Home About us Contact
|
Home About us Contact | ||
|
|
||
Three-dimensional Structure (three-dimensional + structure)
Kinds of Three-dimensional Structure Selected AbstractsPrediction of the Three-Dimensional Structure for the Rat Urotensin,II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic SimulationsCHEMMEDCHEM, Issue 9 2010Soo-Kyung Kim Dr. Abstract Urotensin-II (U-II) has been shown to be the most potent mammalian vasoconstrictor known. Thus, a U-II antagonist might be of therapeutic value in a number of cardiovascular disorders. However, interspecies variability of several nonpeptidic ligands complicates the interpretation of in vivo studies of such antagonists in preclinical animal disease models. ACT058362 is a selective antagonist for the human U-II receptor (hUT2R) with a reported Kd value of ,4,nM in a molecular binding assay, but it is reported to bind weakly to rat UT2R (rUT2R), with a Kd value of ,1,500,nM. In contrast, the arylsulphonamide SB706375 is a selective antagonist against both hUT2R (Kd=,9,nM) and rUT2R (Kd=,21,nM). To understand the species selectivity of the UT2R, we investigated the binding site of ACT058362 and SB706375 in both hUT2R and rUT2R to explain the dramatically lower (,400-fold) affinity of ACT058362 for rUT2R and the similar affinity (,10,nM) of SB706375 for both UT2Rs. These studies used MembStruk and MSCDock to predict the UT2R structure and the binding site of ACT058362 and SB706375. Based on binding energies, we found two binding modes each with D1303.32 as the crucial anchoring point (Ballesteros,Weinstein numbering given in superscript). We predict that ACT058362 (an aryl,amine,aryl or ANA ligand) binds in the transmembrane (TM) 3456 region, while SB706375 (an aryl,aryl,amine or AAN ligand) binds in the TM 1237 region. These predicted sites explain the known differences in binding of the ANA ligand to rat and human receptors, while explaining the similar binding of the AAN compound to rat and human receptors. Moreover the predictions explain currently available structure,activity relationship (SAR) data. To further validate the predicted binding sites of these ligands in hUT2R and rUT2R, we propose several mutations that would help define the structural origins of differential responses between UT2R of different species, potentially indicating novel UT2R antagonists with cross-species high affinity. [source] Three-Dimensional Structure and Thermal Stability Studies of DNA Nanostructures by Energy Transfer SpectroscopyCHEMPHYSCHEM, Issue 10 2010Jong Bum Lee Dr. Structural changes and stability of DNA nanoarchitectures including Y-shaped DNA (see picture), dendrimer-like DNA, and DNA hydrogels are investigated. The results demonstrate the feasibility and flexibility of FRET and NSET (Förster resonance/ nanometal surface- energy transfer) in determining difficult-to-obtain 3D structures and characterizing the thermal responses of DNA nanoarchitectures in real time. [source] Silicon Microstructures: Detachment Lithography of Photosensitive Polymers: A Route to Fabricating Three-Dimensional Structures (Adv. Funct.ADVANCED FUNCTIONAL MATERIALS, Issue 2 2010Mater. The scanning electron microscope image featured on the front cover shows a three-dimensional polydimethylsiloxane (PDMS) molded film bonded on a glass rod. Multilevel silicon structures used to mold the PDMS film were fabricated from successive steps of detachment lithography of photoresist films, which are patterned with lithography and reactive ion etching, as reported by J. Yeom and M. A. Shannon on page 289. The smallest feature on the pyramid is 2 µm in diameter. [source] Detachment Lithography of Photosensitive Polymers: A Route to Fabricating Three-Dimensional StructuresADVANCED FUNCTIONAL MATERIALS, Issue 2 2010Junghoon Yeom Abstract A technique to create arrays of micrometer-sized patterns of photosensitive polymers on the surface of elastomeric stamps and to transfer these patterns to planar and nonplanar substrates is presented. The photosensitive polymers are initially patterned through detachment lithography (DL), which utilizes the difference in adhesion forces to induce the mechanical failure in the film along the edges of the protruded parts of the mold. A polydimethylsiloxane (PDMS) stamp with a kinetically and thermally adjustable adhesion and conformal contact can transfer the detached patterns to etched or curved substrates, as well as planar ones. These printed patterns remain photochemically active for further modification via photolithography, and/or can serve as resists for subsequent etching or deposition, such that photolithography can be used on highly nonconformal and nonplanar surfaces. Various 3D structures fabricated using the process have potential applications in MEMS (micro-electromechanical systems) sensors/actuators, optical devices, and microfluidics. [source] Photosensitive Nanocomposites: Highly Non-Linear Quantum Dot Doped Nanocomposites for Functional Three-Dimensional Structures Generated by Two-Photon Polymerization (Adv. Mater.ADVANCED MATERIALS, Issue 22 201022/2010) Baohua Jia, Min Gu, and co-workers report on p.,2463 on novel quantum dot functionalized photosensitive nanocomposites showing ultrahigh third-order nonlinearity. The cover image shows functional three-dimensional micronano photonic structures, for example, photonic crystals can be fabricated in such active nanocomposites using the versatile two-photon poly-merisation method, opening various possibilities in active micro/nano devices, such as ultrafast switching, signal regeneration, and high speed demultiplexing systems. [source] Highly Non-Linear Quantum Dot Doped Nanocomposites for Functional Three-Dimensional Structures Generated by Two-Photon PolymerizationADVANCED MATERIALS, Issue 22 2010Baohua Jia A nanocomposite consisting of a photosensitive organic,inorganic hybrid polymer functionalized with PbS quantum dots has been developed using a sol,gel process. The uniformly dispersed nanocomposite exhibits ultrahigh third-order non-linearity (,3.2,×,10,12 cm2 W,1) because of the strong quantum confinement of small-sized and narrowly distributed quantum dots. The non-linear nanocomposite has been proven to be suitable for the fabrication of 3D micro/nano photonic devices using two-photon polymerization. The fabricated photonic crystals show stop gaps with more than 60% suppression in transmission at the telecommunications wavelength region. [source] Buckled Bridges Using Film Stress for Three-Dimensional Structures: Effects of Lateral Designs on Vertical Profiles and Dynamic CharacteristicsIEEJ TRANSACTIONS ON ELECTRICAL AND ELECTRONIC ENGINEERING, Issue 2 2010Minoru Sasaki Member Abstract Bridges buckled by film stress can generate a vertical displacement resulting in three-dimensional structures. We have demonstrated a micromirror lifted by buckled bridges and a vertical comb drive actuator. The structures show rounded profiles in a stable manner. The detailed profiles of the bridges and the lifted micromirrors are examined. The relations between the lateral design and its effect on the vertical profile and the dynamic characteristics are studied. Copyright © 2010 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc. [source] Fabrication of Reversely Tapered Three-Dimensional Structures and Their Application to Organic Light-Emitting DiodesADVANCED MATERIALS, Issue 13 2003J. Rhee Cathode separators typically used for patterning metal cathodes of organic light-emitting diodes (OLEDs),see Figure,can be fabricated using a lithography-based technique that allows the construction of reversely tapered 3D structures in one single molding step. The physics involved in making the fabrication of such 3D structures possible is outlined and the efficacy of the separator thus fabricated is demonstrated with an OLED. [source] A Zeolite-Like Zinc Phosphonocarboxylate Framework and Its Transformation into Two- and Three-Dimensional StructuresCHEMISTRY - AN ASIAN JOURNAL, Issue 12 2007Zhenxia Chen Abstract Three zinc phosphonocarboxylates, Zn2(pbc)2,Hdma,H3O,2H2O (1), Zn(pbc),Hdma (2), and Zn4.5(pbc)3(OH)(H2O)0.5,Hdma (3) (H3pbc=4-phosphonobenzoic acid, dma=dimethylamine) were synthesized by the mixed solvothermal reaction of Zn(Ac)2,2H2O and 4-phosphonobenzoic acid in N,N -dimethylformamide (DMF) and water. The zigzag and ladderlike chains completely constructed by triply fused 4-membered rings (denoted SBU-1) are linked by the organic moieties to form the 3D zeolite-like structure 1 and the layered structure 2, respectively. As for structure 3, a new second building unit (SBU-2) formed by the inset of the [Zn3O12] trimer into the 4-membered ring as well as SBU-1 is observed. The connections between the two types of SBUs lead to a "zinc phosphate" layer, which is linked by the organic groups to generate a 3D pillar-layered structure. Both solution-mediated and solid-state transformations of 1 to 2 and 3 were observed. A possible mechanism for the transformation is proposed. Gas sorption studies show that 1 has accessible pores for methanol and water and exhibits size selectivity for alcohols. [source] Three-dimensional structure of the histidine-containing phosphocarrier protein (HPr) from Enterococcus faecalis in solutionFEBS JOURNAL, Issue 3 2001Till Maurer The histidine-containing phosphocarrier protein (HPr) transfers a phosphate group between components of the prokaryotic phosphoenolpyruvate-dependent phosphotransferase system (PTS), which is finally used to phosphorylate the carbohydrate transported by the PTS through the cell membrane. Recently it has also been found to act as an intermediate in the signaling cascade that regulates transcription of genes related to the carbohydrate-response system. Both functions involve phosphorylation/dephosphorylation reactions, but at different sites. Using multidimensional 1H-NMR spectroscopy and angular space simulated annealing calculations, we determined the structure of HPr from Enterococcus faecalis in aqueous solution using 1469 distance and 44 angle constraints derived from homonuclear NMR data. It has a similar overall fold to that found in HPrs from other organisms. Four , strands, A, B, C, D, encompassing residues 2,7, 32,37, 40,42 and 60,66, form an antiparallel , sheet lying opposite the two antiparallel , helices, a and c (residues 16,26 and 70,83). A short , helix, b, from residues 47,53 is also observed. The pairwise root mean square displacement for the backbone heavy atoms of the mean of the 16 NMR structures to the crystal structure is 0.164 nm. In contrast with the crystalline state, in which a torsion angle strain in the active-center loop has been described [Jia, Z., Vandonselaar, M., Quail, J.W. & Delbaere, L.T.J. (1993) Nature (London) 361, 94,97], in the solution structure, the active-site His15 rests on top of helix a, and the phosphorylation site N,1 of the histidine ring is oriented towards the surface, making it easily accessible to the solvent. Back calculation of the 2D NOESY NMR spectra from both the NMR and X-ray structures shows that the active-center structure derived by X-ray crystallography is not compatible with experimental data recorded in solution. The observed torsional strain must either be a crystallization artefact or represents a conformational state that exists only to a small extent in solution. [source] Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95,JOURNAL OF MOLECULAR RECOGNITION, Issue 2 2003Simon S. Terzyan Abstract Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8,×,1.6,×,1.0,mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P212121, with a,=,48.9,Å, b,=,85.2,Å, and c,=,114.0,Å. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293,K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues. Copyright © 2003 John Wiley & Sons, Ltd. [source] Translational Mini-Review Series on Complement Factor H: Structural and functional correlations for factor HCLINICAL & EXPERIMENTAL IMMUNOLOGY, Issue 1 2008C. Q. Schmidt Summary The 155-kDa glycoprotein, complement factor H (CFH), is a regulator of complement activation that is abundant in human plasma. Three-dimensional structures of over half the 20 complement control protein (CCP) modules in CFH have been solved in the context of single-, double- and triple-module segments. Proven binding sites for C3b occupy the N and C termini of this elongated molecule and may be brought together by a bend in CFH mediated by its central CCP modules. The C-terminal CCP 20 is key to the ability of the molecule to adhere to polyanionic markers on self-surfaces where CFH acts to regulate amplification of the alternative pathway of complement. The surface patch on CCP 20 that binds to model glycosaminoglycans has been mapped using nuclear magnetic resonance (NMR), as has a second glycosaminoglycan-binding patch on CCP 7. These patches include many of the residue positions at which sequence variations have been linked to three complement-mediated disorders: dense deposit disease, age-related macular degeneration and atypical haemolytic uraemic syndrome. In one plausible model, CCP 20 anchors CFH to self-surfaces via a C3b/polyanion composite binding site, CCP 7 acts as a ,proof-reader' to help discriminate self- from non-self patterns of sulphation, and CCPs 1,4 disrupt C3/C5 convertase formation and stability. [source] Micro-focus X-ray computed tomography images of the 3D structure of the cranium of a fetus with asymmetric double malformationCONGENITAL ANOMALIES, Issue 1 2006Takashi Shibata ABSTRACT,, Reconstructed micro computed tomography (Micro-CT, µ-CT) images have revealed the detailed three-dimensional structure of the cranium of human fetal congenital anomalies for the first time. The objects were a head and a cervix of female autosite and a parasite consisting of only a head conjoined to the scapular region of the autosite of an asymmetric double malformation (asymmetric conjoined twins, heteropagus twinning) at a gestational age of 8 months. The cranium of the autosite was normal, but that of the parasite was characterized by otocephaly (agnathia, synotia, and monorhina) and almost all the cranial bones were of an abnormal shape. It is suggested that a part of occipital bone (the basioccipital and exoccipital bones), the vomer and cribriform plate were absent and this resulted in the fusion and overlapping of bilateral temporal and craniofacial bones that should have been adjacent to them. This resulted in a reformation and relocation of most of the cranial bones. Micro-CT is a useful tool to visualize the detailed bone structure which has not been clarified by the conventional dissection methods and other imaging technologies and is a powerful instrument for studying congenital anomalies. [source] Characterization of L-plastin interaction with beta integrin and its regulation by micro-calpain,CYTOSKELETON, Issue 5 2010E. Le Goff Abstract Recent evidences suggest that plastin/fimbrin is more than a simple actin cross-linking molecule. In this context and based on the fact that other members of the same family interact with transmembrane proteins, such as integrins, we have investigated a possible interaction between L-plastin and integrins. By combining coimmunoprecipitation of endogenous proteins and in vitro techniques based on solid phase and solution assays, we demonstrate that L-plastin is an additional binding partner for the ,-chain of integrin and confirmed that both proteins display some colocalization. We then show that L-plastin binds to the cytoplasmic domain of ,1 integrin and to ,1 and ,2 peptides. Using recombinant L-plastin domains, we demonstrate that the integrin-binding sites are not located in NH2 terminal part of L-plastin but rather in the two actin-binding domains. Using pull-down, cross-linking experiments, and enzyme-linked immunosorbent assay, we show that the L-plastin/integrin complex is regulated by ,-calpain cleavage and is not directly dissociated by calcium. Indeed, despite the ability of calpain to cleave both proteins, only the cleavage of , integrin hindered the formation of the L-plastin/integrin complex. We discuss these results in the light of the three-dimensional structure of the actin-binding domains of L-plastin. © 2010 Wiley-Liss, Inc. [source] Biosensor Based on Self-Assembling Glucose Oxidase and Dendrimer-Encapsulated Pt Nanoparticles on Carbon Nanotubes for Glucose DetectionELECTROANALYSIS, Issue 6 2007Lihuan Xu Abstract A novel amperometric glucose biosensor based on layer-by-layer (LbL) electrostatic adsorption of glucose oxidase (GOx) and dendrimer-encapsulated Pt nanoparticles (Pt-DENs) on multiwalled carbon nanotubes (CNTs) was described. Anionic GOx was immobilized on the negatively charged CNTs surface by alternatively assembling a cationic Pt-DENs layer and an anionic GOx layer. Transmission electron microscopy images and ,-potentials proved the formation of layer-by-layer nanostructures on carboxyl-functionalized CNTs. LbL technique provided a favorable microenvironment to keep the bioactivity of GOx and prevent enzyme molecule leakage. The excellent electrocatalytic activity of CNTs and Pt-DENs toward H2O2 and special three-dimensional structure of the enzyme electrode resulted in good characteristics such as a low detection limit of 2.5,,M, a wide linear range of 5,,M,0.65,mM, a short response time (within 5,s), and high sensitivity (30.64,,A mM,1,cm,2) and stability (80% remains after 30 days). [source] Malondialdehyde modification of myelin oligodendrocyte glycoprotein leads to increased immunogenicity and encephalitogenicityEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 7 2007Maja Wållberg Abstract Self proteins may become autoantigenic through structural modification. We studied malondialdehydation of recombinant rat (rr) myelin oligodendrocyte glycoprotein (MOG), an autoantigen in multiple sclerosis. Malondialdehyde (MDA) modification changed protein weight and charge, the location of these adducts being mapped by Fourier transform ion cyclotron resonance. Molecular modelling revealed significant differences in the MDA-rrMOG three-dimensional structure. DBA/1 mice immunised with MDA-rrMOG developed greater proliferative responses and more severe experimental autoimmune encephalomyelitis than mice immunised with unmodified rrMOG. MDA-rrMOG was taken up more effectively by antigen-presenting cells (APC), at least partially through scavenger receptors. Exposure to MDA-rrMOG led to increased expression of IL-23, IL-12 and IL-12R, indicating a role not only for increased antigen uptake but also for activation of APC. We thus provide biochemical, structural, immunological and clinical data that suggest that the post-translationally modified form of this myelin autoantigen is a more relevant form of the molecule. [source] Two- and Three-Dimensional Hydrogen-Bonded Networks Built from 1,3,5-[(HO)2(O)P]3C6H3 and 4-(Dimethylamino)pyridineEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2004Michael Mehring Abstract Crystallisation of 3,5-bis(phosphonophenyl)phosphonic acid, 1,3,5-[(HO)2(O)P]3C6H3, from MeOH/H2O in the presence of 4-(dimethylamino)pyridine, 4-(Me2N)C5H4N, gave [1-{(HO)2(O)P}-3,5-{(HO)(O)2P}2C6H3]2,[{4-(Me2N)C5H4NH}+]2 (2) and [1,3-{(HO)2(O)P}2 -5-{(HO)(O)2P}C6H3],[4-(Me2N)C5H4NH]+ (3). Single-crystal X-ray diffraction analyses revealed a two- and a three-dimensional hydrogen-bonded network for compounds 2 and 3, respectively. Compound 2 is composed of layers which are formed by hydrogen-bonded motifs of the type R2,2(8) and R4,4(16). These motifs are connected within the layer by additional hydrogen bonds and the benzene spacer. The cation [4-(Me2N)C5H4NH]+ is located between the layers and determines the interlayer separation of approximately 6.5 Å. In compound 3 a layered network of the hydrogen-bonded building units R2,3(10) was observed. These units are interconnected by four additional hydrogen bonds within the network. The benzene spacer links the adjacent layers to give a three-dimensional structure. Within this network, channels with internal dimensions of ca. 8.5 × 11.3 Å2 which are occupied by the [4-(Me2N)C5H4NH]+ cations were observed. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Syntheses and Crystal Structures of Two Novel Zinc(II) Coordination PolymersEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 14 2003Jun Tao Abstract Two novel zinc(II) coordination polymers, [Zn3(,3 -OH)2(nip)2] (1) and [Zn2(nip)2(4,4,-bpy)3·(OH2)] (2) (H2nip = 5-nitroisophthalic acid, 4,4,-bpy = 4,4,-bipyridyl), were obtained by the hydrothermal reactions of zinc nitrate, 5-nitroisophthalate (nip) (for 1) and zinc nitrate, 5-nitroisophthalate and 4,4,-bipyridyl (for 2). Complex 1 displays a two-dimensional structure that is built from [Zn3(,3 -OH)2]n chains, while complex 2 is a three-dimensional structure formed by the interpenetration of two-dimensional hydrogen-bonded bilayers. The photoluminescent properties of complex 1 have also been investigated. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Neurosphere generation from dental pulp of adult rat incisorEUROPEAN JOURNAL OF NEUROSCIENCE, Issue 3 2008Ryo Sasaki Abstract Dental pulp is a potential source of cells that can be used in cell replacement therapy for various nervous system disorders. Here we report that adult rat dental pulp cells have the ability to form neurospheres when cultured in serum-free culture medium on super-hydrophilic plates. The cells within small spheres continued to grow, and the dental pulp-derived cells generated large spheres. Sphere formation was dependent on exogenously supplied basic-fibroblast growth factor, but not on epidermal growth factor, and the formation and growth of dental pulp-derived spheres were negatively regulated by transforming growth factor-,. Plating cells that were dissociated from spheres on an adhesive substrate resulted in differentiation into Tuj1- and MAP2-positive neuronal cells. Analysis of the three-dimensional structure of dental pulp-derived spheres shows that they contained nestin-positive progenitors, Tuj1-positive neuronal cells and S100-positive glial cells. We found that spheres contained CD81 (TAPA1) and nestin double-positive cells, and identified a small population of CD81 and nestin double-positive cells in the odontoblast layer of the dental pulp. Flow cytometric analysis showed that CD81-positive cells were enriched in the spheres compared with the dental pulp tissue. Bromodeoxyuridine (BrdU) staining showed that nestin- and BrdU-positive cells were located only in the apical portion of the dental pulp, and the apical portion produced a large number of large-sized spheres. These data suggest that the CD81 and nestin double-positive cells localized in the odontoblast layer of the apical portion of the dental pulp may have the ability to grow and form neurospheres. [source] Combined Confocal Microscopy and Stereology: a Highly Efficient and Unbiased Approach to Quantitative Structural Measurement in TissuesEXPERIMENTAL PHYSIOLOGY, Issue 6 2002Katherine Howell Understanding the relationship of the structure of organs to their function is a key component of integrative physiological research. The structure of the organs of the body is not constant but changes, both during growth and development and under conditions of sustained stress (e.g. high altitude exposure and disease). Recently, powerful new techniques have become available in molecular biology, which promise to provide novel insights into the mechanisms and consequences of these altered structure-function relationships. Conventionally structure-function relationships are studied by microscopic examination of tissue sections. However, drawing conclusions about the three-dimensional structure of an organ based on this two-dimensional information frequently leads to serious errors. The techniques of stereology allow precise and accurate quantification of structural features within three-dimensional organs that relate in a meaningful way to integrated function. For example, knowledge of changes in the total surface area of the capillary endothelium in an organ can be related directly to changes in fluid filtration and permeability, or knowledge of total vessel length and mean radius allows deductions about vascular resistance. Confocal microscopy adds enormously to the power of stereological approaches. It reduces the difficulties and labour involved in obtaining suitable images. Moreover, when used in conjunction with new analytical software, it allows convenient application of stereology to small samples and those in which it is essential to maintain a specific orientation for interpretation. The information obtained will allow us to examine in a quantitative manner the altered structure-function relationships produced by manipulation of single genes and regulatory pathways in whole organisms. [source] Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicleFEBS JOURNAL, Issue 4 2008Silvia Vilasi The potent immunomodulatory, anti-inflammatory and procoagulant properties of protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have previously been found to be modulated by a supramolecular monomer,trimer equilibrium. More structural details that integrate experimental data into a predictive framework have recently been reported. Unfortunately, homology modelling and fold-recognition strategies were not successful in creating a theoretical model of the structural organization of SV-IV. It was inferred that the global structure of SV-IV is not similar to that of any protein of known three-dimensional structure. Reversing the classical approach to the sequence,structure,function paradigm, in this paper we report novel information obtained by comparing the physicochemical parameters of SV-IV with two datasets composed of intrinsically unfolded and ideally globular proteins. In addition, we analyse the SV-IV sequence by several publicly available disorder-oriented predictors. Overall, disorder predictions and a re-examination of existing experimental data strongly suggest that SV-IV needs large plasticity to efficiently interact with the different targets that characterize its multifaceted biological function, and should therefore be better classified as an intrinsically disordered protein. [source] Actin-binding domain of mouse plectinFEBS JOURNAL, Issue 10 2004Crystal structure, binding to vimentin Plectin, a large and widely expressed cytolinker protein, is composed of several subdomains that harbor binding sites for a variety of different interaction partners. A canonical actin-binding domain (ABD) comprising two calponin homology domains (CH1 and CH2) is located in proximity to its amino terminus. However, the ABD of plectin is unique among actin-binding proteins as it is expressed in the form of distinct, plectin isoform-specific versions. We have determined the three-dimensional structure of two distinct crystalline forms of one of its ABD versions (pleABD/2,) from mouse, to a resolution of 1.95 and 2.0 Å. Comparison of pleABD/2, with the ABDs of fimbrin and utrophin revealed structural similarity between plectin and fimbrin, although the proteins share only low sequence identity. In fact, pleABD/2, has been found to have the same compact fold as the human plectin ABD and the fimbrin ABD, differing from the open conformation described for the ABDs of utrophin and dystrophin. Plectin harbors a specific binding site for intermediate filaments of various types within its carboxy-terminal R5 repeat domain. Our experiments revealed an additional vimentin-binding site of plectin, residing within the CH1 subdomain of its ABD. We show that vimentin binds to this site via the amino-terminal part of its rod domain. This additional amino-terminal intermediate filament protein binding site of plectin may have a function in intermediate filament dynamics and assembly, rather than in linking and stabilizing intermediate filament networks. [source] The relationship between thermal stability and pH optimum studied with wild-type and mutant Trichoderma reesei cellobiohydrolase Cel7AFEBS JOURNAL, Issue 5 2003Harry Boer The major cellulase secreted by the filamentous fungus Trichoderma reesei is cellobiohydrolase Cel7A. Its three-dimensional structure has been solved and various mutant enzymes produced. In order to study the potential use of T. reesei Cel7A in the alkaline pH range, the thermal stability of Cel7A was studied as a function of pH with the wild-type and two mutant enzymes using different spectroscopic methods. Tryptophan fluorescence and CD measurements of the wild-type enzyme show an optimal thermostability between pH 3.5,5.6 (Tm, 62 ± 2 °C), at which the highest enzymatic activity is also observed, and a gradual decrease in the stability at more alkaline pH values. A soluble substrate, cellotetraose, was shown to stabilize the protein fold both at optimal and alkaline pH. In addition, unfolding of the Cel7A enzyme and the release of the substrate seem to coincide at both acidic and alkaline pH, demonstrated by a change in the fluorescence emission maximum. CD measurements were used to show that the five point mutations (E223S/A224H/L225V/T226A/D262G) that together result in a more alkaline pH optimum [Becker, D., Braet, C., Brumer, H., III, Claeyssens, M., Divne, C., Fagerström, R.B., Harris, M., Jones, T.A., Kleywegt, G.J., Koivula, A., et al. (2001) Biochem. J.356, 19,30], destabilize the protein fold both at acidic and alkaline pH when compared with the wild-type enzyme. In addition, an interesting time-dependent fluorescence change, which was not observed by CD, was detected for the pH mutant. Our data show that in order to engineer more alkaline pH cellulases, a combination of mutations should be found, which both shift the pH optimum and at the same time improve the thermal stability at alkaline pH range. [source] Modeling the three-dimensional structure of H+ -ATPase of Neurospora crassaFEBS JOURNAL, Issue 21 2002Proposal for a proton pathway from the analysis of internal cavities Homology modeling in combination with transmembrane topology predictions are used to build the atomic model of Neurospora crassa plasma membrane H+ -ATPase, using as template the 2.6 Å crystal structure of rabbit sarcoplasmic reticulum Ca2+ -ATPase [Toyoshima, C., Nakasako, M., Nomura, H. & Ogawa, H. (2000) Nature 405, 647,655]. Comparison of the two calcium-binding sites in the crystal structure of Ca2+ -ATPase with the equivalent region in the H+ -ATPase model shows that the latter is devoid of most of the negatively charged groups required to bind the cations, suggesting a different role for this region. Using the built model, a pathway for proton transport is then proposed from computed locations of internal polar cavities, large enough to contain at least one water molecule. As a control, the same approach is applied to the high-resolution crystal structure of halorhodopsin and the proton pump bacteriorhodopsin. This revealed a striking correspondence between the positions of internal polar cavities, those of crystallographic water molecules and, in the case of bacteriorhodopsin, the residues mediating proton translocation. In our H+ -ATPase model, most of these cavities are in contact with residues previously shown to affect coupling of proton translocation to ATP hydrolysis. A string of six polar cavities identified in the cytoplasmic domain, the most accurate part of the model, suggests a proton entry path starting close to the phosphorylation site. Strikingly, members of the haloacid dehalogenase superfamily, which are close structural homologs of this domain but do not share the same function, display only one polar cavity in the vicinity of the conserved catalytic Asp residue. [source] Structural and functional studies of cinnamomin, a new type II ribosome-inactivating protein isolated from the seeds of the camphor treeFEBS JOURNAL, Issue 22 2001Liang Xie Cinnamomin is a new type II ribosome-inactivating protein (RIP). Its A-chain exhibits RNA N -glycosidase activity to inactivate the ribosome and thus inhibit protein synthesis, whereas the glycosylated B-chain is a lectin. The primary structure of cinnamomin, which exhibits approximately 55% identity with those of ricin and abrin, was deduced from the nucleotide sequences of cDNAs of cinnamomin A- and B-chains. It is composed of a total of 549 amino-acid residues: 271 residues in the A-chain, a 14-residue linker and 264 residues in the B-chain. To explore its biological function, the cinnamomin A-chain was expressed in Escherichia coli with a yield of 100 mg per L of culture, and purified through two-step column chromatography. After renaturation, the recovery of the enzyme activity of the expressed A-chain was 80% of that of native A-chain. Based on the modeling of the three-dimensional structure of the A-chain, the functional roles of five amino acids and the only cysteine residues were investigated by site-directed mutagenesis or chemical modification. The conserved single mutation of the five amino-acid residues led to 8,50-fold losses of enzymatic activity, suggesting that these residues were crucial for maintaining the RNA N -glycosidase activity of the A-chain. Most interestingly, the strong electric charge introduced at the position of the single cysteine in A-chain seemed to play a role in enzyme/substrate binding. [source] Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporterFEMS MICROBIOLOGY LETTERS, Issue 2 2001Yumiko Mishima Abstract In a soil isolate, Sphingomonas sp. A1, the transport of a macromolecule (alginate: 27 kDa) is mediated by a pit-dependent ATP-binding cassette (ABC) transporter. The transporter is different from other ABC transporters so far analyzed in that its function is dependent on a pit, a mouth-like organ formed on the cell surface only when cells are compelled to assimilate macromolecules, and in that it allows direct import of macromolecules into cells. The ABC transporter coupled with the pit, which functions as a funnel and/or concentrator of macromolecules to be imported, was designated the ,super-channel', and in this review, we discuss the three-dimensional structure and specific function of the ,super-channel' for macromolecule import found for the first time in a bacterium. [source] Solution structure of a zinc-finger domain that binds to poly-ADP-riboseGENES TO CELLS, Issue 2 2010Shin Isogai Poly-ADP-ribosylation is a unique post-translational modification that controls various nuclear events such as repair of DNA single-strand breaks. Recently, the protein containing the poly-ADP-ribose (pADPr)-binding zinc-finger (PBZ) domain was shown to be a novel AP endonuclease and involved in a cell cycle checkpoint. Here, we determined the three-dimensional structure of the PBZ domain from Drosophila melanogaster CG1218-PA using NMR spectroscopy. The domain folds into a C2H2-type zinc-finger structure in an S configuration, containing a characteristic loop between the zinc-coordinating cysteine and histidine residues. This is distinct from the structure of other C2H2-type zinc fingers. NMR signal changes that occur when pADPr binds to the PBZ domains from CG1218-PA and human checkpoint with FHA (forkhead-associated) and ring finger (CHFR) and mutagenesis suggest that a surface relatively well conserved among PBZ domains may serve as a major interface with pADPr. [source] Molecular analysis of ARSA and PSAP genes in twenty-one Italian patients with metachromatic leukodystrophy: identification and functional characterization of 11 novel ARSA alleles,HUMAN MUTATION, Issue 11 2008Serena Grossi Abstract Metachromatic leukodystrophy (MLD), the demyelinating disorder resulting from impaired sulfatide catabolism, is caused by allelic mutations of the Arylsulfatase A (ARSA) locus except for extremely rare cases of Saposin-B (Sap-B) deficiency. We characterized twenty-one unrelated Italian patients among which seventeen were due to ARSA activity deficiency and 4 others resulted from Saposin-B defect. Overall, we found 20 different mutant ARSA alleles and 2 different Sap-B alleles. The eleven new ARSA alleles (c.53C>A; c.88G>C; c.372G>A; c.409_411delCCC; c.634G>C; [c.650G>A;c.1108C>T]; c.845A>G; c.906G>C; c.919G>T; c.1102-3C>G; c.1126T>A) were functionally characterized and the novel amino acid changes were also modelled into the three-dimensional structure. The present study is aimed at providing a broader picture of the molecular basis of MLD in the Italian population. It also emphasizes the importance of a comprehensive evaluation in MLD diagnosis including biochemical, enzymatic and molecular investigations. © 2008 Wiley-Liss, Inc. [source] Argininosuccinate lyase deficiency: mutational spectrum in Italian patients and identification of a novel ASL pseudogene,HUMAN MUTATION, Issue 7 2007Eva Trevisson Abstract Argininosuccinic aciduria (ASAuria) is an inborn error of metabolism caused by mutations in the argininosuccinate lyase (ASL) gene, which leads to the accumulation of argininosuccinic acid (ASA) in body fluids and severe hyperammonemia. A severe neonatal form and a milder late-onset variant are described. We report a novel ASL pseudogene located in the centromeric region of chromosome 7, 14 novel mutations in the ASL gene, and a novel intronic polymorphism found in a cohort of Italian patients. Our approach relied exclusively on genomic DNA analysis. We found seven missense mutations, two nonsense, three small insertions/deletions, and two splicing mutations. Only two patients harbored previously described mutations, and among the novel variants only two were present in more than one kindred. The pathogenicity of the splicing mutations was demonstrated by a functional splicing assay that employed a hybrid minigene. We also performed molecular modeling using the reported three-dimensional structure of ASL to predict the functional consequences of the missense mutations. There was no genotype,phenotype correlation. Patients with neonatal onset display developmental delay and seizures despite adequate metabolic control. Moreover, hepatomegaly, fibrosis, and abnormal liver function tests are common complications in these patients, but not in patients with the late infancy form. We stress the importance of mutation analysis in patients with ASAuria, to confirm the clinical diagnosis, and to perform DNA-based prenatal diagnosis in future pregnancies of these families. Hum Mutat 28(7), 694,702, 2007. © 2007 Wiley-Liss, Inc. [source] A posteriori error estimation for extended finite elements by an extended global recoveryINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 8 2008Marc Duflot Abstract This contribution presents an extended global derivative recovery for enriched finite element methods (FEMs), such as the extended FEM along with an associated error indicator. Owing to its simplicity, the proposed scheme is ideally suited to industrial applications. The procedure is based on global minimization of the L2 norm of the difference between the raw strain field (C,1) and the recovered (C0) strain field. The methodology engineered in this paper extends the ideas of Oden and Brauchli (Int. J. Numer. Meth. Engng 1971; 3) and Hinton and Campbell (Int. J. Numer. Meth. Engng 1974; 8) by enriching the approximation used for the construction of the recovered derivatives (strains) with the gradients of the functions employed to enrich the approximation employed for the primal unknown (displacements). We show linear elastic fracture mechanics examples, both in simple two-dimensional settings, and for a three-dimensional structure. Numerically, we show that the effectivity index of the proposed indicator converges to unity upon mesh refinement. Consequently, the approximate error converges to the exact error, indicating that the error indicator is valid. Additionally, the numerical examples suggest a novel adaptive strategy for enriched approximations in which the dimensions of the enrichment zone are first increased, before standard h - and p -adaptivities are applied; we suggest to coin this methodology e-adaptivity. Copyright © 2008 John Wiley & Sons, Ltd. [source] | |||||||||||||||||||||||||||||||||||||||||||