with model peptides derived from the C-terminal globular domain of the prion protein, hPrP [173-195], and that interaction concerns residues within the C-terminal half of the helix 2, a short region previously indicated as endowed with ambivalent conformational behavior and implicated in PrP conversion to the beta-sheet-rich, infective scrapie variant. Data have been confirmed by binding studies with the N-terminal truncated 180-195 variant that displays a dissociation constant of 483 +/- 30 nM. Remarkably, TC does not influence the structure of the N-terminally fluoresceinated peptides that both show alpha-helical conformations. Docking calculations and molecular dynamics simulations suggest a direct, strong interaction of the antibiotic with exposed side chain functional groups of threonines 190-193 on the solvent-exposed surface of helix 2.

Amino Acid Sequence↗
PubMed1996

An integrative framework for explaining reactions to decisions: interactive effects of outcomes and procedures.

The authors suggest that procedural and distributive factors interactively combine to influence individuals' reactions to their encounters with other people, groups, and organizations. Results from 45 independent samples (reviewed herein) show that (a) level of procedural justice is more positively related to individuals' reactions when outcome fairness or valence is relatively low and (b) level of outcome fairness or valence is more positively related to individuals' reactions when procedural justice is relatively low. They present various explanations of the interaction effect. Theoretical progress may be achieved through future efforts to delineate the conditions under which each of the explanations is more versus less likely to account for the interaction.

Attitude↗
PubMed2001

Feynman's path-integral approach for intense-laser-atom interactions.

Atoms interacting with intense laser fields can emit electrons and photons of very high energies. An intuitive and quantitative explanation of these highly nonlinear processes can be found in terms of a generalization of classical Newtonian particle trajectories, the so-called quantum orbits. Very few quantum orbits are necessary to reproduce the experimental results. These orbits are clearly identified, thus opening the way for an efficient control as well as previously unknown applications of these processes.

Journal Article↗
PubMed2005

Imaging molecular interactions in living cells.

Hormones integrate the activities of their target cells through receptor-modulated cascades of protein interactions that ultimately lead to changes in cellular function. Understanding how the cell assembles these signaling protein complexes is critically important to unraveling disease processes, and to the design of therapeutic strategies. Recent advances in live-cell imaging technologies, combined with the use of genetically encoded fluorescent proteins, now allow the assembly of these signaling protein complexes to be tracked within the organized microenvironment of the living cell. Here, we review some of the recent developments in the application of imaging techniques to measure the dynamic behavior, colocalization, and spatial relationships between proteins in living cells. Where possible, we discuss the application of these different approaches in the context of hormone regulation of nuclear receptor localization, mobility, and interactions in different subcellular compartments. We discuss measurements that define the spatial relationships and dynamics between proteins in living cells including fluorescence colocalization, fluorescence recovery after photobleaching, fluorescence correlation spectroscopy, fluorescence resonance energy transfer microscopy, and fluorescence lifetime imaging microscopy. These live-cell imaging tools provide an important complement to biochemical and structural biology studies, extending the analysis of protein-protein interactions, protein conformational changes, and the behavior of signaling molecules to their natural environment within the intact cell.

Animals↗
PubMed2005

Meeting report: Structural determination of environmentally responsive proteins.

The three-dimensional structure of gene products continues to be a missing lynchpin between linear genome sequences and our understanding of the normal and abnormal function of proteins and pathways. Enhanced activity in this area is likely to lead to better understanding of how discrete changes in molecular patterns and conformation underlie functional changes in protein complexes and, with it, sensitivity of an individual to an exposure. The National Institute of Environmental Health Sciences convened a workshop of experts in structural determination and environmental health to solicit advice for future research in structural resolution relative to environmentally responsive proteins and pathways. The highest priorities recommended by the workshop were to support studies of structure, analysis, control, and design of conformational and functional states at molecular resolution for environmentally responsive molecules and complexes; promote understanding of dynamics, kinetics, and ligand responses; investigate the mechanisms and steps in posttranslational modifications, protein partnering, impact of genetic polymorphisms on structure/function, and ligand interactions; and encourage integrated experimental and computational approaches. The workshop participants also saw value in improving the throughput and purity of protein samples and macromolecular assemblies; developing optimal processes for design, production, and assembly of macromolecular complexes; encouraging studies on protein-protein and macromolecular interactions; and examining assemblies of individual proteins and their functions in pathways of interest for environmental health.

Environmental Health↗
PubMed2002

Interactions between heterotypic stressors and corticosterone reveal integrative mechanisms for controlling corticotropin-releasing hormone gene expression in the rat paraventricular nucleus.

Although the convergence of neural and humoral afferent information onto paraventricular neuroendocrine corticotropin-releasing hormone (CRH) neurons is a major determinant for adaptive stress responses, the underlying integrative mechanisms are poorly understood. To dissect the relative contributions made by neural afferents and corticosterone to these processes, we determined how the concurrent application of two heterotypic physiological stressors, chronic dehydration (produced by drinking hypertonic saline) and sustained hypovolemia (produced by subcutaneous injections of polyethylene glycol), is interpreted by the synthetic and secretory activity of CRH neurons using in situ hybridization and plasma ACTH measurements. These two stressors are encoded by relatively simple, distinct, and well defined sets of neural afferents to CRH neurons. Both increase plasma corticosterone, but they have opposing actions on CRH gene expression when applied separately. In the first experiment, we showed that chronic dehydration suppresses CRH gene transcription after hypovolemia, but not the preproenkephalin and c-fos mRNA responses or ACTH secretion. In the second, we showed that negative feedback actions of corticosterone do not suppress CRH gene activation after hypovolemia, but instead determine the prestress lower limit of a range within which the CRH gene then responds. Collectively, these data show that at least two processes are integrated to control how the CRH gene responds to multiple stimuli. First, the presence of corticosterone, which although permissive for appropriately activating the CRH gene during hypovolemia, does not mediate the suppressed gene response. Second, neural afferent-driven processes that encode dehydration play a central role in suppressing CRH activation.

Administration, Oral↗
PubMed1993

Restorative dentistry. Interactions with periodontics.

The integration of periodontal considerations with restorative planning is now the standard of care. Instilling motivation toward prevention continues to be one of our most challenging goals. A stable healthy periodontium and minimum restorative needs are the resulting rewards. With the use of available knowledge and microbial testing for both periodontitis and caries susceptibility, we now can offer our patients a higher likelihood of success in retaining natural teeth and implants.

Dental Caries↗
PubMed2006

KlRHO1 and KlPKC1 are essential for cell integrity signalling in Kluyveromyces lactis.

Cell integrity in yeasts is ensured by a rigid cell wall whose synthesis is triggered by a MAP kinase-mediated signal-transduction cascade. Upstream regulatory components of this pathway in Saccharomyces cerevisiae involve a single protein kinase C, which is regulated by interaction with the small GTPase Rho1. Here, two genes were isolated which encode these proteins from Kluyveromyces lactis (KlPKC1 and KlRHO1). Sequencing showed ORFs which encode proteins of 1,161 and 208 amino acids, respectively. The deduced proteins shared 59 and 85 % overall amino acid identities, respectively, with their homologues from S. cerevisiae. Null mutants in both genes were non-viable, as shown by tetrad analyses of the heterozygous diploid strains. Overexpression of the KlRHO1 gene under the control of the ScGAL1 promoter severely impaired growth in both S. cerevisiae and K. lactis. On the other hand, a similar construct with KlPKC1 did not show a pronounced phenotype. Two-hybrid analyses showed interaction between Rho1 and Pkc1 for the K. lactis proteins and their S. cerevisiae homologues. A green fluorescent protein (GFP) fusion to the C-terminal end of KlPkc1 located the protein to patches in the growing bud, and at certain stages of the division process also to the bud neck. N-terminal GFP fusions to KlRho1 localized mainly to the cell surface (presumably the cytoplasmic side of the plasma membrane) and to the vacuole, with some indications of traffic from the former to the latter. Thus, KlPkc1 and KlRho1 have been shown to serve vital functions in K. lactis, to interact in cell integrity signalling and to traffic between the plasma membrane and the vacuole.

Amino Acid Sequence↗
PubMed2004

Control of yeast filamentous-form growth by modules in an integrated molecular network.

On solid growth media with limiting nitrogen source, diploid budding-yeast cells differentiate from the yeast form to a filamentous, adhesive, and invasive form. Genomic profiles of mRNA levels in Saccharomyces cerevisiae yeast-form and filamentous-form cells were compared. Disparate data types, including genes implicated by expression change, filamentation genes known previously through a phenotype, protein-protein interaction data, and protein-metabolite interaction data were integrated as the nodes and edges of a filamentation-network graph. Application of a network-clustering method revealed 47 clusters in the data. The correspondence of the clusters to modules is supported by significant coordinated expression change among cluster co-member genes, and the quantitative identification of collective functions controlling cell properties. The modular abstraction of the filamentation network enables the association of filamentous-form cell properties with the activation or repression of specific biological processes, and suggests hypotheses. A module-derived hypothesis was tested. It was found that the 26S proteasome regulates filamentous-form growth.

Cell Cycle↗
PubMed2005

A contribution to the theory of preferential interaction coefficients.

A simple and complete derivation of the relation between concentration-based preferential interaction coefficients and integrals over the relevant pair correlation functions is presented for the first time. Certain omissions from the original treatment of pair correlation functions in multicomponent thermodynamics are also addressed. Connections between these concentration-based quantities and the more common molality-based preferential interaction coefficients are also derived. The pair correlation functions and preferential interaction coefficients of both solvent (water) and cosolvent (osmolyte) in the neighborhood of a macromolecule contain contributions from short-range repulsions and generic long-range attractions originating from the macromolecule, as well as from osmolyte-solvent exchange reactions beyond the macromolecular surface. These contributions are evaluated via a heuristic analysis that leads to simple insightful expressions for the preferential interaction coefficients in terms of the volumes excluded to the centers of the water and osmolyte molecules and a sum over the contributions of exchanging sites in the surrounding solution. The preferential interaction coefficients are predicted to exhibit the experimentally observed dependence on osmolyte concentration. Molality-based preferential interaction coefficients that were reported for seven different osmolytes interacting with bovine serum albumin are analyzed using the this formulation together with geometrical parameters reckoned from the crystal structure of human serum albumin. In all cases, the excluded volume contribution, which is the volume excluded to osmolyte centers minus that excluded to water centers in units of V1, exceeds in magnitude the contribution of the exchange reactions. Under the assumption that the exchange contribution is dominated by sites in the first surface-contiguous layer, the ratio of the average exchange constant to its neutral random value is determined for each osmolyte. These ratios all lie in the range 1.0 +/- 0.15, which indicates rather slight deviations from random occupation near the macromolecular surface. Finally, a mechanism is proposed whereby the chemical identity of an osmolyte might be concealed from partially ordered multilayers of water in clefts, grooves, and pits, and its consequences are noted.

Algorithms↗
PubMed2000

CBP (CREB binding protein) integrates NF-kappaB (nuclear factor-kappaB) and glucocorticoid receptor physical interactions and antagonism.

Nuclear factor-kappaB (NF-kappaB) and the glucocorticoid receptor (GR) are transcription factors with opposing actions in the modulation of immune/inflammatory responses. NF-kappaB induces the expression of proinflammatory genes, while GR suppresses immune function in part by suppressing expression of the same genes. Previously, we demonstrated that physiological antagonism between NF-kappaB and GR is due to a mutual transcriptional antagonism that requires the p65 subunit of NF-kappaB and multiple domains of GR (1). To elucidate the mechanism(s) of NF-kappaB p65 and GR transcriptional antagonism, we analyzed the interactions of wild-type p65 and p65 RHD (rel homology domain, a dominant negative mutant of p65 which lacks a transactivation domain) with GR. We show that p65RHD blocks p65-mediated transactivation, yet does not block the repression of GR transactivation by p65, indicating that transcriptional activity by p65 is not required to repress GR function. Both p65 and p65 RHD physically interact with GR, but only intact p65 represses GR-mediated signaling, implicating the p65 transactivation domain in the transcriptional repression of GR. To further characterize p65-GR interactions, we examined the role of the transcriptional co-integrator CREB binding protein (CBP) in their mutual antagonism. GR-mediated repression of p65 transactivation and p65-mediated repression of GR transactivation, as well as the physical interaction between NF-kappaB and GR, are enhanced by CBP. GR bound to the antagonist RU 486, although transcriptionally inactive, retains the ability to repress p65 transactivation. However, CBP does not physically interact with antagonist-bound GR and does not enhance its repressive effect on p65. These data suggest that CBP functions as an integrator of p65/GR physical interaction, rather than as a limiting cofactor for which p65 and GR compete.

Animals↗
PubMed2005

Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-Ter complex.

The arrest of DNA replication in Escherichia coli is triggered by the encounter of a replisome with a Tus protein-Ter DNA complex. A replication fork can pass through a Tus-Ter complex when traveling in one direction but not the other, and the chromosomal Ter sites are oriented so replication forks can enter, but not exit, the terminus region. The Tus-Ter complex acts by blocking the action of the replicative DnaB helicase, but details of the mechanism are uncertain. One proposed mechanism involves a specific interaction between Tus-Ter and the helicase that prevents further DNA unwinding, while another is that the Tus-Ter complex itself is sufficient to block the helicase in a polar manner, without the need for specific protein-protein interactions. This review integrates three decades of experimental information on the action of the Tus-Ter complex with information available from the Tus-TerA crystal structure. We conclude that while it is possible to explain polar fork arrest by a mechanism involving only the Tus-Ter interaction, there are also strong indications of a role for specific Tus-DnaB interactions. The evidence suggests, therefore, that the termination system is more subtle and complex than may have been assumed. We describe some further experiments and insights that may assist in unraveling the details of this fascinating process.

Amino Acid Sequence↗
PubMed2006

The scope of integrated modelling: system boundaries, sub-systems, scales and disciplines.

Integrated modelling has become an urgent issue of urban drainage and wastewater treatment planning. The scope of integrated modelling, system boundaries and disciplines to be involved are addressed in view of future developments and new paradigms in urban drainage, demanding the inclusion of the full urban water cycle. A system analysis is demonstrated to identify relevant sub-systems and components, processes and interactions within the urban water system. The permissibility to exclude subsystems or neglect interactions is evaluated. Integrated modelling of urban water system is characterised as an ambitious task in regard to system complexity, heterogeneous scales and interface problems. The methodical status quo is characterised in preliminary approaches towards integrated modelling. It is concluded that it does not seem promising to create and apply one entity model for the scope of integrated urban water modelling. Instead, the development of adequate and efficient IT frameworks is identified as the key issue of integrated modelling. Harmonising interfaces to facilitate the linking of existing models is presented as the objective of a European research project HarmonlT and the U.S. EPA Multimedia Integrated Modelling System project MIMS.

Cities↗