SEARCH · PubMed Health

Results for “Unique interface”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41Linked to original sources

PubMed2000

LaminOss immediate-load implants: II. Clinical considerations of osteocompression.

The sinusoidal thread design of the LaminOss (Impladent Ltd, Holliswood, NY) osteocompressive immediate-load implant is structured with minimal shear interface to function in horizontal planes and stimulate bone growth by the action of streaming potentials at the implant thread surface area. This implant design, when used with a unique surgical instrumentation technique, allows maximum bone to be molded and compacted circumferentially around the sinusoidal implant threads. The surgical technique of bone lamination around larger implant horizontal planes (or load-bearing areas) creates a stable foundation for placing this implant into immediate function. For the past 10 years this surgical procedure has provided patients with immediate function the day of implant placement. The clinical advantage of immediate implant loading enhances care acceptance and patient satisfaction.

Bite Force↗

PubMed2004

Identification of novel synthetic organic compounds with supersonic gas chromatography-mass spectrometry.

Several novel synthetic organic compounds were successfully analyzed with a unique type of GC-MS titled Supersonic GC-MS following a failure in their analysis with standard GC-MS. Supersonic GC-MS is based on interfacing GC and MS with a supersonic molecular beam (SMB) and on electron ionization of sample compounds as vibrationally cold molecules while in the SMB, or by cluster chemical ionization. The analyses of novel synthetic organic compounds significantly benefited from the extended range of compounds amenable to analyses with the Supersonic GC-MS. The Supersonic GC-MS enabled the analysis of thermally labile compounds that usually degrade in the GC injector, column and/or ion source. Due to the high carrier gas flow rate at the injector liner and column these compounds eluted without degradation at significantly lower elution temperatures and the use of fly-through EI ion source eliminated any sample degradation at the ion source. The cold EI feature of providing trustworthy enhanced molecular ion (M+), complemented by its optional further confirmation with cluster CI was highly valued by the synthetic organic chemists that were served by the Supersonic GC-MS. Furthermore, the provision of extended mass spectral structural, isomer and isotope information combined with short (a few minutes) GC-MS analysis times also proved beneficial for the analysis of unknown synthetic organic compounds. As a result, the synthetic organic chemists were provided with both qualitative and quantitative data on the composition of their synthetic mixture, and could better follow the path of their synthetic chemistry. Ten cases of such analyses are demonstrated in figures and discussed.

Gas Chromatography-Mass Spectrometry↗

PubMed1986

Spread monolayers of proteins.

The study of spread monolayers of proteins is of interest for understanding the fundamental behavior of proteins as well as the many phenomena resulting from their ubiquitous presence at interfaces in nature. Spread monolayers of proteins is a branch of the developing field of membrane mimetic chemistry. In recent times, it has been somewhat neglected in comparison to other branches (such as bilayers, liposomes and vesicles), despite the unique advantage that the arrangement and packing of molecules in monolayers may be measured and controlled. Methods for spreading proteins and techniques used for their manipulation are outlined. As well as the more traditional methods (such as surface pressure, potential and viscosity), more recent innovations, including removal of monolayers on slides for study by radiotracer techniques, electron diffraction and infrared (IR) spectroscopy, are discussed. Direct optical methods for the study of monolayers in situ are also available (e.g., multiple reflectance spectroscopy, ellipsometry). The use of measurements in the low pressure region to measure molecular weights is discussed. At higher pressures, configurational changes, surface coagulation and desorption are all observed. Experimental and theoretical work on the desorption of proteins from the air/water interface is reviewed. The introduction of multicompartment film balances has proved valuable for the study of reactions occurring in monolayers. This instrumentation has been applied to the study of enzyme reactions at the surface, of direct relevance to reactions where the enzyme is immobilized in the cell membrane. Some applications of monolayer studies are briefly illustrated with reference to biological membranes, foams and emulsions and biomedical problems.

Protein Conformation↗

PubMed2004

Functional renormalization group and the field theory of disordered elastic systems.

We study elastic systems, such as interfaces or lattices, pinned by quenched disorder. To escape triviality as a result of "dimensional reduction," we use the functional renormalization group. Difficulties arise in the calculation of the renormalization group functions beyond one-loop order. Even worse, observables such as the two-point correlation function exhibit the same problem already at one-loop order. These difficulties are due to the nonanalyticity of the renormalized disorder correlator at zero temperature, which is inherent to the physics beyond the Larkin length, characterized by many metastable states. As a result, two-loop diagrams, which involve derivatives of the disorder correlator at the nonanalytic point, are naively "ambiguous." We examine several routes out of this dilemma, which lead to a unique renormalizable field theory at two-loop order. It is also the only theory consistent with the potentiality of the problem. The beta function differs from previous work and the one at depinning by novel "anomalous terms." For interfaces and random-bond disorder we find a roughness exponent zeta=0.208 298 04epsilon+0.006 858epsilon(2), epsilon=4-d. For random-field disorder we find zeta=epsilon/3 and compute universal amplitudes to order O(epsilon(2)). For periodic systems we evaluate the universal amplitude of the two-point function. We also clarify the dependence of universal amplitudes on the boundary conditions at large scale. All predictions are in good agreement with numerical and exact results and are an improvement over one loop. Finally we calculate higher correlation functions, which turn out to be equivalent to those at depinning to leading order in epsilon.

Journal Article↗

PubMed1996

Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences.

Protein structures generally consist of favorable folding motifs formed by specific arrangements of secondary structure elements. Similar architectures can be adopted by different amino acids sequences, although the details of the structures vary. It has long been known that despite the sequence variability, there is a striking preferential conservation of the hydrophobic character of the amino acids at the buried positions of these folding motifs. Differences in the sizes of the side-chains are accommodated by movements of the secondary structure elements with respect to each other, leading to compact packing. Scanning protein-protein interfaces reveals that similar architectures are also observed at and around their interacting surfaces, with preservation of the hydrophobic character, although not to the same extent. The general forces that determine the origin of the native structures of proteins have been investigated intensively. The major non-bonded forces operating on a protein chain as it folds into a three-dimensional structure are likely to be packing, the hydrophobic effect, and electrostatic interactions. While the substantial hydrophobic forces lead to a compact conformation, they are also nonspecific and cannot serve as a guide to a conformationally unique structure. For the general folding problem, it thus appears that packing is a prime candidate for determining a particular fold. Specific hydrogen-bonding patterns and salt-bridges have also been proposed to play a role. Inspection of protein-protein interfaces reveals that the hallmarks governing single chain protein structures also determine their interactions, suggesting that similar principles underlie protein folding and protein-protein associations. This review focuses on some aspects of protein-protein interfaces, particularly on the architectures and their interactions. These are compared with those present in protein monomers. This task is facilitated by the recently compiled, non-redundant structural dataset of protein-protein interfaces derived from the crystallographic database. In particular, although current view holds that protein-protein interfaces and interactions are similar to those found in the conformations of single-chain proteins, this review brings forth the differences as well. Not only is it logical that such differences would exist, it is these differences that further illuminate protein folding on the one hand and protein-protein recognition on the other. These are also particularly important in considering inhibitor (ligand) design.

Amino Acids↗

PubMed2004

HIVbase: a PC/Windows-based software offering storage and querying power for locally held HIV-1 genetic, experimental and clinical data.

BACKGROUND: Human immunodeficiency virus (HIV) research involves ongoing, repetitious sequencing of the HIV genome and the massive accumulation of associated investigational data. As a result, the storage of annotated DNA and/or protein sequences, as well as information retrieval, have become increasingly difficult tasks, with scientists extracting less information from their collected data than they should. OBJECTIVES: Our objective was to design and develop a software package to aid researchers in the storage, analysis and exploration of their HIV-associated data. RESULTS: HIVbase contains familiar, easy-to-use interfaces and functionality for integrating many types of disparate data. The software contains tools that allow for the mass import of raw genetic data, eliminate repetitious sequence translations, have the ability to identify automatically and store HIV regions of interest from nucleic acid or protein sequences, allow for the export of data in commonly used analysis-ready formats, and for unique querying approaches.

Algorithms↗

PubMed2006

The transmembrane domain of the oncogenic mutant ErbB-2 receptor: a structure obtained from site-specific infrared dichroism and molecular dynamics.

ErbB-2 is a member of the family of epidermal growth factor receptors, which shows an oncogenic mutation in the rat gene neu, Val664Glu in the transmembrane domain that causes permanent dimerisation and subsequently leads to uncontrollable cell division and tumour formation. We have obtained the alpha-helical structure of the mutant transmembrane domain dimer experimentally with site-specific infrared dichroism (SSID) based on six transmembrane peptides with 13C18O carbonyl group-labelled residues. The derived orientational data indicate a local helix tilt ranging from 28(+/-6) degrees to 22(+/-4) degrees. Altogether using orientational constraints from SSID and experimental alpha-helical constraints while performing a systematic conformational search including molecular dynamics simulation in a lipid bilayer, we have obtained a unique experimentally defined atomic structure. The resulting structure consists of a right handed alpha-helical bundle with the residues Ile659, Val663, Leu667, Ile671, Val674 and Leu679 in the dimerisation interface. The right-handed bundle is in contrast to the left-handed structures obtained in previous modelling efforts. In order to facilitate tight helical packing, the spacious Glu664 residues do not interact directly but with water molecules that enter the bilayer.

Animals↗

PubMed2004

Crystal structure of the putative adapter protein MTH1859.

MTH1859 from Methanobacterium thermoautotrophicum is a 77 residue protein representing a conserved family of functionally uncharacterized proteins. We solved the crystal structure of MTH1859 by single wavelength anomalous diffraction phasing using selenomethionine labeled protein. MTH1859 adopts a mainly anti-parallel all-beta-fold. The beta-sheet is heavily bent to form a U-structure that is closed through a loop. The monomer structure possesses similarities to the photoreaction center (PRC) domain fold, but the protein employs a unique oligomerization scheme. Two monomers of MTH1859 occupy the asymmetric unit and dimerize in a head-to-head fashion. Crystal packing interactions identify a second protein-protein interaction interface at the MTH1859 tails which can simultaneously bind two partner molecules. These interactions lead to the formation of a honeycomb structure and suggest that the family of MTH1859-like proteins might function as adapters for protein complex assembly.

Adaptor Proteins, Signal Transducing↗

PubMed2003

Bacillus subtilis SecA ATPase exists as an antiparallel dimer in solution.

SecA ATPase promotes the biogenesis of membrane and secretory proteins into and across the cytoplasmic membrane of Eubacteria. SecA binds to translocon component SecYE and substrate proteins and undergoes ATP-dependent conformational cycles that are coupled to the stepwise translocation of proteins. Our recent crystal structure of B. subtilis SecA [Hunt, J. F., Weinkauf, S., Henry, L., Fak, J. J., McNicholas, P., Oliver, D. B., and Deisenhofer, J. (2002) Science 297, 2018-2026] showed two different dimer interactions in the lattice which both buried significant solvent-accessible surface area in their interface and could potentially be responsible for formation of the physiological dimer in solution. In this paper, we utilize fluorescence resonance energy transfer methodology with genetically engineered SecA proteins containing unique pairs of tryptophan and fluorophore-labeled cysteine residues to determine the oligomeric structure of SecA protein in solution. Our results show that of the two dimers interactions observed in the crystal structure, SecA forms an antiparallel dimer in solution that maximizes the buried solvent-accessible surface area and intermolecular contacts. At the submicromolar protein concentrations used in the fluorescence experiments, we saw no evidence for the formation of higher-order oligomers of SecA based on either the alternative dimer or the 3(1) helical fiber observed in the crystal lattice. Our studies are consistent with previous ones demonstrating the existence of a dimerization determinant within the C-domain of SecA as well as those documenting the interaction of N- and C-domains of SecA. Our results also provide a valuable starting point for a determination of whether the subunit status of SecA changes during the protein translocation as well as studies designed to elucidate the conformational dynamics of this multidomain protein during its translocation cycle.

Adenosine Triphosphatases↗

PubMed2004

The structure of (3R)-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Pseudomonas aeruginosa.

Type II fatty acid biosynthesis systems are essential for membrane formation in bacteria, making the constituent proteins of this pathway attractive targets for antibacterial drug discovery. The third step in the elongation cycle of the type II fatty acid biosynthesis is catalyzed by beta-hydroxyacyl-(acyl carrier protein) (ACP) dehydratase. There are two isoforms. FabZ, which catalyzes the dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP, is a universally expressed component of the bacterial type II system. FabA, the second isoform, as has more limited distribution in nature and, in addition to dehydration, also carries out the isomerization of trans-2- to cis-3-decenoyl-ACP as an essential step in unsaturated fatty acid biosynthesis. We report the structure of FabZ from the important human pathogen Pseudomonas aeruginosa at 2.5 A of resolution. PaFabZ is a hexamer (trimer of dimers) with the His/Glu catalytic dyad located within a deep, narrow tunnel formed at the dimer interface. Site-directed mutagenesis experiments showed that the obvious differences in the active site residues that distinguish the FabA and FabZ subfamilies of dehydratases do not account for the unique ability of FabA to catalyze isomerization. Because the catalytic machinery of the two enzymes is practically indistinguishable, the structural differences observed in the shape of the substrate binding channels of FabA and FabZ lead us to hypothesize that the different shapes of the tunnels control the conformation and positioning of the bound substrate, allowing FabA, but not FabZ, to catalyze the isomerization reaction.

Amino Acid Sequence↗

PubMed2006

PREDITOR: a web server for predicting protein torsion angle restraints.

Every year between 500 and 1000 peptide and protein structures are determined by NMR and deposited into the Protein Data Bank. However, the process of NMR structure determination continues to be a manually intensive and time-consuming task. One of the most tedious and error-prone aspects of this process involves the determination of torsion angle restraints including phi, psi, omega and chi angles. Most methods require many days of additional experiments, painstaking measurements or complex calculations. Here we wish to describe a web server, called PREDITOR, which greatly accelerates and simplifies this task. PREDITOR accepts sequence and/or chemical shift data as input and generates torsion angle predictions (with predicted errors) for phi, psi, omega and chi-1 angles. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions. The method is fast (<40 s per protein) and accurate, with 88% of phi/psi predictions being within 30 degrees of the correct values, 84% of chi-1 predictions being correct and 99.97% of omega angles being correct. PREDITOR is 35 times faster and up to 20% more accurate than any existing method. PREDITOR also provides accurate assessments of the torsion angle errors so that the torsion angle constraints can be readily fed into standard structure refinement programs, such as CNS, XPLOR, AMBER and CYANA. Other unique features to PREDITOR include dihedral angle prediction via PDB structure mapping, automated chemical shift re-referencing (to improve accuracy), prediction of proline cis/trans states and a simple user interface. The PREDITOR website is located at: http://wishart.biology.ualberta.ca/preditor.

Internet↗

PubMed2000

Reinterpretation of a Kardar-Parisi-Zhang equation-based classification

The velocity versus tilt behavior, on which the Kardar-Parisi-Zhang (KPZ) equation-based quenched Edward-Wilkinson-directed percolation depinning (QEW-DPD) classification scheme of models of rough interface growth in a medium with quenched disorder is based, is reinterpreted. The consideration of the screen grid of pixels in computer simulation interface propagation allows an explanation of tilt-velocity behavior without assuming vanishing or divergence in the depinning transition of the KPZ parameter lambda which is found to have a unique, measurable value in DPD. Random field Ising model-like velocity-tilt behavior in the QEW class is shown to either correspond to zero lambda. The possibility of obtaining low velocity v(m) behavior from the KPZ method raises some interesting questions about the depinning transition.

Journal Article↗

PubMed1999

Secretion of cryparin, a fungal hydrophobin.

Cryparin is a cell-surface-associated hydrophobin of the filamentous ascomycete Cryphonectria parasitica. This protein contains a signal peptide that directs it to the vesicle-mediated secretory pathway. We detected a glycosylated form of cryparin in a secretory vesicle fraction, but secreted forms of this protein are not glycosylated. This glycosylation occurred in the proprotein region, which is cleaved during maturation by a Kex2-like serine protease, leaving a mature form of cryparin that could be isolated from both the cell wall and culture medium. Pulse-chase labeling experiments showed that cryparin was secreted through the cell wall, without being bound, into the culture medium. The secreted protein then binds to the cell walls of C. parasitica, where it remains. Binding of cryparin to the cell wall occurred in submerged culture, presumably because of the lectin-like properties unique to this hydrophobin. Thus, the binding of this hydrophobin to the cell wall is different from that of other hydrophobins which are reported to require a hydrophobic-hydrophilic interface for assembly.

Ascomycota↗

PubMed1995

Role of the astronaut in operating the Advanced Fluid Physics Module.

The role of man in space is investigated in the operation of the Advanced Fluid Physics Module (AFPM), a scientific instrument dedicated to fluid physics research in a microgravity environment and flown on the Spacelab D2 mission. The astronaut involvement is addressed by applying the criteria of the THURIS study, conducted by NASA for the optimization of future manned space flights. Outcomes of the THURIS study are first summarized. The AFPM characteristics and interfaces are briefly presented. The five experiments performed on board Spacelab D2 are introduced and the involvement of the astronaut is described. Finally, THURIS criteria are applied to an AFPM experiment scenario. Results show that, of all the activities involved in the AFPM nominal operation, two thirds are related to hardware manipulation and to procedure following, while the last third uses the unique astronaut intellectual capabilities, making his presence in orbit mandatory for successful experiment completion.

Astronauts↗

PubMed1998

Unique activation of matrix metalloproteinase-9 within human liver metastasis from colorectal cancer.

Experimental in vitro and animal data support an important role for matrix metalloproteinases (MMPs) in cancer invasion and metastasis via proteolytic degradation of the extracellular matrix (ECM). Our previous data have shown that MMP-9 mRNA is localized to the interface between liver metastasis and normal liver tissue, indicating that MMP-9 may play an important role in liver metastasis formation. In the present study, we analysed the cellular enzymatic expression of MMP-9 in 18 human colorectal cancer (CRC) liver metastasis specimens by enzyme-linked immunosorbent assay (ELISA) and zymography. ELISA analysis reveals that the latent form of MMP-9 is present in both liver metastasis and paired adjacent normal liver tissue. The mean level of the latent form of MMP-9 is 580+/-270 ng per mg total tissue protein (mean+/-s.e.) in liver metastasis vs 220+/-90 in normal liver tissue. However, this difference is not significantly different (P = 0.26). Using gelatin zymography, the 92-kDa band representative of the latent form is present in both liver metastasis and normal liver tissue. However, the 82 kDa band, representative of the active form of MMP-9, was seen only in liver metastasis. This was confirmed by Western blot analysis. Our observation of the unique presence of the active form of MMP-9 within liver metastasis suggests that proMMP-9 activation may be a pivotal event during CRC liver metastasis formation.

Blotting, Western↗

PubMed2004

APD: the Antimicrobial Peptide Database.

An antimicrobial peptide database (APD) has been established based on an extensive literature search. It contains detailed information for 525 peptides (498 antibacterial, 155 antifungal, 28 antiviral and 18 antitumor). APD provides interactive interfaces for peptide query, prediction and design. It also provides statistical data for a select group of or all the peptides in the database. Peptide information can be searched using keywords such as peptide name, ID, length, net charge, hydrophobic percentage, key residue, unique sequence motif, structure and activity. APD is a useful tool for studying the structure-function relationship of antimicrobial peptides. The database can be accessed via a web-based browser at the URL: http://aps.unmc.edu/AP/main.html.

Amino Acid Motifs↗

PubMed2006

Human PXR forms a tryptophan zipper-mediated homodimer.

The human nuclear receptor pregnane X receptor (PXR) responds to a wide variety of potentially harmful chemicals and coordinates the expression of genes central to xenobiotic and endobiotic metabolism. Structural studies reveal that the PXR ligand binding domain (LBD) uses a novel sequence insert to form a homodimer unique to the nuclear receptor superfamily. Terminal beta-strands from each monomeric LBD interact in an ideal antiparallel fashion to bury potentially exposed surface beta-strands, generating a 10-stranded intermolecular beta-sheet. Conserved tryptophan and tyrosine residues lock across the dimer interface and provide the first tryptophan-zipper (Trp-Zip) interaction observed in a native protein. We show using analytical ultracentrifugation that the PXR LBD forms a homodimer in solution. We further find that removal of the interlocking aromatic residues eliminates dimer formation but does not affect PXR's ability to interact with DNA, RXRalpha, or ligands. Disruption of the homodimer significantly reduces receptor activity in transient transfection experiments, however, and effectively eliminates the receptor's recruitment of the transcriptional coactivator SRC-1 both in vitro and in vivo. Taken together, these results suggest that the unique Trp-Zip-mediated PXR homodimer plays a role in the function of this nuclear xenobiotic receptor.

DNA↗

PubMed1984

Cells of the fetomaternal interface: their role in the maintenance of viviparous pregnancy.

An immune system capable of discriminating between self and nonself evolved in nature long before the appearance of the viviparous mode of pregnancy, which brings maternal cells into a direct physical contact with genetically disparate cells of fetal origin. In the hemochorial type of placentation, the former include cells of the maternal immune system. This article briefly reviews the possible mechanisms that may protect the semiallogeneic conceptus in nature, with special reference to the role of the cells at the fetomaternal interface. We also present some new data on the antigenicity of pre- and postimplantation trophoblast cells and the immunobiology of decidual cells. Systemic changes in the maternal immune system appear to represent homeostatic responses to the presence of a semiallogeneic conceptus, unrelated to its protection; mechanisms for this protection must reside locally at the fetomaternal interface. We find that the lack of immunogenicity of the outer (trophoblast) cells of the preimplantation blastocyst can be explained by a transient disappearance of the major histocompatibility (MHC) antigens on their cell surface. However, following implantation and the formation of the placenta, class 1 MHC antigens reappear on certain classes of trophoblast cells, i.e., labyrinthine and spongiotrophoblast cells of the murine placenta. Similarly, cytotrophoblast cells of the early human placenta exhibit the presence of class 1 MHC antigens. An absence of class 2 MHC antigens despite the presence of class 1 antigens cannot entirely explain the lack of trophoblast immunogenicity. A local immunosuppression mediated by trophoblast cells themselves as well as maternal cells of hemopoietic origin in the decidua remain as a strong possibility. Typical decidual cells appear to play a central role in the maintenance of pregnancy because of their numerous functions: nutritive, endocrine, and immunoregulatory. Our studies reveal that they are descendants of bone-marrow-derived precursors, have unique surface markers recognizable with monoclonal antibodies nonreactive with other hemopoietic cell lineages, and have the ability to abrogate mixed lymphocyte reactions in vitro in a genetically unrestricted manner. Further studies directed at the cells of the fetomaternal interface should provide a better insight into the mode of survival of the nature's most commonplace allograft.

Animals↗