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PubMed1987

An intact heavy chain at the actin-subfragment 1 interface is required for ATPase activity of scallop myosin.

Scallop S1 has a region sensitive to tryptic hydrolysis not found thus far in S1s of other species, located 65K from the N-terminus as determined by SDS/polyacrylamide-gel electrophoresis. In the presence of actin the S1 heavy chain is preferentially cleaved at this site. The high-salt EDTA and calcium ATPase activities of the nicked 65K-31K S1 are abolished. This inactivation is not due to denaturation, conformational effects of actin, or to light chain dissociation. The unique proteolytic site of scallop S1 is adjacent to a peptide involved in actin-S1 interaction in scallop and rabbit but it is far removed from the nucleotide-binding site in the linear amino acid sequence. We conclude that proteolysis inactivates the high-salt ATPase activities through a connection mediated by tertiary interactions. Such a connection provides a structural correlate for the known reciprocal relationship between the nucleotide and actin affinities of myosin.

Actins↗

PubMed1994

Backscattering and transmission through a high Z interface as a measure of electron beam energy.

The ratio of electron beam transmission (Tr) and backscattering (Bs) is used as a measure of beam energy. With a proper thickness of high Z medium placed at the surface of a low Z homogeneous medium, it is observed that the function log(Tr/Bs) is a linear function of electron energy. This method is applied to electrons produced with scattering foil and pulse-swept (scanned) beams for the nominal energies ranging from 6 to 20 MeV. This technique provides a unique alternative method which is easy, simple, and accurate within +/- 3% for estimation of electron beam energy.

Electrons↗

PubMed2000

Human immunodeficiency virus type 1 reverse transcriptase dimer destabilization by 1-[Spiro[4"-amino-2",2" -dioxo-1",2" -oxathiole-5",3'-[2', 5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]]]-3-ethylthy mine.

The nonnucleoside inhibitor binding pocket is a well-defined region in the p66 palm domain of the human immunodeficiency virus type-1 reverse transcriptase (HIV-1 RT). This binding pocket opens toward the interface of the p66/p51 heterodimer and we have investigated whether ligand binding at or near this site induces structural changes that have an impact on the dimeric structure of HIV-1 RT. 1-[2',5'-bis-O-(tert-butyldimethylsilyl]-3'-spiro-5' '-(4' '-amino-1' ',2' '-oxathiole-2' ',2' '-dioxide)-3-ethylthymine (TSAOe(3)T) was found to destabilize the subunit interactions of both the p66/p51 heterodimer and p66/p66 homodimer enzymes. The Gibbs free energy of dimer dissociation (DeltaG(D)(H)2(O)) is decreased with increasing concentrations of TSAOe(3)T, resulting in a loss in dimer stability of 4.0 and 3.2 kcal/mol for the p66/p51 and p66/p66 HIV-1 RT enzymes, respectively. This loss of energy is not sufficient to induce the dissociation of the subunits in the absence of denaturant. This destabilizing effect seems to be unique for TSAOe(3)T, since neither the tight-binding inhibitor UC781 nor nevirapine showed any effects on the stability of HIV-1 RT dimers. TSAOe(3)T was unable to destabilize the subunit interactions of the E138K mutant enzyme, which exhibits significant resistance to TSAOe(3)T inhibition. Molecular modeling of TSAOm(3)T into the nonnucleoside inhibitor binding pocket of wild-type RT suggests that it makes significant interactions with the p51 subunit of the enzyme, a feature that has not been observed with other types of nonnucleoside inhibitors. The observed destabilization of the dimeric HIV-1 RT may result from structural/conformational perturbations at the reverse transcriptase subunit interface.

Anilides↗

PubMed2003

Intravascular palpography for high-risk vulnerable plaque assessment.

BACKGROUND: The composition of an atherosclerotic plaque is considered more important than the degree of stenosis. An unstable lesion may rupture and cause an acute thrombotic reaction. Most of these lesions contain a large lipid pool covered by an inflamed thin fibrous cap. The stress in the cap increases with decreasing cap thickness and increasing macrophage infiltration. Intravascular ultrasound (IVUS) palpography might be an ideal technique to assess the mechanical properties of high-risk plaques. TECHNIQUE: Palpography assesses the local mechanical properties of tissue using its deformation caused by the intraluminal pressure. IN VITRO VALIDATION: The technique was validated in vitro using diseased human coronary and femoral arteries. Especially between fibrous and fatty tissue, a highly significant difference in strain (p = 0.0012) was found. Additionally, the predictive value to identify the vulnerable plaque was investigated. A high-strain region at the lumen-vessel wall boundary has an 88% sensitivity and 89% specificity for identifying such plaques. IN VIVO VALIDATION: In vivo, the technique was validated in an atherosclerotic Yucatan minipig animal model. This study also revealed higher strain values in fatty than fibrous plaques (p < 0.001). The presence of a high-strain region at the lumenplaque interface has a high predictive value to identify macrophages. PATIENT STUDIES: Patient studies revealed high-strain values (1-2%) in thin-cap fibrous atheroma. Calcified material showed low strain values (0-0.2%). With the development of three-dimensional (3-D) palpography, identification of highstrain spots over the full length of a coronary artery becomes available. CONCLUSION: Intravascular palpography is a unique tool to assess lesion composition and vulnerability. The development of 3-D palpography provides a technique that may develop into a clinical tool to identify the high-risk plaque.

Animals↗

PubMed2005

High-resolution crystal structures of Desulfovibrio vulgaris (Hildenborough) nigerythrin: facile, redox-dependent iron movement, domain interface variability, and peroxidase activity in the rubrerythrins.

High-resolution crystal structures of Desulfovibrio vulgaris nigerythrin (DvNgr), a member of the rubrerythrin (Rbr) family, demonstrate an approximately 2-A movement of one iron (Fe1) of the diiron site from a carboxylate to a histidine ligand upon conversion of the mixed-valent ([Fe2(II),Fe1(III)]) to diferrous states, even at cryogenic temperatures. This Glu<-->His ligand "toggling" of one iron, which also occurs in DvRbr, thus, appears to be a characteristic feature of Rbr-type diiron sites. Unique features of DvNgr revealed by these structures include redox-induced flipping of a peptide carbonyl that reversibly forms a hydrogen bond to the histidine ligand to Fe1 of the diiron site, an intra-subunit proximal orientation of the rubredoxin-(Rub)-like and diiron domains, and an electron transfer pathway consisting of six covalent and two hydrogen bonds connecting the Rub-like iron with Fe2 of the diiron site. This pathway can account for DvNgr's relatively rapid peroxidase turnover. The characteristic combination of iron sites together with the redox-dependent iron toggling between protein ligands can account for the selectivity of Rbrs for hydrogen peroxide over dioxygen.

Bacterial Proteins↗

PubMed2004

Pro7.33(303) of the human GnRH receptor regulates selective binding of mammalian GnRH.

Mammalian gonadotropin releasing hormone (GnRH) receptors have a conserved acidic residue (Glu7.32(301) or Asp7.32(302)) in extracellular loop (ECL) three that confers selectivity for mammalian GnRH, which has Arg8. Comparison of mammalian and non-mammalian GnRH receptors suggested that the acidic residue is not the only determinant of ligand selectivity in mammalian receptors. The acidic residue is followed by a conserved Pro7.33 in mammalian GnRH receptors, but not non-mammalian receptors. Unique structural constraints imposed by Pro residues suggested that Pro7.33 determines selective binding of Arg8-containing GnRH, by stabilising the conformation of the third extracellular loop of the receptor. Substituting Pro7.33(303) or introducing Pro to position 7.31 decreased affinity for GnRH, but not analogs lacking Arg8. Substituting Pro7.33(303) changed the predicted alpha-helix content of the loop-helix interface. These results show that Pro7.33(303) of the human GnRH receptor is required for selective high affinity binding of mammalian GnRH and supports the hypothesis that Pro7.33(303) stabilises a loop conformation that is necessary for selective ligand binding.

Amino Acid Sequence↗

PubMed2002

A model for constitutive lutropin receptor activation based on molecular simulation and engineered mutations in transmembrane helices 6 and 7.

Many naturally occurring and engineered mutations lead to constitutive activation of the G protein-coupled lutropin receptor (LHR), some of which also result in reduced ligand responsiveness. To elucidate the nature of interhelical interactions in this heptahelical receptor and changes thereof accompanying activation, we have utilized site-directed mutagenesis on transmembrane helices 6 and 7 of rat LHR to prepare and characterize a number of single, double, and triple mutants. The potent constitutively activating mutants, D556(6.44)H and D556(6.44)Q, were combined with weaker activating mutants, N593(7.45)R and N597(7.49)Q, and the loss-of-responsiveness mutant, N593(7.45)A. The engineered mutants have also been simulated using a new receptor model based on the crystal structure of rhodopsin. The results suggest that constitutive LHR activation by mutations at Asp-556(6.44) is triggered by the breakage or weakening of the interaction found in the wild type receptor between Asp-556(6.44) and Asn-593(7.45). Whereas this perturbation is unique to the activating mutations at Asp-556(6.44), common features to all of the most active LHR mutants are the breakage of the charge-reinforced H-bonding interaction between Arg-442(3.50) and Asp-542(6.30) and the increase in solvent accessibility of the cytosolic extensions of helices 3 and 6, which probably participate in the receptor-G protein interface. Asn-593(7.45) and Asn-597(7.49) also seem to be necessary for the high constitutive activities of D556(6.44)H and D556(6.44)Q and for full ligand responsiveness. The new theoretical model provides a foundation for further experimental work on the molecular mechanism(s) of receptor activation.

Amino Acid Substitution↗

PubMed2006

CutDB: a proteolytic event database.

Beyond the well-known role of proteolytic machinery in protein degradation and turnover, many specialized proteases play a key role in various regulatory processes. Thousands of highly specific proteolytic events are associated with normal and pathological conditions, including bacterial and viral infections. However, the information about individual proteolytic events is dispersed over multiple publications and is not easily available for large-scale analysis. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. CutDB is publicly available at http://cutdb.burnham.org.

Animals↗

PubMed1997

Design strategies of sea urchin teeth: structure, composition and micromechanical relations to function.

The teeth of sea urchins comprise a variety of different structural entities, all of which are composed of magnesium-bearing calcite together with a small amount of organic material. The teeth are worn down continuously, but in such a way that they remain sharp and functional. Here we describe aspects of the structural, compositional and micromechanical properties of the teeth of Paracentrotus lividus using scanning electron microscopy, infrared spectrometry, atomic absorption. X-ray diffraction and microindentation. The S-shaped single crystalline calcitic fibres are one of the main structural elements of the tooth. They extend from the stone part to the keel. The diameter of the fibres increases gradually from less than 1 micron at the stone tip to about 20 microns at the keel end, while their MgCO3 contents decrease from about 13 mol% to about 4.5 mol%. Each fibre is coated by a thin organic sheath and surrounded by polycrystalline calcitic discs containing as much as 35 mol% MgCO3. This structure constitutes a unique kind of gradient fibre-reinforced ceramic matrix composite, whose microhardness and toughness decrease gradually from the stone part to the keel. Primary plates are also important structural elements of the tooth. Each primary plate has a very unusual sandwich-like structure with a calcitic envelope surrounding a thin apparently amorphous CaCO3 layer. This central layer, together with the primary plate/disc interface, improves the toughness of this zone by stopping and blunting cracks. The self-sharpening function of the teeth is believed to result from the combination of the geometrical shape of the main structural elements and their spatial arrangement, the interfacial strength between structural elements, and the hardness gradient extending from the working stone part to the surrounding zones. The sea urchin tooth structure possesses an array of interesting functional design features, some of which may possibly be applicable to materials science.

Animals↗

PubMed2003

Microscopical evaluation of neural connectivity between paired stages of Eudiplozoon nipponicum (Monogenea: Diplozoidae).

Diplozoidae monogeneans am fish-gill ectoparasites comprising 2 individuals fused in so-called permanent copula. This unique situation occurs when 2 larvae (diporpee) make contact on the host gin, such that their union triggers maturation into an individual adult worm. The present study examined paired stages of Eudiplozoon nipponioun microscopicaily to ascertain whether somatic fusion involves neural connectivity between these 2 heterogenic larvae. Neuronal pathways were demonstrated in whole-mount preparations of the worm, using indirect immunocytochemical techniques interfaced with confocal scanning laser microscopy for peptidergic and serotoninergic innervations and enzyme cytochemical methodology and light microscopy for cholinergic component. Elements of the central nervous systems of paired worms are connected by commissures in the region of fusion so that the 2 systems are in structural continuity. Interindividual connections were mast apparent between corresponding ventral nerve cords. All 3 classes of neuronal mediators were identified throughout both central and peripheral connections of the 2 nervous systems. The anatomical complexity and apparent plasticity of the diplozoon nervous system suggest that it has a pivotal role not only in motility, feeding, and reproductive behavious but also in the events of larval pairing and somatic fusion.

Animals↗

PubMed2003

[Dedifferentiated chondrosarcoma of bone--report of 5 cases and literature review with emphasis on histogenesis].

Five cases of dedifferentiated chondrosarcoma of bone are presented. Three women and two men of age ranging from 57-72 years (median 63 years) suffered from tumors located in femur (2), scapula (1), humerus (1) and pelvis (1). They were all bulky tumors destroying the bones and infiltrating into the adjacent soft tissues in maximum diameter from 5-20 cm (median 12 cm). Both the short clinical histories lasting from 2-24 months (median 5 months) and persistent pains unrelieved by acylpirin were constant findings in all the cases. Four patients died of metastatic disease (mainly to lungs) with median survival of 8 months. All cases were the so-called "de novo" dedifferentiated chondrosarcomas without clinical or morphological evidence of the primarily benign or malignant chondroid lesions. The tumors displayed a typical dual composition with an abrupt interface between chondroid and nonchondroid components. The chondroid tissue resembled G1 chondrosarcoma in three cases, G2-3 chondrosarcoma in two cases. The second nonchondroid mesenchymal portion had the appearance of undifferentiated pleomorphic sarcoma in three cases, rhabdoid and giant cell tumor-like in one case. The new data and evidence provided by molecular biology dramatically changed the opinions of histogenesis of this unique neoplasm. At present, there is a generally accepted idea of common origin of both portions from a primitive stem cell. Therefore, this peculiar tumors should not be viewed merely as dedifferentiated conventional chondrosarcomas.

Aged↗

PubMed2004

Structural and functional heterogeneity in the CD200R family of immunoregulatory molecules and their expression at the feto-maternal interface.

PROBLEM: We have shown that CD200Fc, a chimeric molecule including the extracellular domain of CD200 and a murine immunoglobulin (Ig)G2a Fc region, regulates immune responses and prevents T helper (Th)1 cytokine-triggered spontaneous abortions in mice. CD200 is expressed on a subpopulation of uterine decidua cells and on trophoblast, both in the mouse and human. The receptor(s) for CD200, CD200R(s), was not previously well-characterized. METHODS: 5'-rapid amplification of cDNA ends (RACE), cDNA and genomic DNA clone analysis were used to identify a family of CD200Rs on mouse chromosome 16, juxtaposed to the CD200 gene, named CD200R1, R2, R3, and R4. Northern blot and reverse transcriptase polymerase chain reaction (RT-PCR) analysis was used to detect expression of different CD200R subtypes in different organs. Rabbit polyclonal and rat monoclonal antibodies (mAbs) to CD200R isoforms was used for fluorescence-activated cell sorter (FACS) analysis, to test for immunomodulatory effects on allogeneic mixed-lymphocyte responses in vitro, and for immunohistochemistry. RESULTS: The CD200Fc was able to interact physically with each of the CD200Rs expressed on the cell surface. Northern blot and RT-PCR analyses indicated distinct patterns of CD200R isoform mRNA expression in different tissues and FACS analyses confirmed unique cell- and tissue-specific expression of the different CD200Rs. mAbs directed against the different isoforms modified the development of in vitro alloimmune responses. The addition of anti-CD200R1/R4 elicited immunomodulatory responses in vitro comparable to findings with CD200Fc, but different from the effects of anti-CD200R2-3. CONCLUSIONS: These data provide evidence for a family of CD200R molecules in the mouse genome and defines the existence of previously unrecognized diversity in the CD200/CD200R immunomodulatory gene member family. Although this gene member family is clustered in the genome, the different CD200Rs and CD200 exhibit distinct expression patterns and functional properties. Restricted CD200R isoform expression at the feto-maternal interface suggests CD200:CD200R interactions may serve important function(s) determining the successful outcome of pregnancy.

Amino Acid Sequence↗

PubMed1994

Biomineralization: new directions in crystal science.

Effective protocols for controlling crystal structure, size, and morphology attract considerable interest given the requirement for particles of modal size and shape in many areas of materials fabrication and the importance of crystallochemical selectivity in determining the exploitable properties of inorganic solids. For this reason biomineralization merits particular attention since many biominerals are deposited in a highly controlled manner to produce crystals which are uniformly sized and crystallographically unique. Studies of biominerals have revealed that while a complex array of strategies have evolved for regulating their formation, one feature is common to the biological paradigm; interactions between organized biopolymeric assemblies and the nascent inorganic solids play a pivotal role in controlling the crystallization process. In order to gain a better understanding of the molecular interactions which take place at organic-inorganic interface and address the fundamental chemical problems of biomineralization, a crystal chemical approach has been adopted. Organized organic assemblies (phospholipid vesicles, Langmuir monolayers, polypetide templates) of precise molecular design (head group identity, packing conformation, peptide sequence, etc.) were assayed for their effectiveness in controlling the nucleation and growth of inorganic solids. This work has established that through systematic changes in the nature of the organic matrix the size, crystallographic orientation, and growth of the mineral phase can be controlled. Critical to this process was the translation of specific molecular information at the organic-inorganic interface: epitaxial alignment, stereochemical complementarity, and electrostatic interactions were an essential feature of this recognition event.

Animals↗

PubMed1998

Measurement of sealing resistance of cell-electrode interfaces in neuronal cultures using impedance spectroscopy.

Sealing resistance is highly significant with respect to the electrical neuron-electrode contact because it decreases the stimulation threshold of neurons cultured on a planar micro-electrode array. A method is proposed for measurement of the sealing resistance using impedance spectroscopy. The effect of the sealing resistance on the total impedance spectrum of a cell-electrode interface is modelled for complete coverage of the electrode by the cell. Sensitivity analysis demonstrates that the impedance spectrum is determined by four parameters: two electrode parameters, the sealing resistance and the shunt capacitance between the lead of the electrode and the culture medium. Experimental verification of the model is performed by simultaneous measurement of the impedance spectrum and electrode coverage. A good and unique fit between the simulated and measured impedance spectra was obtained by varying the two electrode parameters and the sealing resistance.

Animals↗

PubMed2001

Cubilin, a multifunctional epithelial receptor: an overview.

Cubilin is a 460-kDa endocytic receptor coexpressed with megalin, a multiligand receptor of the low-density lipoprotein receptor gene family, at the apical pole of epithelial cells in the renal proximal convoluted tubule, visceral yolk sac, ileum, and placenta. The structure of cubilin is unique: it lacks a transmembrane domain and requires megalin for its internalization. The accumulation of 27 interactive CUB domains provides the potential for multiple, possibly independent interactions and functions. Cubilin is involved in the intestinal absorption of vitamin B12, the catabolism of apolipoprotein A-I by the proximal convoluted tubule and more generally in renal protein reabsorption. The role of cubilin on fetomaternal interfaces is not defined but may be related to its ability to bind and internalize high density lipoproteins.

Animals↗

PubMed2005

Crystal structure of the ENT domain of human EMSY.

EMSY is a recently discovered gene encoding a BRCA2-associated protein and is amplified in some sporadic breast and ovarian cancers. The EMSY sequence contains no known domain except for a conserved approximately 100 residue segment at the N terminus. This so-called ENT domain is unique in the human genome, although multiple copies are found in Arabidopsis proteins containing members of the Royal family of chromatin remodelling domains. Here, we report the crystal structure of the ENT domain of EMSY, consisting of a unique arrangement of five alpha-helices that fold into a helical bundle arrangement. The fold shares regions of structural homology with the DNA-binding domain of homeodomain proteins. The ENT domain forms a homodimer via the anti-parallel packing of the extended N-terminal alpha-helix of each molecule. It is stabilized mainly by hydrophobic residues at the dimer interface and has a dissociation constant in the low micromolar range. The dimerisation of EMSY mediated by the ENT domain could provide flexibility for it to bind two or more different substrates simultaneously.

Binding Sites↗

PubMed2006

Solution structure of the Hdm2 C2H2C4 RING, a domain critical for ubiquitination of p53.

Regulation of the transcriptional response to the tumor suppressor p53 occurs at many levels, including control of its transcriptional activity, and of its stability and concentration within the cell. p53 stability is regulated by the protein Hdm2, an E3 ubiquitin ligase that binds to p53 and promotes its ubiquitination and degradation. The C-terminal domain of Hdm2, which is critical for this activity, has been classified as a RING domain on the basis of sequence homology, although it lacks the canonical set of zinc ligands (RING domains typically have C3HC4 or C4C4 zinc coordination). Here, we report the solution structure of the C2H2C4 RING domain of Hdm2(429-491), which reveals a symmetrical dimer with a unique cross-brace zinc-binding scheme. Each subunit has one Cys4 Zn site and one His2Cys2 Zn site. The global fold of each subunit is similar to those reported for other RING domains, with a compact betabetaalphabeta fold, a small hydrophobic core, and two Zn ions, which are essential for maintaining the domain structure. The dimer structure is maintained by an extensive interface that buries a large hydrophobic area on each subunit. It has been proposed that Hdm2 and its homologue HdmX form a stable heterodimer through their RING domains, resulting in a synergistic increase in observed E3 activity. To test this proposal, we prepared an HdmX RING construct and showed by NMR titration that it forms a tight 1:1 complex with the Hdm2 RING. The resonances most perturbed by heterodimer formation are located within the subunit interface of the homodimer, far removed from the surface expected to form the docking site of the E2 ubiquitin-conjugating enzyme, providing a structure-based rationale for the function of the RING domains in p53 ubiquitination.

Amino Acid Sequence↗

PubMed2005

Structure determination of protein/RNA complexes by NMR.

Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently solved in our laboratory, the nucleolin RBD12/b2NRE and Rnt1p dsRBD/snR47h complexes. Topics covered are protein and RNA preparation, complex formation, identification of the protein/RNA interface, protein and RNA resonance assignment, intermolecular NOE assignment, and structure calculation and analysis.

Magnetic Resonance Spectroscopy↗