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PubMed2004

Biochemical and structural basis for partially redundant enzymatic and transcriptional functions of DCoH and DCoH2.

An inherited form of diabetes, maturity-onset diabetes of the young type 3 (MODY3), results from mutations in the transcriptional activator, hepatocyte nuclear factor-1alpha (HNF1alpha). Transcription by HNF1alpha is stimulated by the bifunctional coactivator DCoH (dimerization cofactor of HNF1). Strikingly, an HNF1alpha deletion in mice causes more severe phenotypes than a DCoH deletion. It has been hypothesized that a DCoH homolog, DCoH2, partially complements the DCoH deletion. To test this idea, we determined the biochemical properties and the 1.6-A-resolution crystal structure of DCoH2. Like DCoH, DCoH2 forms a tetramer, displays pterin-4alpha-carbinolamine dehydratase activity, and binds HNF1alpha in vivo and in vitro. DCoH and DCoH2 adopt identical folds with structural differences confined largely to the protein surfaces and the tetramer interface. In contrast to the hyperstable DCoH tetramer, DCoH2 readily disproportionates and forms a 2:2 complex with HNF1 in vitro. Phylogenetic analysis reveals six major subfamilies of DCoH proteins, including unique DCoH and DCoH2 branches in metazoans. These results suggest distinct roles for DCoH and DCoH2. Differences in conserved surface residues could mediate binding to different effectors. We propose that HNF1alpha binding kinetics may distinguish regulation by DCoH2, under thermodynamic control, from regulation by DCoH, under kinetic control.

Amino Acid Sequence↗

PubMed2003

Identification of a family of endocytic proteins that define a new alpha-adaptin ear-binding motif.

Endocytosis by clathrin-coated vesicles (CCVs) is an important mechanism mediating protein internalization. Here, we show that two proteins identified through a proteomics analysis of CCVs are new components of the endocytic machinery. The proteins, named NECAP (adaptin-ear-binding coat-associated protein) 1 and 2, are paralogues that display no sequence similarity or common domains with any known protein. Both are enriched in CCV coats, and further analysis of the brain-enriched isoform, NECAP 1, shows its partial localization to clathrin-coated pits and direct binding to the globular ear domain of the alpha-adaptin subunit (alpha-ear) of the adaptor protein 2 (AP-2) complex. Intriguingly, this interaction is mediated by a new motif, WVQF, that uses a distinct alpha-ear interface relative to known alpha-ear-binding partners. Disruption of this interaction blocks clathrin-mediated endocytosis. Together, our studies identify a new family of endocytic proteins that define a unique AP-2-binding motif.

Adaptor Protein Complex alpha Subunits↗

PubMed2000

The structural basis of substrate activation in yeast pyruvate decarboxylase. A crystallographic and kinetic study.

The crystal structure of the complex of the thiamine diphosphate dependent tetrameric enzyme pyruvate decarboxylase (PDC) from brewer's yeast strain with the activator pyruvamide has been determined to 2.4 A resolution. The asymmetric unit of the crystal contains two subunits, and the tetrameric molecule is generated by crystallographic symmetry. Structure analysis revealed conformational nonequivalence of the active sites. One of the two active sites in the asymmetric unit was found in an open conformation, with two active site loop regions (residues 104-113 and 290-304) disordered. In the other subunit, these loop regions are well-ordered and shield the active site from the bulk solution. In the closed enzyme subunit, one molecule of pyruvamide is bound in the active site channel, and is located in the vicinity of the thiazolium ring of the cofactor. A second pyruvamide binding site was found at the interface between the Pyr and the R domains of the subunit in the closed conformation, about 10 A away from residue C221. This second pyruvamide molecule might function in stabilizing the unique orientation of the R domain in this subunit which in turn is important for dimer-dimer interactions in the activated tetramer. No difference electron density in the close vicinity of the side chain of residue C221 was found, indicating that this residue does not form a covalent adduct with an activator molecule. Kinetic experiments showed that substrate activation was not affected by oxidation of cysteine residues and therefore does not seem to be dependent on intact thiol groups in the enzyme. The results suggest that a disorder-order transition of two active-site loop regions is a key event in the activation process triggered by the activator pyruvamide and that covalent modification of C221 is not required for this transition to occur. Based on these findings, a possible mechanism for the activation of PDC by its substrate, pyruvate, is proposed.

Catalytic Domain↗

PubMed2004

Two structural features of lambda integrase that are critical for DNA cleavage by multimers but not by monomers.

Despite many years of genetic and biochemical studies on the lambda integrase (Int) recombination system, it is still not known whether the Int protein is competent for DNA cleavage as a monomer. We have addressed this question, as part of a larger study of Int functions critical for the formation of higher-order complexes, by isolating "multimer-specific" mutants. We identify a pair of oppositely charged residues, E153 and R169, that comprise an intermolecular salt bridge within a functional Int multimer. Mutation of either of these residues significantly reduces both the cleavage of full-att sites and the resolution of Holliday junctions without compromising the cleavage of half-att site substrates. Allele-specific suppressor mutations were generated at these residues. Their interaction with wild-type Int on preformed Holliday junctions indicates that the mutated residues comprise an intermolecular salt bridge. We have also shown that the most C-terminal seven residues of Int, which comprise another previously identified subunit interface, inhibit DNA cleavage by monomeric but not multimeric Int. Taken together, our results lead us to conclude that Int can cleave DNA as a monomer. We also identify and discuss unique structural features of Int that act negatively to reduce its activity as a monomer and other features that act positively to enhance its activity as a multimer.

Amino Acid Substitution↗

PubMed2000

Unique protein determinants of the subtype-selective ligand responses of the estrogen receptors (ERalpha and ERbeta ) at AP-1 sites.

The two subtypes of human estrogen receptor, alpha (hERalpha) and beta (hERbeta), regulate transcription at an AP-1 response element differently in response to estradiol and the anti-estrogens tamoxifen and raloxifene. To better understand the protein determinants of these differences, chimeric and deletional mutants of the N-terminal domain and the F region of ERalpha and ERbeta were made and tested in transient transfection assays at the classical estrogen response element (ERE) site as well as at an AP-1 site. Although the same regions on each receptor subtype appeared to be primarily responsible for estradiol activation at an ERE and in HeLa cells, major differences between ERalpha and ERbeta mutants were seen in the estrogen and anti-estrogen responses at an AP-1 site. This differential ligand response maps to the N-terminal domain and the F region. These results suggest that different estrogenic and anti-estrogenic ligands use different mechanisms of activation and inhibition at the AP-1 site. In contrast to previous studies, this work also shows that many of subtype-specific responses are not transferred to the other subtype by swapping the N-terminal domain of the receptor. This implies that there are other unique surfaces presented by each subtype outside of the N-terminal domain, and these surfaces can play a role in subtype-selective signaling. Together, these data suggest a complex interface between ligand, response element, and receptor that underlies ligand activation in estrogen signaling pathways.

Base Sequence↗

PubMed2001

Evidence for a novel GTPase priming step in the SRP protein targeting pathway.

Protein targeting by the signal recognition particle (SRP) pathway requires the interaction of two homologous GTPases that reciprocally regulate each other's GTPase activity, the SRP signal peptide- binding subunit (SRP54) and the SRP receptor alpha-subunit (SRalpha). The GTPase domain of both proteins abuts a unique 'N domain' that appears to facilitate external ligand binding. To examine the relationship between the unusual regulation and unique architecture of the SRP pathway GTPases, we mutated an invariant glycine in Escherichia coli SRP54 and SRalpha orthologs ('Ffh' and 'FtsY', respectively) that resides at the N-GTPase domain interface. A G257A mutation in Ffh produced a lethal phenotype. The mutation did not significantly affect Ffh function, but severely reduced interaction with FtsY. Likewise, mutation of FtsY Gly455 produced growth defects and inhibited interaction with Ffh. The data suggest that Ffh and FtsY interact only in a 'primed' conformation which requires interdomain communication. Based on these results, we propose that the distinctive features of the SRP pathway GTPases evolved to ensure that SRP and the SR engage external ligands before interacting with each other.

Alleles↗

PubMedDate not supplied

Detection of interictal spikes and artifactual data through orthogonal transformations.

This study introduces an integrated algorithm based on the Walsh transform to detect interictal spikes and artifactual data in epileptic patients using recorded EEG data. The algorithm proposes a unique mathematical use of Walsh-transformed EEG signals to identify those criteria that best define the morphologic characteristics of interictal spikes. EEG recordings were accomplished using the 10-20 system interfaced with the Electrical Source Imaging System with 256 channels (ESI-256) for enhanced preprocessing and on-line monitoring and visualization. The merits of the algorithm are: (1) its computational simplicity; (2) its integrated design that identifies and localizes interictal spikes while automatically removing or discarding the presence of different artifacts such as electromyography, electrocardiography, and eye blinks; and (3) its potential implication to other types of EEG analysis, given the mathematical basis of this algorithm, which can be patterned or generalized to other brain dysfunctions. The mathematics that were applied here assumed a dual role, that of transforming EEG signals into mutually independent bases and in ascertaining quantitative measures for those morphologic characteristics deemed important in the identification process of interictal spikes. Clinical experiments involved 31 patients with focal epilepsy. EEG data collected from 10 of these patients were used initially in a training phase to ascertain the reliability of the observable and formulated features that were used in the spike detection process. Three EEG experts annotated spikes independently. On evaluation of the algorithm using the 21 remaining patients in the testing phase revealed a precision (positive predictive value) of 92% and a sensitivity of 82%. Based on the 20- to 30-minute epochs of continuous EEG recording per subject, the false detection rate is estimated at 1.8 per hour of continuous EEG. These are positive results that support further development of this algorithm for prolonged EEG recordings on ambulatory subjects and to serve as a support mechanism to the decisions made by EEG experts.

Action Potentials↗

PubMed2001

Avian haemoglobins and structural basis of high affinity for oxygen: structure of bar-headed goose aquomet haemoglobin.

Haemoglobin from the bar-headed goose (Anser indicus) has higher oxygen affinity than that from its lowland relatives such as greylag goose (A. anser). The crystal structure of bar-headed goose aquomet haemoglobin was determined at 2.3 A resolution and compared with the structures of the goose oxy, human, horse and other avian haemoglobins and the sequences of other avian haemoglobins. Four amino-acid residues differ between greylag goose and bar-headed goose haemoglobins, among which Alaalpha119 and Aspbeta125 in bar-headed goose haemoglobin reduces the contacts between the alpha(1) and beta(1) subunits compared with Pro and Glu, respectively, and therefore may increase the oxygen affinity by loosening the alpha(1)beta(1) interface. Compared with human oxy haemoglobin, the relative orientation of two alphabeta dimers in the bar-headed goose aquomet and oxy Hbs are rotated by about 4 degrees, indicating a unique quaternary structural difference from the typical R state. This new 'R(H)' state is probably correlated with the higher oxygen affinity of bar-headed goose haemoglobin.

Animals↗

PubMed1994

PERIODIC AIR-BREATHING BEHAVIOUR IN A PRIMITIVE FISH REVEALED BY SPECTRAL ANALYSIS

The ventilatory patterns of air-breathing fish are commonly described as 'arrhythmic' or 'irregular' because the variable periods of breath-holding are punctuated by seemingly unpredictable air-breathing events (see Shelton et al. 1986). This apparent arrhythmicity contrasts with the perceived periodism or regularity in the gill ventilation patterns of some fish and with lung ventilation in birds and mammals. In this sense, periodism refers to behaviour that occurs with a definite, recurring interval (Bendat and Piersol, 1986). The characterisation of aerial ventilation patterns in fish as 'aperiodic' has been generally accepted on the basis of qualitative examination and it remains to be validated with rigorous testing. The bowfin, Amia calva (L.), is a primitive air-breathing fish that makes intermittent excursions to the airwater interface to gulp air, which is transferred to its well-vascularized gas bladder. Its phylogenetic position as the only extant member of the sister lineage of modern teleosts affords a unique opportunity to examine the evolution of aerial ventilation and provides a model for the examination of ventilatory patterns in primitive fishes. To establish whether Amia calva exhibit a particular pattern of air-breathing, we examined time series records of aerial ventilations from undisturbed fish over long periods (8 h). These records were the same as those used to calculate average ventilation intervals under a variety of experimental conditions (Hedrick and Jones, 1993). Their study also reported the occurrence of two distinct breath types. Type I breaths were characterised by an exhalation followed by an inhalation, whereas type II breaths were characterised by inhalation only. It was also hypothesized that the type I breaths were employed to meet oxygen demands, whereas the type II breaths were used to regulate gas bladder volume. However, they did not investigate the potential presence of a periodic ventilatory pattern. We now report the results of just such an analysis of ventilatory pattern that demonstrates a clear periodism to air-breathing in a primitive fish.

Journal Article↗

PubMed2004

The NLM Gateway: something old, something new.

The NLM Gateway is a single Web interface for searching multiple NLM databases. While the majority of the available databases can be accessed directly via their own Web sites, such as PubMed, there are three databases that are unique to the NLM Gateway, including the ever-expanding OLDMEDLINE files. Thus, the Gateway is a necessary tool for librarians and researchers to be familiar with and have handy.

Internet↗

PubMed2004

Conotoxins and structural biology: a prospective paradigm for drug discovery.

Understanding the interactions between activating or antagonizing ligands and their cognate receptors at a molecular level offers promise for the development of pharmacological therapeutics for CNS disorders. The discovery of novel molecules that are capable of discriminating between the varied molecular subunits or isoforms of ion channels should provide a more detailed understanding of the pathophysiology of many CNS disorders. Abundant natural sources of pharmacologically active agents that demonstrate this refined selectivity and specificity are found in the animal toxins of venomous species including: snakes, spiders and the marine snail of the genus Conus. The uniquely fascinating combinatorial ability of the marine snail, genus Conus to modify the pharmacological properties of these neurotoxins or conopeptides within its venom is depicted throughout this review. The myriad of posttranslational modifications and disulfide bonded architectures that have been identified in the conopeptides, are described with an emphasis on the unique pharmacological properties and receptor target specificities that have been ascribed to each of these modifications. The ability of NMR spectroscopy to provide three-dimensional structural information within the interaction interface for both the ligand and target protein following complex formation and its application to conopeptide drug discovery are discussed. Similarly, the strength of merging NMR spectroscopy data with ab initio "restrained soft-docking" for rational pharmacophore design and the identification of lead compounds from in silico library screens will also be discussed. The initial phases of this stratagem are illustrated using two toxin antagonists and the recently determined structure of the KcsA potassium channel. These data exemplify the utility of this approach in elucidating important molecular interfaces of specific toxin-receptor/ion channel complexes, which can be further exploited in drug discovery initiatives.

Animals↗

PubMed2026

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases.

MOTIVATION: Epigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. RESULTS: We developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG- searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. AVAILABILITY AND IMPLEMENTATION: The eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

DNA methylation↗

PubMed1998

Reconstructing the protein-water interface.

Using molecular dynamics simulations of fully hydrated proteins and analysis of crystal structures contained in the Protein Data Bank, we develop a transferable set of perpendicular radial distribution functions for water molecules around globular proteins. These universal functions may be used to reconstruct the unique three-dimensional solvent density distribution around every individual protein with a modest error. We discuss potential applications of this solvent treatment in protein x-ray crystallographic refinements and in theoretical modeling. We also present a fast, grid-based algorithm for construction of the perpendicular solvent density distributions.

Algorithms↗

PubMed1999

alpha6 Integrin is regulated with lens cell differentiation by linkage to the cytoskeleton and isoform switching.

The developing chicken embryo lens provides a unique model for examining the relationship between alpha6 integrin expression and cell differentiation, since multiple stages of differentiation are expressed concurrently at one stage of development. We demonstrate that alpha6 integrin is likely to mediate the inductive effects of laminin on lens differentiation as well as to function in a matrix-independent manner along the cell-cell interfaces of the differentiating cortical lens fiber cells. Both alpha6 isoform expression and its linkage to the cytoskeleton were regulated in a differentiation-specific manner. The association of alpha6 integrin with the Triton-insoluble cytoskeleton increased as the lens cells differentiated, reaching its highest levels in the cortical fiber region where the lens fiber cells are formed. In this region of the lens alpha6 integrin was uniquely localized along the cell-cell borders of the differentiating fiber cells, similar to beta1. alpha6beta4, the primary transmembrane protein of hemidesmosomes, is also expressed in the lens, but in the absence of hemidesmosomes. Differential expression of alpha6A and alpha6B isoforms with lens cell differentiation was seen at both the mRNA and the protein levels. RT-PCR studies demonstrated that alpha6B was the predominant isoform expressed both early in development, embryonic day 4, and in the epithelial regions of the day 10 embryonic lens. Isoform switching, with alpha6A now the predominant isoform, occurred in the fiber cell zones. Immunoprecipitation studies showed that alpha6B, which is characteristic of undifferentiated cells, was expressed by the lens epithelial cells but was dramatically reduced in the lens fiber zones. Expression of alpha6B began to drop as the cells initiated their differentiation and then dropped precipitously in the cortical fiber zone. In contrast, expression of the alpha6A isoform remained high until the cells became terminally differentiated. alpha6A was the predominant isoform expressed in the cortical fiber region. The down-regulation of alpha6B relative to alpha6A provides a developmental switch in the process of lens fiber cell differentiation.

Animals↗

PubMed2006

RepairNET: a bioinformatics toolbox for functional exploration of DNA damage response.

DNA damage response is one of the essential cellular mechanisms to maintaining the genomic integrity of the cell. Aberrations in the mechanism of DNA damage response often result in cancer. We describe here RepairNET, a protein-protein interaction network associated with the DNA damage response. RepairNET is assembled from the published literature by using a protocol that involved computational data mining of the MEDLINE and manual curation. This network represents the current knowledge on the intrinsic signaling pathways related to the DNA damage response process. RepairNET currently contains more than 1,200 proteins with over 2,300 functional interactions. A number of web-interface tools have been implemented to facilitate a user-friendly environment. The users can navigate through the cellular network associated with the DNA damage response via a Java-based interactive graphical interface. In order to help users explore the functional relationships between the interacting proteins, we have assigned functional domains to the proteins in RepairNET based on their sequences. A total of 365 unique functional domains are assigned. RepairNET is available online at http://guanyin.chem.temple.edu/RepairNET.html. It could become an essential resource center for cancer research, providing clues to understanding the functional relationship between proteins in the network, and to building scientific models for the mechanism of DNA damage response and cancer proliferation.

Adaptor Proteins, Signal Transducing↗

PubMed1975

Community mental health and the community college.

This paper represents one solution to the present mental health dilemma facing today's colleges and universities--static or declining services in the face of increased student needs. What is unique to this solution is that it developed out of a collaborative interaction between a community college and a prototype of a community mental health center in the same geographical area. Multiple interfaces between systems and various members within these systems were established in an effort to provide improved mental health services and the training of all personnel so involved to a higher level of professional functioning.

Community Mental Health Services↗

PubMed2004

Crystal structure of the Bowman-Birk inhibitor from barley seeds in ternary complex with porcine trypsin.

The structure and function of Bowman-Birk inhibitors (BBIs) from dicotyledonous plants such as soybean have been studied extensively. In contrast, relatively little is known about the BBIs from monocotyledonous plants such as barley, which differ from dicot BBIs in size and tertiary structure. The BBI from barley seeds (BBBI) consists of 125 amino acid residues with two separate inhibitory loops. Previously we determined the high-resolution structure of a 16 kDa BBBI in the free state. The BBBI folds into two compact domains (N and C domain) with tertiary structures that are similar to that of the 8 kDa BBI from dicots. Here we report the structure of a 1:2 complex between BBBI and porcine pancreatic trypsin (PPT) at 2.2 A resolution. This structure confirms that several regions, including the inhibitory loops in the free BBBI structure, show exceptionally low temperature factors and a distorted conformation due to crystalline packing in the lattice. Extensive analysis of the interaction between BBBI and trypsin, and comparison with other known canonical inhibitor-protease complexes, reveals that the mode of interaction between BBBI and PPT is similar to that of known serine protease inhibitors, as expected; however, several unique features are also identified in the primary binding sites near the inhibitory loops as well as in additional binding sites. The carboxy-terminal tail of the inhibitor extends into the interface between the two trypsin molecules and interacts with both of them simultaneously. The longest distance between the two P1 residues (Arg17 and Arg76) in the complex structure is approximately 34 A, which is shorter than in the free inhibitor, but it is still possible for BBBI to bind and inhibit two trypsin molecules simultaneously and independently.

Amino Acid Sequence↗

PubMed2005

Ocular pharmacokinetics of moxifloxacin after topical treatment of animals and humans.

The ocular penetration and pharmacokinetics of moxifloxacin in comparison to other fluoroquinolones (ofloxacin, ciprofloxacin, gatifloxacin, norfloxacin, levofloxacin, and lomefloxacin) have been determined by in vitro and ex vivo techniques, as well as in animal and human studies. This article reviews the original pharmacokinetics work performed by Alcon and other studies reported in the ocular fluoroquinolone literature. The results consistently demonstrate higher maximum concentrations for moxifloxacin relative to the other fluoroquinolones in ocular tissues with levels well above its minimum inhibitory concentrations for relevant ocular pathogens. This superior performance is due to the unique structure of moxifloxacin that combines high lipophilicity for enhanced corneal penetration with high aqueous solubility at physiological pH. The latter property creates a high concentration gradient at the tear film/corneal epithelial interface providing a driving force for better ocular penetration for moxifloxacin. In addition, the higher concentration of moxifloxacin in VIGAMOX (i.e., 0.5% vs. 0.3%) allows more antibiotic to be available to ocular tissues. It is clear from the array of studies summarized in this report that moxifloxacin penetrates ocular tissues better (two- to three-fold) than gatifloxacin, ciprofloxacin, ofloxacin, or levofloxacin. This consistent, enhanced penetration of topical moxifloxacin offers powerful advantages for ophthalmic therapy.

Administration, Topical↗