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Transmembrane helix-helix interactions: comparative simulations of the glycophorin a dimer.

The glycophorin helix dimer is a paradigm for the exploration of helix-helix interactions in integral membrane proteins. Two NMR structures of the dimer are known, one in a detergent micelle and one in a lipid bilayer. Multiple (4 x 50 ns) molecular dynamics simulations starting from each of the two NMR structures, with each structure in either a dodecyl phosphocholine (DPC) micelle or a dimyristoyl phosphatidylcholine (DMPC) bilayer, have been used to explore the conformational dynamics of the helix dimer. Analysis of the helix-helix interaction, mediated by the GxxxG sequence motif, suggests convergence of the simulations to a common model. This is closer to the NMR structure determined in a bilayer than to micelle structure. The stable dimer interface in the final simulation model is characterized by (i) Gly/Gly packing and (ii) Thr/Thr interhelix H-bonds. These results demonstrate the ability of extended molecular dynamics simulations in a lipid bilayer environment to refine membrane protein structures or models derived from experimental data obtained in protein/detergent micelles.

Cell Membrane↗

Structure of the OmpA-like domain of RmpM from Neisseria meningitidis.

RmpM is a putative peptidoglycan binding protein from Neisseria meningitidis that has been shown to interact with integral outer membrane proteins such as porins and TonB-dependent transporters. Here we report the 1.9 A crystal structure of the C-terminal domain of RmpM. The 150-residue domain adopts a betaalphabetaalphabetabeta fold, as first identified in Bacillus subtilis chorismate mutase. The C-terminal RmpM domain is homologous to the periplasmic, C-terminal domain of Escherichia coli OmpA; these domains are thought to be responsible for non-covalent interactions with peptidoglycan. From the structure of the OmpA-like domain of RmpM, we suggest a putative peptidoglycan binding site and identify residues that may be essential for binding. Both the crystal structure and solution experiments indicate that RmpM may exist as a dimer. This would promote more efficient peptidoglycan binding, by allowing RmpM to interact simultaneously with two glycan chains through its C-terminal, OmpA-like binding domain, while its (structurally uncharacterized) N-terminal domain could stabilize oligomers of porins and TonB-dependent transporters in the outer membrane.

Amino Acid Sequence↗

Genetic modifiers of cardiac arrhythmias.

Rhythmic contraction of a four-chambered mammalian heart is a highly coordinated process, requiring a functional conduction system. Both acquired and inherited forms of arrhythmia can be life threatening, and are major causes of mortality and morbidity in developed nations. Knowledge derived from human genetics and from studies of mouse genetic models has led to the discovery of multiple molecular defects responsible for arrhythmogenesis, including mutations in ion channels, cytoplasmic ion-channel-interacting proteins, gap-junction proteins, transcription factors and, most recently, a kinase subunit. However, phenotypic expression of a given mutation does not always appear to be uniform in human patients, implying a contribution from environmental factors and/or the presence of other genetic modifiers. Accumulating evidence suggests that 'multiple hits' affecting the interaction and integrity of multiple pathways might be responsible for many forms of arrhythmia.

AMP-Activated Protein Kinase Kinases↗

Structural determinants of the rigidity of the red cell membrane.

Although the stability and viscoelasticity of the red cell membrane are undoubtedly governed by the membrane's underlying protein skeleton, the mechanism by which this network controls elasticity is uncertain. The structural constraints, that impose end-to-end spacing on the spectrin molecules well below that in free solution, may impart rubbery (entropic) elasticity to the system. However, other enthalpic and entropic contributions due to interactions between spectrin chains or between spectrin and other proteins, the lipid bilayer or the solvent must also prevail. To relate structural features to elasticity, explicit measurements of membrane rigidity are required. The most widely used measurement is that of the membrane shear elastic modulus by micropipette aspiration. Analysis of genetic variants of membrane structure have shown that the density of spectrin is directly correlated with membrane rigidity. Although cross-linking of the skeleton increases rigidity, interruption of the continuity of the network by dissociating spectrin tetramers into dimers does not reduce rigidity as might be expected. On the other hand, external ligands that cause new interactions between integral proteins and the skeletal network do increase rigidity. Moreover, hereditary ovalocytes, which have a deletion of 9 amino acids from band 3 at the first point of entry into the membrane, are extremely rigid. This mutation is associated with decreased translational and rotational mobility of the band 3, and may impair flexural freedom of its cytoplasmic domain. It thus appears that elasticity may be regulated not only by the structure of the spectrin network, but also by its interactions with and freedom of motion relative to the lipid bilayer.

Chemical Phenomena↗

Functional interaction in establishment of ribosomal integrity between small subunit protein rpS6 and translational regulator rpL10/Grc5p.

Functional ribosomes synthesize proteins in all living cells and are composed of two labile associated subunits, which are made of rRNA and ribosomal proteins. The rRNA of the small 40S subunit (SSU) of the functional eukaryotic 80S ribosome decodes the mRNA molecule and the large 60S subunit (LSU) rRNA catalyzes protein synthesis. Recent fine structure determinations of the ribosome renewed interest in the role of ribosomal proteins in modulation of the core ribosomal functions. RpL10/Grc5p is a component of the LSU and is a multifunctional translational regulator, operating in 60S subunit biogenesis, 60S subunit export and 60S subunit joining with the 40S subunit. Here, we report that rpL10/Grc5p functionally interacts with the nuclear export factor Nmd3p in modulation of the cellular polysome complement and with the small subunit protein rpS6 in subunit joining and differential protein expression.

Base Sequence↗

A coupling mechanism to inter-relate regulatory with haem-haem interactions of haemoglobin.

The Me2+ (Zn2+ or Mg2+)-dependent increase in the oxygenation of Haemoglobin (Hb) is examined theoretically using an overview in scale of the interface of the alpha 1 beta 2 dimer of Hb. A model was developed showing that 2,3 DPG and Me2+ would maintain a pH-modulated mutually exclusive relationship as ligands of Hb because they both share a common binding His-beta (2)143. A symmetric relationship applies to alpha 2 beta 1. One atom of metal, within each dimer, would compete in turn with each of the haem groups to sequentially dislocate both proximal histidines during the transition from deoxyHb to oxyHb. Hence, the pH-modulated reaction path of the multiple equilibrium of Hb would integrate the interactions of either one 2,3 DPG with four histidines for the increase of hindrance effects, or the interactions of two Me2+ with four haem groups to increase their affinity for O2. The model predicts that increases in pO2 would increase the affinity of Hb for Me2+ and therefore for O2, simultaneously decreasing its affinity for 2,3 DPG and protons.

2,3-Diphosphoglycerate↗

The relationship of role-related variables to job satisfaction and commitment to the organization in a restructured hospital environment.

BACKGROUND AND PURPOSE: Many factors in today's hospitals can influence how physical therapists view their work experience. Changing roles, with the accompanying stress, and professionalism may contribute to a therapist's perception of his or her job and the organization in which he or she works. In this study, the relationship between changes in physical therapist role behaviors following hospital restructuring and 2 work-related outcomes--job satisfaction and commitment to the organization--was studied. The influence of stress and occupational commitment on these outcomes also was examined. SUBJECTS AND METHODS: Through a survey of 273 hospital-based physical therapists, changes in physical therapist role behaviors, levels of stress, occupational commitment, job satisfaction, and commitment to the organization following restructuring were identified and examined. RESULTS: Six role behavior dimensions reflecting professional and organizational responsibilities were identified from the data. After controlling for sample demographics, the professional role behaviors, specifically those reflecting interaction and integration with other practitioners, appeared to exert a small, but positive, influence on job satisfaction and commitment to the organization. In addition, occupational commitment had a positive influence, whereas stress had a negative influence on job satisfaction and commitment to the organization. DISCUSSION AND CONCLUSION: Multiple aspects of a clinician's role could influence job satisfaction and commitment to the organization following hospital restructuring. The most influential factor was stress, which often accompanies organizational change. However, the positive influence of occupational commitment and the role behaviors that involve increased interaction with other people reflect professional role characteristics described in the Guide to Physical Therapist Practice were noted.

Adult↗

Lipid-mediated protein interaction in membranes.

This study describes the effects ensuing from a non-specific interaction between membrane integral proteins and the surrounding lipids. The results are obtained using an appropriate molecular field theory to describe the ordering of membrane lipids. The modification of the lipid structure near a protein molecule, while most pronounced within the annulus of the first neighbour molecules, extends two or three layers beyond the annulus. The ordering of lipids within the annulus has a modified temperature dependence, and becomes a continuous function of temperature for low lipid/protein ratios. The change in order of lipid molecules surrounding a protein leads to an indirect, lipid-mediated interaction between membrane integral proteins. This interaction depends sensitively on the bulk lipid order. Under favourable circumstances, it gives rise to protein aggregation.

Binding Sites↗

Ferrichrome transport in Escherichia coli K-12: altered substrate specificity of mutated periplasmic FhuD and interaction of FhuD with the integral membrane protein FhuB.

FhuD is the periplasmic binding protein of the ferric hydroxamate transport system of Escherichia coli. FhuD was isolated and purified as a His-tag-labeled derivative on a Ni-chelate resin. The dissociation constants for ferric hydroxamates were estimated from the concentration-dependent decrease in the intrinsic fluorescence intensity of His-tag-FhuD and were found to be 0.4 microM for ferric aerobactin, 1.0 microM for ferrichrome, 0.3 microM for ferric coprogen, and 5.4 microM for the antibiotic albomycin. Ferrichrome A, ferrioxamine B, and ferrioxamine E, which are poorly taken up via the Fhu system, displayed dissociation constants of 79, 36, and 42 microM, respectively. These are the first estimated dissociation constants reported for a binding protein of a microbial iron transport system. Mutants impaired in the interaction of ferric hydroxamates with FhuD were isolated. One mutated FhuD, with a W-to-L mutation at position 68 [FhuD(W68L)], differed from wild-type FhuD in transport activity in that ferric coprogen supported promotion of growth of the mutant on iron-limited medium, while ferrichrome was nearly inactive. The dissociation constants of ferric hydroxamates were higher for FhuD(W68L) than for wild-type FhuD and lower for ferric coprogen (2.2 microM) than for ferrichrome (156 microM). Another mutated FhuD, FhuD(A150S, P175L), showed a weak response to ferrichrome and albomycin and exhibited dissociation constants two- to threefold higher than that of wild-type FhuD. Interaction of FhuD with the cytoplasmic membrane transport protein FhuB was studied by determining protection of FhuB degradation by trypsin and proteinase K and by cross-linking experiments. His-tag-FhuD and His-tag-FhuD loaded with aerobactin specifically prevented degradation of FhuB and were cross-linked to FhuB. FhuD loaded with substrate and also FhuD free of substrate were able to interact with FhuB.

Base Sequence↗

Systematic identification and characterization of regulators of aryl hydrocarbon receptor signaling.

The human aryl hydrocarbon receptor (AHR) integrates chemical signals derived from the environment, gut microbes, and endogenous sources to regulate processes ranging from intestinal barrier integrity to xenobiotic detoxification. Despite strong evidence that dysregulation of AHR signaling is a causal factor in metabolic and autoimmune disorders, we currently lack a comprehensive understanding of the factors that regulate AHR activity in human cells. Here, we use genome-scale CRISPR screening to systematically identify regulators of AHR signaling in hepatocytes. The resulting datasets recapitulate the core AHR signaling pathway and identify a large network of regulators. Many of these factors have roles beyond AHR signaling, reflecting that AHR signaling is deeply integrated into human cell biology. We further dissect this network to reveal novel modes of regulation of AHR expression, protein levels, and signaling. For example, we find that the E3 ubiquitin ligase UBR5 sustains AHR signaling by counteracting degradation of ligand-bound AHR. Finally, we identify components of the AHR regulatory network that are specific to cell types and ligands as potential nodes to manipulate AHR signaling in a targeted manner for therapeutic benefit. Overall, our results define the regulatory network that underpins AHR activation, with implications for our understanding of host-microbe interactions and integrative chemosensation and the etiology of metabolic and inflammatory disorders.

Journal Article↗

Java experiments for introductory cognitive psychology courses.

Interactive on-line experiments provide a unique and useful method for communicating material to students that is otherwise cumbersome and often confusing. The Java programming language is particularly suited for Internet-based programming applications of this sort because it bypasses many technical issues, including resource availability, security, and cross-platform compatibility. In most cases, topics appropriate to this medium of presentation should (1) not be easily demonstrated by other means, (2) represent an important finding in the field, and (3) be robust with respect to variations in both participants and equipment. The present paper outlines the integration of interactive experiments into an introductory cognitive psychology classroom, describing several experiments currently available on the World-Wide Web (WWW). Evaluation of the technical aspects of the technology as well as expansion of the format to other courses is discussed.

Cognitive Science↗

Subunit b of the membrane moiety (F0) of ATP synthase (F1F0) from Escherichia coli is indispensable for H+ translocation and binding of the water-soluble F1 moiety.

The ATP synthase complex, designated F1F0, of Escherichia coli is composed of a water-soluble portion (F1; membrane-associated ATPase, EC 3.6.1.3) with ATP-hydrolyzing activity and a membrane-integrated part (F0) with H+-translocating activity. F0 is built up from three kinds of subunits (a, b, and c). We have isolated the F0 portion directly from membranes of an E. coli strain (KY 7485) that overproduces the enzyme several fold. Subunit b was extracted from purified F0 by two methods. One method included prolonged incubation of the F0 complex in the presence of trichloroacetate (2.5 M) and the separation of subunit b and an a-c complex by gel filtration. Alternatively, subunit b was extracted by deoxycholate and separated from the a-c complex by hydrophobic-interaction chromatography. Integrated into liposomes, the a-c complex exhibited neither H+ uptake nor binding of F1. However, a functional F0 complex was reconstituted by adding stoichiometric amounts of subunit b to the a-c complex.

ATP Synthetase Complexes↗

Rgg144/SHP144-controlled streptolancidin D mediates intra-species competition in Streptococcus pneumoniae with cumulative effect from other bacteriocins and fratricide.

UNLABELLED: Streptococcus pneumoniae is a major colonizer of the human nasopharynx, where inter- and intra-strain competition plays a critical role in shaping population structure and influencing vaccine outcomes. Bacteriocins are key mediators of intra-species competition, yet many of their functions and regulatory mechanisms remain poorly understood. Here, we identify and characterize streptolancidin D, a previously uncharacterized bacteriocin encoded by the sldA-T locus, and demonstrate its contribution to pneumococcal competition. Using isogenic streptolancidin-producing and non-producing variants of a naturally colonizing strain, we show that sldA-T contributes to the inhibition of competitor strains in in vitro biofilms and during murine co-colonization. Importantly, streptolancidin D also inhibited in vitro a subset of genetically diverse pneumococcal isolates representing multiple serotypes, whereas non-producing variants showed no activity. This indicates that its effect is broad and not restricted to isogenic interactions. Genomic analysis of over 7,500 pneumococcal genomes revealed that sldA-T is present in ~12% of isolates, with lineage-associated distribution patterns, and is consistently encoded downstream of the Rgg144/SHP144 quorum sensing system. We further demonstrate that sldA-T is regulated by this system, with sldA-T promoter activity abolished in a SHP-deficient background and partially restored by exogenous peptide stimulation. Finally, we show that streptolancidin D acts in concert with other bacteriocin systems and competence-mediated fratricide, highlighting a multifactorial antimicrobial strategy that enhances pneumococcal competitiveness. Overall, our findings identify a quorum sensing-regulated bacteriocin that contributes to pneumococcal competition and helps shape population dynamics. IMPORTANCE: Bacteriocins are central to bacterial competition and niche occupation, particularly in structured environments like the human nasopharynx. While several pneumococcal bacteriocins have been characterized, the functions of many remain unknown, limiting our understanding of how these systems shape strain fitness and population dynamics. We characterize streptolancidin D, a bacteriocin that enhances intraspecies competitiveness in vitro and in vivo and contributes to the inhibition of genetically diverse pneumococcal strains. We demonstrate that its expression is tightly regulated by the conserved Rgg144/SHP144 quorum sensing system and that the locus is distributed and shows synteny across multiple pneumococcal lineages. Our findings reveal that streptolancidin D operates within a broader network of bacteriocins and competence-associated mechanisms that collectively shape competitive interactions. By integrating genomic, functional, and regulatory analyses, this work expands the known repertoire of pneumococcal antimicrobial systems and provides new insights into the mechanisms underpinning competition and population structure in S. pneumoniae.

Bacteriocins↗

Sea urchin spectrin in oogenesis and embryogenesis: a multifunctional integrator of membrane-cytoskeletal interactions.

Using indirect immunofluorescence microscopy on semithin cryosections of maturing ovarian tissue, eggs, and developing embryos, we have mapped the cellular distribution and dynamic redistribution of spectrin in oogenesis and early embryogenesis. During oogenesis, spectrin is initially found in the cortex of oogonia and previtellogenic oocytes, and later accumulates in the cytoplasm of vitellogenic oocytes on the surfaces of cortical granules, pigment granules/acidic vesicles, and yolk platelets. Following egg activation, spectrin undergoes a rapid redistribution coincident with three major developmental events including: (1) restructuring of the cell surface, (2) translocation of pigment granules/acidic vesicles to the cortex during the first cell cycle, and (3) amplification of the embryo's surface during the rapid cleavage phase of early embryogenesis. The synthesis and storage of spectrin during oogenesis appears to prime the egg with a preestablished pool of membrane-cytoskeletal precursor for use during embryogenesis. Results from this study support the hypothesis that spectrin may function as a key integrator and modulator of multiple membrane-cytoskeletal functions during embryonic growth and cellular differentiation.

Animals↗

Phase-oriented treatment of structural dissociation in complex traumatization: overcoming trauma-related phobias.

The theory of structural dissociation of the personality proposes that patients with complex trauma-related disorders are characterized by a division of their personality into different prototypical parts, each with its own psychobiological underpinnings. As one or more apparently normal parts (ANPs), patients have a propensity toward engaging in evolutionary prepared action systems for adaptation to daily living to guide their actions. Two or more emotional parts (EPs) are fixated in traumatic experience. As EPs, patients predominantly engage action systems related to physical defense and attachment cry. ANP and EP are insufficiently integrated, but interact and share a number of dispositions of the personality (e.g., speaking). All parts are stuck in maladaptive action tendencies that maintain dissociation, including a range of phobias, which is a major focus of this article. Phase-oriented treatment helps patients gradually develop adaptive mental and behavioral actions, thus overcoming their phobias and structural dissociation. Phase 1, symptom reduction and stabilization, is geared toward overcoming phobias of mental contents, dissociative parts, and attachment and attachment loss with the therapist. Phase 2, treatment of traumatic memories, is directed toward overcoming the phobia of traumatic memories, and phobias related to insecure attachment to the perpetrator(s), particularly in EPs. In Phase 3, integration and rehabilitation, treatment is focused on overcoming phobias of normal life, healthy risk-taking and change, and intimacy. To the degree that the theory of structural dissociation serves as an integrative heuristic for treatment, it should be compatible with other theories that guide effective treatment of patients with complex dissociative disorders.

Adaptation, Psychological↗

H. influenzae Consortium: integrative study of H. influenzae-human interactions.

Developments in high-throughput analysis tools coupled with integrative computational techniques have enabled biological studies to reach new levels. The ability to correlate large volumes of diverse data types into cohesive models of organism function has spawned a new systematic approach to biological investigation. The creation of a new consortium has been proposed to investigate a single organism utilizing these comprehensive approaches. The Haemophilus influenzae Consortium (HIC) would be comprised of five laboratories, each providing separate and complementary areas of expertise in the study of Haemophilus influenzae (HI). The 5-year study proposes to develop coherent models of HI, both as a stand-alone organism, and more importantly, as a human pathogen. Studies in growth condition specificity followed by genomic, metabolic, and proteomic experimentation will be combined and integrated through computational and experimental analyses to form dynamic and predictive models of HI and its responses. Data from the HIC will allow greater understanding of cellular behavior, pathogen-host interactions, bacterial infection, and provide future scientific endeavors with a template for studies of other pathogens.

Bacterial Adhesion↗

Somitogenesis.

We are still far from understanding "somitogenesis" as a whole, but there is an emerging picture of the tissue interactions and molecular mechanisms that underlie and govern various aspects of this essential multistep patterning process in vertebrates. The ability to form segmental units appears to be a property specific to the paraxial mesoderm (as opposed to lateral or limb mesoderm), and this ability is probably acquired during early development, when paraxial mesoderm is specified and emerges from the primitive streak. Signaling molecules expressed in the primitive streak and tail bud are prime candidates involved in specifying paraxial (as well as other mesodermal) fates. Increasing levels of signaling molecules may be required in posterior regions of the embryo, and combinatorial signals may be essential to specify the paraxial mesoderm along the entire anterior-posterior axis. However, most of the pivotal signals, and the ways in which they are integrated and interact, remain enigmatic. Once the paraxial mesoderm is formed, segmentation proceeds largely without the requirement for continuous interactions with surrounding tissues. Somitomeres represent a morphologic pattern in the mesenchymal presomitic mesoderm, but their significance for somite formation is unclear. Molecular patterns are established in the presomitic mesoderm and probably are of functional significance. Cell interactions within the paraxial mesoderm appear to be involved in forming segment borders and ensuring their maintenance during subsequent differentiation of somites. These interactions are, at least in part, mediated by components of the conserved Notch signaling pathway, which may have multiple functions during somitogenesis. Epithelial somites are clearly a result of segmentation, but epithelialization is not the mechanism to form segments, supporting the idea that the basic mechanisms that govern segmentation in the mesoderm of vertebrates are very similar in different species despite divergent types of resulting segments (i.e., epithelial somites versus rotated myotomes). Concomitantly with segmentation, segment polarity and positional specification are established. How these processes are linked to, and depend on, each other is unknown, as is how they are regulated and how segmentation is coordinated on both sides of the neural tube. In contrast to early patterning in the presomitic mesoderm, patterning of the mature somites during their subsequent differentiation is the result of extensive tissue interactions. Virtually all tissues in close proximity to somites provide signals that are involved in induction or inhibition of particular differentiation pathways, but how these pathways are initiated is less clear. Some of the molecules mediating inductive signals and tissue interactions are known, and a growing number of candidate genes are potentially involved in regulating various steps of somitogenesis. The roles of these genes have yet to be analyzed. In addition, the molecular genetic analysis of mutations affecting somitogenesis, which were collected in the mouse and more recently in the zebrafish (Driever et al., 1996; Haffter et al., 1996; van Eeden et al., 1996), promises to add important new insights into this process. Much remains to be done, but the tools are at hand to provide further understanding of the molecular mechanisms underlying somitogenesis.

Animals↗

A functional neuroimaging study of motivation and executive function.

Executive functions, such as working memory, must intersect with functions that determine value for the organism. Functional imaging work in humans and single-unit recordings in non-human primates provide evidence that PFC might integrate motivational context with working memory. With functional magnetic resonance imaging (fMRI), we addressed the question of motivation and working memory, using a trial-related design in an object-working memory task. The design permitted the analysis of BOLD signal at separate stages, corresponding to encoding, maintenance, and retrieval. Subjects were motivated by a financial incentive during the task, such that they could gain a high or a low reward. The two different levels of reward also entailed greater or lesser risk of losing money for incorrect responses. In the high, relative to the low, reward condition, subjects shifted response bias, and showed a trend to greater sensitivity. We found main effects in fMRI BOLD signal for reward, which overlapped with BOLD effects for maintenance of information, in the right superior frontal sulcus and bilateral intraparietal sulcus. We also found an interaction between reward and retrieval from working memory in the right dorsolateral prefrontal cortex. Main effects of load and reward occurred in adjacent regions of the ventrolateral PFC during retrieval. The data demonstrate that when subjects perform a simple working memory task, financial incentives motivate performance and interact with some of the same neural networks that process various stages of working memory. Areas of overlap and interaction may integrate information about value, or they may represent a general effect of motivation increasing neural effort.

Adult↗