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PubMed2000

Localization of agonist and competitive antagonist binding sites on nicotinic acetylcholine receptors.

Identification of all residues involved in the recognition and binding of cholinergic ligands (e.g. agonists, competitive antagonists, and noncompetitive agonists) is a primary objective to understand which structural components are related to the physiological function of the nicotinic acetylcholine receptor (AChR). The picture for the localization of the agonist/competitive antagonist binding sites is now clearer in the light of newer and better experimental evidence. These sites are located mainly on both alpha subunits in a pocket approximately 30-35 A above the surface membrane. Since both alpha subunits are identical, the observed high and low affinity for different ligands on the receptor is conditioned by the interaction of the alpha subunit with other non-alpha subunits. This molecular interaction takes place at the interface formed by the different subunits. For example, the high-affinity acetylcholine (ACh) binding site of the muscle-type AChR is located on the alphadelta subunit interface, whereas the low-affinity ACh binding site is located on the alphagamma subunit interface. Regarding homomeric AChRs (e.g. alpha7, alpha8, and alpha9), up to five binding sites may be located on the alphaalpha subunit interfaces. From the point of view of subunit arrangement, the gamma subunit is in between both alpha subunits and the delta subunit follows the alpha aligned in a clockwise manner from the gamma. Although some competitive antagonists such as lophotoxin and alpha-bungarotoxin bind to the same high- and low-affinity sites as ACh, other cholinergic drugs may bind with opposite specificity. For instance, the location of the high- and the low-affinity binding site for curare-related drugs as well as for agonists such as the alkaloid nicotine and the potent analgesic epibatidine (only when the AChR is in the desensitized state) is determined by the alphagamma and the alphadelta subunit interface, respectively. The case of alpha-conotoxins (alpha-CoTxs) is unique since each alpha-CoTx from different species is recognized by a specific AChR type. In addition, the specificity of alpha-CoTxs for each subunit interface is species-dependent. In general terms we may state that both alpha subunits carry the principal component for the agonist/competitive antagonist binding sites, whereas the non-alpha subunits bear the complementary component. Concerning homomeric AChRs, both the principal and the complementary component exist on the alpha subunit. The principal component on the muscle-type AChR involves three loops-forming binding domains (loops A-C). Loop A (from mouse sequence) is mainly formed by residue Y(93), loop B is molded by amino acids W(149), Y(152), and probably G(153), while loop C is shaped by residues Y(190), C(192), C(193), and Y(198). The complementary component corresponding to each non-alpha subunit probably contributes with at least four loops. More specifically, the loops at the gamma subunit are: loop D which is formed by residue K(34), loop E that is designed by W(55) and E(57), loop F which is built by a stretch of amino acids comprising L(109), S(111), C(115), I(116), and Y(117), and finally loop G that is shaped by F(172) and by the negatively-charged amino acids D(174) and E(183). The complementary component on the delta subunit, which corresponds to the high-affinity ACh binding site, is formed by homologous loops. Regarding alpha-neurotoxins, several snake and alpha-CoTxs bear specific residues that are energetically coupled with their corresponding pairs on the AChR binding site. The principal component for snake alpha-neurotoxins is located on the residue sequence alpha1W(184)-D(200), which includes loop C. In addition, amino acid sequence 55-74 from the alpha1 subunit (which includes loop E), and residues gammaL(119) (close to loop F) and gammaE(176) (close to loop G) at the low-affinity binding site, or deltaL(121) (close to the homologous region of loop G) at the high-affinity binding site, are i

Animals↗

PubMed1987

Cellular electrophysiology of coronary artery ligation in chronic pressure overload.

We evaluated ischemia-induced cellular electrophysiologic abnormalities in chronic pressure overload ventricular myocardium in vitro. Left ventricular systolic hypertension was induced in cats via partial supracoronary aortic constriction (overload); at 1 1/2-3 months, resulting pressure overload was accompanied by ventricular hypertrophy (25-35% by weight) and patchy endocardial fibrosis. Two hours of subsequent acute myocardial ischemia (ischemia) was imposed on overload (ischemia/overload) via total occlusion of distal branches of the left coronary artery system. Spontaneous premature depolarizations in vitro were increased in ischemia/overload compared to control, ischemia or overload alone; bursts of spontaneous, repetitive depolarizations were also unique to these preparations. Multiple site recordings of endocardial transmembrane action potentials overlying the borders (interface) of fibrotic areas in ischemia/overload demonstrated numerous electrophysiologic abnormalities, including several not observed in control, ischemia or overload. Unique to the border areas of ischemia/overload preparations was the presence of maintained but depressed resting potential without action potentials; also, the incidence of depolarizations at the onset of the plateau phase was highest in these preparations. In non-fibrotic areas, electrophysiologic properties including resting potential and action potential amplitude and rate of rise were diminished in ischemia/overload compared to ischemia or overload preparations. These data demonstrate that acute myocardial ischemia in the setting of chronic pressure overload leads to additional cellular electrophysiologic abnormalities compared to ischemia or overload alone.

Action Potentials↗

PubMed2004

Therapeutic targeting of prostate cancer.

An inaugural conference in Tucson Arizona on May 6-9, 2004 brought together more than 70 clinical and basic scientists to discuss recent research advances in understanding and targeting the progression of the human prostate cancer. The informal meeting was unique in that it provided the opportunity for discussion and interaction between these different groups of scientists whose paths rarely cross. The goal of the meeting was to develop new and novel approaches in understanding the human prostate cancer in order to uncover therapeutic targets. Faculty from six different cancer centers were represented including Memorial Sloan-Kettering Cancer Center (New York, NY); Arizona Cancer Center (Tucson, AZ); Fred Hutchinson Cancer Center (Seattle, WA); Chao Family Comprehensive Cancer Center (Irvine, CA); the Sydney Kimmel Cancer Center (San Diego, CA); Jonsson Comprehensive Cancer Center, University of California (Los Angeles, CA); and University of Massachusetts Memorial Cancer Center (Worcester, MA). Several important concepts emerged from this meeting as a result of the basic and clinical science interface. These concepts include: (1) Human prostate cancer has unique biological features as compared to other human epithelial malignancies; (2) Tumor plasticity is evident early in prostate cancer progression as evidenced by alterations in the extracellular matrix; (3) New therapeutic strategies should include the co-targeting of the stroma and prostate cancer; (4) Cell-cell and cell-ECM adhesion switching are reversible phenotypes evident early in human prostate tumor progression; (5) The discovery of molecular signatures including genomic or proteomic patterns for the discrimination of indolent versus aggressive disease is a potentially powerful tool and requires multifactorial approaches for success; and (6) New biomarkers and innovative tissue specific imaging modalities for human prostate cancer are being developed that may aid in a more accurate assessment of prostate cancer in patients.

Animals↗

PubMed2006

Interfacing microchip capillary electrophoresis with electrospray ionization mass spectrometry.

Microfluidic devices are a unique enabling technology for chemical separations, modification, and synthesis that are ideally suited for the manipulation of low volume samples on the order of a few nanoliters in volume. Complex patterns of capillary-sized channels with zero dead volume connections are the distinguishing features of many microfluidic devices. Concurrently, mass spectrometry has undergone further development, and is now arguably the method of choice for structural characterization of mass- and volume-limited samples. The production of ions in the gas phase from the solution phase is critical for direct coupling of fluidic devices with the mass spectrometer, and the electrospray ionization (ESI) sources are well suited for this application. Micro- and nanoflow ESI interfaces are ideal for these applications as they cover flow rate ranges from the hundreds to a few nanoliters per minute, which are the same as the flow rates used by most microfluidic devices. Herein, the assembly and operation of a simple ESI interface for coupling a microfluidic device and mass spectrometer is described.

Electrophoresis, Microchip↗

PubMed2006

Apolipoprotein B is conformationally flexible but anchored at a triolein/water interface: a possible model for lipoprotein surfaces.

Apolipoprotein B (apoB) is one of a unique group of proteins that form and bind to fat droplets, stabilize the emulsified fat, and direct their metabolism. ApoB, secreted on lipoproteins (emulsions), remains bound during lipid metabolism yet exhibits conformational flexibility. It has amphipathic beta-strand (AbetaS)-rich domains and amphipathic alpha-helix (AalphaH)-rich domains. We showed that two consensus AbetaS peptides of apoB bound strongly to hydrophobic interfaces [triolein/water (TO/W) and dodecane/water], were elastic, and were not pushed off the interface when the surface was compressed. In contrast, an AalphaH peptide modeling helical parts of apoB was forced off the TO/W interface by compression and readsorbed when the interface was expanded. In this report, the surface behavior of apoB-100 was studied at the TO/W interface. Solubilized apoB lowered the interfacial tension of TO/W in a concentration-dependent fashion. At equilibrium tension, if the surface was compressed, part of apoB was pushed off but quickly readsorbed when the surface was expanded. Even when the surface area was compressed by approximately 55%, part of the apoB molecule remained bound. The maximum surface pressure that apoB could withstand without being partially ejected was 13 mN/m. ApoB showed high elasticity at the TO/W interface. Based on studies of the consensus AbetaS and AalphaH peptides, we suggest that AbetaSs anchor apoB and are its nonexchangeable motif, whereas its conformational flexibility arises from both the elastic nature of the AbetaS and the ability of AalphaH domains of the molecule to desorb and readsorb rapidly in response to surface pressure changes.

Adsorption↗

PubMed1997

A new adhesive bonding material for the cementation of implantable devices in otologic surgery.

BACKGROUND: Presently, there are no U.S. Food and Drug Administration (FDA)-approved adhesive bone cements for the surgical fixation of prosthetic materials in the middle ear. A promising new cement, 4-META/MMA-TBB opaque resin, has shown remarkable adhesive properties as a bone cement in vivo. The cement is composed of 4-methacryloyloxyethyl trimellitate anhydride (4-META) and methyl methacrylate (MMA) as monomers and tri-n-butyl borane (TBB) as an initiator. METHODS: An electromagnetic semiimplantable hearing device presently under development was implanted into the middle ear of six cats using 4-META/MMA-TBB resin to cement a titanium-encased magnet to the incus. The animals were subsequently killed (at a mean of 9.6 months) to assess the (temporal bones and specifically the magnet-incus complex in each animal. RESULTS: The titanium-encapsulated magnet was firmly adherent to all incuses without any failure of the cement-bone interface. Histopathologic examination of the implanted temporal bones demonstrated lack of middle ear inflammation. Transmission electron microscopy of the incuses demonstrated a unique "hybrid layer" in the bone-side subsurface of the bone-cement interface that elucidates the mechanism of interfacial adhesion. CONCLUSIONS: Our investigation highlights the special biomechanical properties as well as the biocompatibility of 4-META/ MMA-TBB resin that make it an attractive bone-bonding agent for use in otologic surgery, including its potential usefulness during ossicular reconstruction.

Animals↗

PubMed1996

A protocol for maintaining multidatabase referential integrity.

The bioinformatics community is becoming increasingly reliant on the creation of links among biological databases (DBs) as a foundation for DB interoperability. For example, a link might be created from a protein in one DB (such as PIR), to a gene in another DB (such as GDB), by storing the unique identifier (id) of the gene object within an attribute of the protein object. User interfaces can then support navigation from the protein to the gene, and multiDB queries can join the protein with the gene. The unique id of the gene is serving as a foreign key. However, a variety of factors, such as changes in the underlying biology, can cause object ids to become invalid, thus producing invalid links among DBs. Invalid links are a violation of multidatabase referential integrity. We propose a network protocol whereby a database administrator can provide information about changes to the identifiers of objects in their database via Internet, to allow other databases to maintain referential integrity. We request comments from the bioinformatics community for the purpose of building a consensus on the proposed protocol.

Computational Biology↗

PubMedDate not supplied

Scalable WIM: effective exploration in large-scale astrophysical environments.

Navigating through large-scale virtual environments such as simulations of the astrophysical Universe is difficult. The huge spatial range of astronomical models and the dominance of empty space make it hard for users to travel across cosmological scales effectively, and the problem of wayfinding further impedes the user's ability to acquire reliable spatial knowledge of astronomical contexts. We introduce a new technique called the scalable world-in-miniature (WIM) map as a unifying interface to facilitate travel and wayfinding in a virtual environment spanning gigantic spatial scales: Power-law spatial scaling enables rapid and accurate transitions among widely separated regions; logarithmically mapped miniature spaces offer a global overview mode when the full context is too large; 3D landmarks represented in the WIM are enhanced by scale, positional, and directional cues to augment spatial context awareness; a series of navigation models are incorporated into the scalable WIM to improve the performance of travel tasks posed by the unique characteristics of virtual cosmic exploration. The scalable WIM user interface supports an improved physical navigation experience and assists pragmatic cognitive understanding of a visualization context that incorporates the features of large-scale astronomy.

Journal Article↗

PubMed1994

Tumor-associated antigens recognized by human monoclonal antibodies.

BACKGROUND: Nonhuman monoclonal antibodies (MoAbs) of desired specificities have been studied in cancer treatment and tumor targeting with minimal success. Attempts of using humanized chimeric antibodies have not improved significantly their clinical applications. We have engaged in the development of human MoAbs by incorporating the in vitro immunization protocols to the nodal lymphocytes of cancer patients. Three human MoAbs thus generated were found to be strongly reactive with various human malignancies. The antigens recognized by the three antibodies were selected for immunochemical and biochemical characterizations. METHODS: The antigens investigated were AgSK1, PA 1-2 and PA 3-1. The patterns of each antigen expression in various human cancer cell lines were studied by the immunocytochemical staining technique. The expression of AgSK1 in association with cellular proliferation was examined by the flow cytometry analysis. In studying the biochemical natures of these antigens, their sensitivities toward various chemical and physical treatments were determined. The antigens that were shown to be proteins were subjected to SDS-PAGE and Western blot for estimations of molecular weights. RESULTS: The AgSK1 was detected in 10 human carcinoma cell lines but in none of the melanoma cell lines. This suggests that SK1 may be an epithelial or carcinoma marker. The phenotypic expressions of AgSK1 were shown to be associated with proliferation of carcinoma cells. Biochemically AgSK1 was a sialophycoprotein with an estimated molecular weight of 42-44 kilodaltons (kDa). HuMAb PA1-2 demonstrated a unique staining pattern at both the cytoplasmic and intercellular interface. The stained filamentlike structures extending from cell to cell indicated that Ag PA1-2 might play a role in cellular interactions. Biochemically, Ag PA1-2 appeared to be an asialocarbohydrate. The Ag PA3-1 was a cytoplasmic glycoprotein expressed by all 13 cell lines. The estimated molecular weights of PA3-1 were 164, 104, and 40 kDa. CONCLUSIONS: Tumor-associated antigens recognized by the human MoAbs may be more relevant clinically than those recognized by the mouse immune system. Carcinoma-specific human MoAbs are desirable for cancer treatment and tumor localization.

Antibodies, Monoclonal↗

PubMed1996

An improved accuracy six-load component pedal dynamometer for cycling.

This paper describes a new six-load component pedal dynamometer designed for study of knee overuse injury in cycling. A unique capability of the dynamometer is the ability to interface with multiple pedal platforms of varying height while maintaining a desired elevation of the foot above the pedal spindle axis. The dynamometer was designed using a concept described in an earlier article by Quinn and Mote (1991, Exp. Mech. 30, 40-48) which measures shear strain across multiple, thin cross-sections. An optimal design technique was used for choosing dimensions of the load measuring cross-sections. A dynamometer was designed and built using the optimal results. Calibration, accuracy results, and sample data are presented. A comparison of accuracy reveals that the new dynamometer is more accurate than previously reported instruments.

Bicycling↗

PubMed1993

The skin immune system: progress in cutaneous biology.

The skin is an active, and in many ways unique, immunological microenvironment quite different from the other primary interfaces between the body and the environment (namely the mucosae). Here Jan D. Bos and Martien L. Kapsenberg identify the components of the skin immune system and describe the inflammatory and immunological responses that they can mount. New findings with regard to the immunophysiology and physiopathology of the human integument are emphasized.

Autoimmune Diseases↗

PubMed2004

Structural basis of heteromeric smad protein assembly in TGF-beta signaling.

The formation of protein complexes between phosphorylated R-Smads and Smad4 is a central event in the TGF-beta signaling pathway. We have determined the crystal structure of two R-Smad/Smad4 complexes, Smad3/Smad4 to 2.5 angstroms, and Smad2/Smad4 to 2.7 angstroms. Both complexes are heterotrimers, comprising two phosphorylated R-Smad subunits and one Smad4 subunit, a finding that was corroborated by isothermal titration calorimetry and mutational studies. Preferential formation of the R-Smad/Smad4 heterotrimer over the R-Smad homotrimer is largely enthalpy driven, contributed by the unique presence of strong electrostatic interactions within the heterotrimeric interfaces. The study supports a common mechanism of Smad protein assembly in TGF-beta superfamily signaling.

Animals↗

PubMed2006

Classification of protein-DNA complexes based on structural descriptors.

We attempt to classify protein-DNA complexes by using a set of 11 descriptors, mainly characterizing protein-DNA interactions, including the number of atomic contacts at major and minor grooves, conformational deviations from standard B- and A-DNA forms, widths of DNA grooves, GC content, specificity measures of direct and indirect readouts, and buried surface area at the complex interface. The cluster analyses were carried out for a unique set of 62 complexes including a variety of protein motifs, and 7 distinct clusters were revealed from the analyses. We found that some proteins with the same motif are classified into different clusters, whereas different proteins with distinct motifs are classified into the same cluster. These results suggest that the conventional motif-based classification of DNA binding proteins may not necessarily correspond to structural and functional properties of protein-DNA complexes, and that the present classification will help to identify common properties and rules that govern protein-DNA recognition.

Cluster Analysis↗

PubMed1998

Nonradioactive in situ hybridization for detection of hydrophobin mRNA in the phytopathogenic fungus Claviceps purpurea during infection of rye.

Hydrophobins are unique fungal extracellular proteins that produce amphipathic films at interfaces, mediate contact to hydrophobic surfaces and are known to be important in phytopathogenicity. In the pathogenic ascomycete Claviceps purpurea, causing ergot disease in grasses and cereals and ergotism in livestock, a gene encoding an extraordinary type of hydrophobin has been detected, which appeared to be induced during alkaloid synthesis in axenic culture of an ergot-alkaloid producing strain of Claviceps (V. Garre and P. Tudzynski, pers. communication; Arntz and Tudzynski, 1997, Curr. Genet. 31, 357-360). To elucidate presence and function of this hydrophobin during infection of rye, the nonradioactive in situ hybridization technique was successfully adapted to the fungal organism and optimized in the pathogenic interaction system. Semithin cryosections proved to be suitable for microscopical gene expression analysis using immune-mediated alkaline-phosphatase staining for detection of digoxigenin-labeled cRNA probes. Specific hybridization of the prepared antisense riboprobe to hydrophobin mRNA was confirmed in nonradioactive Northern blots. While permeabilization by proteinase K had only a minor effect, the inclusion of detergent into the hybridization solutions enhanced specific RNA-RNA hybridization under maximum stringency. Hydrophobin mRNA was found in fungal cells, growing in axenic culture. In the disease cycle, hydrophobin transcripts were localized in abundance during vegetative fructification in conidiophores that actively produced conidia. No signals were observed in sclerotial hyphae during formation of the alkaloid-containing ergots, although they fluoresced intensely during total RNA detection using acridine orange. Notably, in situ hybridization experiments resulted in specific signals during early infection and colonization phases in the external mycelia and in hyphae penetrating the host epidermal layer. The presumed role of the hydrophobin gene product in ergot pathogenicity is discussed with respect to the described spatio-temporal distribution of the hydrophobin transcripts.

Claviceps↗

PubMed1994

Construction of a synthetic gene for the metalloregulatory protein MerR and analysis of regionally mutated proteins for transcriptional regulation.

The transcriptional control protein MerR is a metalloregulatory switch, activating transcription of a mercury resistance operon in the presence of mercuric ions and repressing transcription in their absence. We report here the construction and utilization of a synthetic merR gene and a single-copy merT'-lacZ fusion reporter for mutagenic analysis of the MerR protein's function. Site-directed mutagenesis of clustered acidic residues within the central region of the MerR protein indicated that these residues are important to the protein's ability to repress transcription. Quadruple or sextuple mutations involving residues E83 and E84 and other nearby acidic residues result in a repression-deficient (RD) phenotype. One of the mutant proteins was purified and shown by gel shift assay to retain binding to its operator DNA with an affinity similar to wild-type protein, suggesting that transcriptional repression does not correlate with MerR binding affinity. A small region of merR corresponding to residues 81-92 also was mutagenized in a search for other RD mutants and for mutants displaying sufficient transcriptional activation in the absence of mercuric ion to be classified as constitutive activation (CA) mutants. In this case, oligonucleotide-directed randomization of the target region and a screening/selection protocol were employed. Sixteen different mutants with an RD phenotype were identified, as well as eight different mutants with a CA phenotype. A high frequency of S87C mutations is evident in the RD set of mutants. The CA mutants have a high incidence of S86C and A89V mutations. The CA double mutant S86C/A89V was purified and found to bind to its DNA site with an affinity similar to that of the wild-type protein. Chemical nuclease activity assays indicate that the nonmercurated S86C/A89V CA mutant has a DNA distortion activity identical to that of mercurated wild-type MerR. A unique disulfide bond bridging this CA mutant's dimer interface was found and is proposed to constrain protein conformation in a manner analogous to mercuric ion binding in the wild-type protein.

Amino Acid Sequence↗

PubMed2005

Protein driven patterning of self-assembled cubosomic nanostructures: long oriented nanoridges.

Self-assembly lipid/protein cubosomic nanostructures are generated at high hydration level (dispersion of 5% lipid only) and examined by freeze-fracture electron microscopy (FF-EM) and synchrotron X-ray diffraction (XRD). The fracture surface of the three-dimensional (3D) soft-matter membranous assembly reveals starlike nanopatterns of oriented 100-nm-long cubosomic nanoridges with lateral periodicity defined by their 21-nm diameters. The average water channel radius in these liquid crystalline cubosomic nanoarchitectures, determined by high-resolution FF-EM and XRD, is 18.0 Angstrom. The protein-directed fragmentation of a diamond-type lipid cubic phase at high hydration can induce 3D patterns of oriented nanoporous building blocks, which are a unique example of tertiary organization of functionalized fluid lipid/water interfaces.

Chemistry, Physical↗

PubMed2006

Versatile fabrication of distorted cubic mesoporous silica film using CTAB together with a hydrophobic organic additive.

We have succeeded in the fabrication of distorted cubic R-3m mesoporous silica film with 3D open mesostructure providing high pore accessibility from the surface-air interface of the film. The film fabrication involves a unique approach of adding 1,3,5- triisopropylbenzene (TIPB) to the silica/cetyltrimethylammoniumbromide (CTAB) coating sol during its preparation. The addition of TIPB induces the formation of spheroid micelles, promoting R-3m mesostructure in the film. This phase does not exist in the corresponding binary phase diagram of CTAB surfactant.

Journal Article↗

PubMed2005

Nanomaterial-based electrochemical biosensors.

The unique properties of nanoscale materials offer excellent prospects for interfacing biological recognition events with electronic signal transduction and for designing a new generation of bioelectronic devices exhibiting novel functions. In this Highlight I address recent research that has led to powerful nanomaterial-based electrical biosensing devices and examine future prospects and challenges. New nanoparticle-based signal amplification and coding strategies for bioaffinity assays are discussed, along with carbon-nanotube molecular wires for achieving efficient electrical communication with redox enzyme and nanowire-based label-free DNA sensors.

Biosensing Techniques↗