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Monomeric Form (monomeric + form)
Selected AbstractsRegulation of monomeric dynein activity by ATP and ADP concentrationsCYTOSKELETON, Issue 4 2001Katsuyuki Shiroguchi Abstract Axonemal dyneins are force-generating ATPases that produce ciliary and flagellar movement. A dynein has large heavy chain(s) in which there are multiple (4,6) ATP-binding consensus sequences (P-loops) as well as intermediate and light chains, constituting a very large complex. We purified a monomeric form of dynein (dynein- a) that has at least three light chains from 14S dyneins of Tetrahymena thermophila and characterized it. In in vitro motility assays, dynein- a rotated microtubules around their longitudinal axis as well as translocated them with their plus-ends leading. ATPase activity at 1 mM ATP was doubled in the presence of a low level of ADP (, 20 ,M). Both ATPase activity and translocational velocities in the presence of ADP (, 20 ,M) fit the Michaelis-Menten equation well. However, in the absence of ADP (< 0.1 ,M), neither of the activities followed the Michaelis-Menten-type kinetics, probably due to the effect of two ATP-binding sites. Our results also indicate that dynein- a has an ATP-binding site that is very sensitive to ADP and affects ATP hydrolysis at the catalytic site. This study shows that a monomeric form of a dynein molecule regulates its activity by direct binding of ATP and ADP to itself, and thus the dynein molecule has an intramolecular regulating system. Cell Motil. Cytoskeleton 49:189,199, 2001. © 2001 Wiley-Liss, Inc. [source] Aegyptin displays high-affinity for the von Willebrand factor binding site (RGQOGVMGF) in collagen and inhibits carotid thrombus formation in vivoFEBS JOURNAL, Issue 2 2010Eric Calvo Aegyptin is a 30 kDa mosquito salivary gland protein that binds to collagen and inhibits platelet aggregation. We have studied the biophysical properties of aegyptin and its mechanism of action. Light-scattering plot showed that aegyptin has an elongated monomeric form, which explains the apparent molecular mass of 110 kDa estimated by gel-filtration chromatography. Surface plasmon resonance identified the sequence RGQOGVMGF (where O is hydroxyproline) that mediates collagen interaction with von Willebrand factor (vWF) as a high-affinity binding site for aegyptin, with a KD of approximately 5 nm. Additionally, aegyptin interacts with the linear peptide RGQPGVMGF and heat-denatured collagen, indicating that the triple helix and hydroxyproline are not a prerequisite for binding. However, aegyptin does not interact with scrambled RGQPGVMGF peptide. Aegyptin also recognizes the peptides (GPO)10 and GFOGER with low affinity (,m range), which respectively represent glycoprotein VI and integrin ,2,1 binding sites in collagen. Truncated forms of aegyptin were engineered, and the C-terminus fragment was shown to interact with collagen and to attenuate platelet aggregation. In addition, aegyptin prevents laser-induced carotid thrombus formation in the presence of Rose Bengal in vivo, without significant bleeding in rats. In conclusion, aegyptin interacts with distinct binding sites in collagen, and is useful tool to inhibit platelet,collagen interaction in vitro and in vivo. Structured digital abstract ,,MINT-7299280, MINT-7299290: Collagen (uniprotkb:P02461) binds (MI:0407) to Aegyptin (uniprotkb:O01949) by enzyme linked immunosorbent assay (MI:0411) ,,MINT-7298991, MINT-7299153, MINT-7299208: Collagen (uniprotkb:P02452) binds (MI:0407) to Aegyptin (uniprotkb:O01949) by surface plasmon resonance (MI:0107) ,,MINT-7299266: Collagen (uniprotkb:P02452) binds (MI:0407) to Aegyptin (uniprotkb:O01949) by fluorescence microscopy (MI:0416) ,,MINT-7299256: Collagen (uniprotkb:P02452) binds (MI:0407) to Aegyptin (uniprotkb:O01949) by solid phase assay (MI:0892) [source] The Alzheimer ,-peptide shows temperature-dependent transitions between left-handed 31 -helix, ,-strand and random coil secondary structuresFEBS JOURNAL, Issue 15 2005Jens Danielsson The temperature-induced structural transitions of the full length Alzheimer amyloid ,-peptide [A,(1,40) peptide] and fragments of it were studied using CD and 1H NMR spectroscopy. The full length peptide undergoes an overall transition from a state with a prominent population of left-handed 31 (polyproline II; PII)-helix at 0 °C to a random coil state at 60 °C, with an average ,H of 6.8 ± 1.4 kJ·mol,1 per residue, obtained by fitting a Zimm,Bragg model to the CD data. The transition is noncooperative for the shortest N-terminal fragment A,(1,9) and weakly cooperative for A,(1,40) and the longer fragments. By analysing the temperature-dependent 3JHNH, couplings and hydrodynamic radii obtained by NMR for A,(1,9) and A,(12,28), we found that the structure transition includes more than two states. The N-terminal hydrophilic A,(1,9) populates PII-like conformations at 0 °C, then when the temperature increases, conformations with dihedral angles moving towards ,-strand at 20 °C, and approaches random coil at 60 °C. The residues in the central hydrophobic (18,28) segment show varying behaviour, but there is a significant contribution of ,-strand-like conformations at all temperatures below 20 °C. The C-terminal (29,40) segment was not studied by NMR, but from CD difference spectra we concluded that it is mainly in a random coil conformation at all studied temperatures. These results on structural preferences and transitions of the segments in the monomeric form of A, may be related to the processes leading to the aggregation and formation of fibrils in the Alzheimer plaques. [source] Mass spectrometry study of ecto-5,-nucleotidase from bull seminal plasmaFEBS JOURNAL, Issue 16 2000Carlo Fini The structure of ecto-5,-nucleotidase from bull seminal plasma, containing a glycosyl-phosphatidylinositol anchor, was studied using mass spectrometry. MALDI-MS analysis of intact protein indicated a mass of 65 568.2 Da for the monomeric form, and it also showed a heterogeneous population of glycoforms with the glycosidic moiety accounting for ,,6000 Da. MALDI-MS analysis showed that Asn53, Asn311, Asn333 and Asn403 were four sites of N -glycosylation. GC-MS analysis provided information on the glycosidic structures linked to the four asparagines. Asn53, Asn311 and Asn333 were linked to high-mannose saccharide chains, whereas the glycan chains linked to Asn403 contained a heterogeneous mixture of oligosaccharides, the high-mannose type structure being the most abundant and hybrid or complex type glycans being minor components. By combining enzymatic and/or chemical hydrolysis with GC-MS analysis, detailed characterization of the glycosyl-phpsphatidylinositol anchor was obtained. MALDI spectral analysis indicated that the glycosyl-phosphatidylinositol core contained EtN(P)Man3GlcNH2 -myo-inositol(P)-glycerol, principally modified by stearoyl and palmitoyl residues or by stearoyl and myristoyl residues to a minor extent. Moreover, 1-palmitoylglycerol and 1-stearoylglycerol outweighed 2-palmitoylglycerol and 2-stearoylglycerol. The combination of chemical and enzymatic digestions of the protein with the mass spectral analysis yielded a complete pattern of S,S bridges. The protein does not contain free thiols and its eight cysteines are linked by intramolecular disulfide bonds, the pairs being: Cys51,Cys57, Cys353,Cys358, Cys365,Cys387 and Cys476,Cys479. This work resolves details of the structure of ecto-5,-nucleotidase, with particular regard to the localization and composition of the glycidic moiety, number and localization of the disulfide bridges and characterization of the glycosyl-phosphatidylinositol anchor. [source] Physical characterization of plakophilin 1 reconstituted with and without zincFEBS JOURNAL, Issue 14 2000Ilse Hofmann Plakophilin 1 (PKP1) belongs to the arm -repeat protein family which is characterized by the presence of a conserved 42-amino-acid motif. Despite individual members of the family containing a similar type of structural domain, they exhibit diverse cellular functions. PKP1 is ubiquitously expressed in human tissues and, depending on the type of cell, found prominently in the karyoplasm and/or in desmosomes. In surface plasmon resonance detection experiments, we noticed that PKP1 specifically bound zinc but not calcium or magnesium. Therefore we have used circular dichroism spectroscopy, limited proteolysis, analytical ultracentrifugation, electron microscopy and dynamic light scattering to establish the physical properties of recombinant PKP1 depending on the presence or absence of zinc. The , helix content of PKP1 was considerably higher when reconstituted with zinc than without. By atomic absorption spectroscopy 7.3 atoms zinc were shown to be tightly associated with one molecule of wild-type PKP1. The zinc-reconstituted protein formed globular particles of 21.9 ± 8.4 nm diameter, as measured by electron microscopy after glycerol spraying/rotary metal shadowing. In parallel, the average sedimentation coefficient (s20,w) for zinc-containing PKP1 was 41S and its diffusion coefficient, as obtained by dynamic light scattering, 1.48 × 10,7 cm2·s,1. The molecular mass of 2.44 × 106 obtained from s and D yields an average stoichiometry of 30 for the PKP1 oligomer. In contrast, PKP1, reconstituted without zinc, contained no significant amount of zinc, sedimented with 4.6S, and was present in monomeric form as determined by sedimentation equilibrium centrifugation. [source] Interpretation of biological activity data of bacterial endotoxins by simple molecular models of mechanism of actionFEBS JOURNAL, Issue 3 2000Vladimir Frecer Lipid A moiety has been identified as the bioactive component of bacterial endotoxins (lipopolysaccharides). However, the molecular mechanism of biological activity of lipid A is still not fully understood. This paper contributes to understanding of the molecular mechanism of action of bacterial endotoxins by comparing molecular modelling results for two possible mechanisms with the underlying experimental data. Mechanisms of action involving specific binding of lipid A to a protein receptor as well as nonspecific intercalation into phospholipid membrane of a host cell were modelled and analysed. As the cellular receptor for endotoxin has not been identified, a model of a peptidic pseudoreceptor was proposed, based on molecular structure, symmetry of the lipid A moiety and the observed character of endotoxin-binding sites in proteins. We have studied the monomeric form of lipid A from Escherichia coli and its seven synthetic analogues with varying numbers of phosphate groups and correlated them with known biological activities determined by the Limulus assay. Gibbs free energies associated with the interaction of lipid A with the pseudoreceptor model and intercalation into phospholipid membrane calculated by molecular mechanics and molecular dynamics methods were used to compare the two possible mechanisms of action. The results suggest that specific binding of lipid A analogues to the peptidic pseudoreceptor carrying an amphipathic cationic binding pattern BHPHB (B, basic; H, hydrophobic; P, polar residue, respectively) is energetically more favourable than intercalation into the phospholipid membrane. In addition, binding affinities of lipid A analogues to the best minimum binding sequence KFSFK of the pseudoreceptor correlated with the experimental Limulus activity parameter. This correlation enabled us to rationalize the observed relationship between the number and position of the phosphate groups in the lipid A moiety and its biological activity in terms of specific ligand,receptor interactions. If lipid A,receptor interaction involves formation of phosphate-ammonium ion-pair(s) with cationic amino-acid residues, the specific mechanism of action was fully consistent with the underlying experimental data. As a consequence, recognition of lipid A variants by an amphipathic binding sequence BHPHB of a host-cell protein receptor might represent the initial and/or rate-determining molecular event of the mechanism of action of lipid A (or endotoxin). The insight into the molecular mechanism of action and the structure of the lipid A-binding pattern have potential implications for rational drug design strategies of endotoxin-neutralizing agents or binding factors. [source] Detection and structural features of the ,B2-B3-crystallin heterodimer by radical probe mass spectrometry (RP-MS)JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 5 2009Hélène Diemer Abstract The predilection of the ,-crystallin B2 subunit to interact with the ,B3 subunit rather than self associate is evident by the detection of the ,B2-B3-crystallin heterodimer by native gel electrophoresis and electrospray ionisation time-of-flight (ESI-TOF) mass spectrometry under non denaturing conditions. The complex has been detected for the first time and its molecular mass is measured to be 47 450 ± 1 Da. Radical probe mass spectrometry (RP-MS) was subsequently applied to investigate the nature of the heterodimer through the limited oxidation of the subunits in the complex. Two peptide segments of the ,B2 subunit and six of the ,B3 subunit were found to oxidise, with far greater oxidation observed within the ,B3 versus the ,B2 subunit. This, and the observation that the oxidation data of ,B2 subunit is inconsistent with the structure of the ,B2 monomer, demonstrates that the protection of ,B2 is conferred by its association with ,B3 subunit within the heterodimer where only the residues of, and towards, its N -terminal domain remain exposed to solvent. The results suggest that the ,B2 subunit adopts a more compacted form than in its monomeric form in order for much of its structure to be enveloped by the ,B3 subunit within the heterodimer. Copyright © 2009 John Wiley & Sons, Ltd. [source] Molecular mass determination of plasma-derived glycoproteins by ultraviolet matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with internal calibrationJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 11 2002Omar Belgacem Abstract Human plasma-derived antithrombin III (AT-III), factor IX (FIX) and vitronectin (VN) were characterized as native glycoproteins and in their de- N -glycosylated form by means of MALDI mass spectrometry. The average molecular masses of the three complex glycoproteins were determined applying internal calibration with high-mass, well-defined protein calibrants. Internal calibration generated for the 47 kDa yeast protein enolase a mass precision in the continuous and delayed extraction mode of ±0.12 and ±0.022%, respectively. The achievable mass accuracy for such a high-mass, unmodified protein was in the range of 0.02% in the continuous mode, which turned out to be better than in the delayed extraction mode. Purification of all (glyco) proteins (even the calibration proteins) by means of ZipTip® technology and direct elution with a solvent system containing the appropriate MALDI matrix turned out to be a prerequisite to measure the exact molecular masses with an internal calibration. The average molecular masses of the two different forms of AT-III, namely AT-III, and AT-III,, were shown to be 57.26 and 55.04 kDa, respectively. The 2.22 kDa mass difference is attributed to the known difference in carbohydrate content at one specific site (Asn-135). After exhaustive de- N -glycosylation (by means of PNGase F) of the ,- and ,-form and subsequent MALDI-MS analysis, average molecular masses of 48.96 and 48.97 kDa, respectively, were obtained. These values are in good agreement (,0.15%) with the calculated molecular mass (49.039 kDa) of the protein part based on SwissProt data. The molecular mass of the heavily post-translational modified glycoprotein FIX was found to be 53.75 kDa with a peak width at 10% peak height of 4.5 kDa, because of the presence of many different posttranslational modifications (N - and O -glycosylation at multiple sites, sulfation, phosphorylation, hydroxylation and numerous ,-carboxyglutamic acids). MALDI-MS molecular mass determination of the native, size-exclusion chromatography-purified, VN sample revealed that the glycoprotein was present as dimer with molecular mass of 117.74 kDa, which could be corroborated by non-reducing SDS-PAGE. After sample treatment with guanidine hydrochloride and mass spectrometric analysis, a single, new main component was detected. The molecular mass turned out to be 59.45 kDa, representing the monomeric form of VN, known as V75. The determined molecular mass value was shown to be on one hand lower than from SDS-PAGE and on the other higher than the calculated amino acid sequence molecular mass (52 277 Da), pointing to the well-known SDS-PAGE bias and to considerable post-translational modifications. Further treatment of the sample with a reducing agent and subsequent MALDI-MS revealed two new components with molecular masses of 49.85 and 9.41 kDa, corresponding to V65 and V10 subunits of VN. PNGase F digest of the V75 and V65 units and MS analysis, exhibiting a molecular mass reduction of 6.37 kDa in both cases, verified the presence of a considerable amount of N -glycans. Copyright © 2002 John Wiley & Sons, Ltd. [source] The peptaibol antiamoebin as a model ion channel: similarities to bacterial potassium channels,JOURNAL OF PEPTIDE SCIENCE, Issue 11-12 2003Andrias O. O'Reilly Abstract Antiamoebin (AAM) is a polypeptide antibiotic that is capable of forming ion channels in phospholipid membranes; planar bilayer studies have suggested the channels are octamers. The crystal structure of a monomeric form of AAM has provided the basis for molecular modelling of an octameric helical bundle channel. The channel model is funnel-shaped due to a substantial bend in the middle of the polypeptide chain caused by the presence of several imino acids. Inter-monomer hydrogen bonds orientate a ring of glutamine side chains to form a constriction in the pore lumen. The channel lumen is lined both by side chains of Gln11 and by polypeptide backbone carbonyl groups. Electrostatic calculations on the model are compatible with a channel that transports cations across membranes. The AAM channel model is compared with the crystal structures of two bacterial (KcsA and MthK) potassium channels. AAM and the potassium channels exhibit common functional features, such as cation-selectivity and similar single channel conductances. Common structural features include being multimers, each formed from a bundle of eight transmembrane helices, with lengths roughly comparable to the thickness of lipid bilayers. In addition, they all have aromatic amino acids that lie at the bilayer interfaces and which may aid in the stabilization of the transmembrane helices, as well as narrower constrictions that define the ion binding sites or selectivity filters in the pore lumen. The commonality of structural and functional features in these channels thus suggests that antiamoebin is a good, simple model for more complex bacterial and eukaryotic ion channels, capable of providing insight into details of the mechanisms of ion transport and multimeric channel stability. Copyright © 2003 European Peptide Society and John Wiley & Sons, Ltd. [source] Evaluation of novel alginate foams as drug delivery systems in antimicrobial photodynamic therapy (aPDT) of infected wounds,An in vitro study: Studies on curcumin and curcuminoides XLJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 8 2010Anne Bee Hegge Abstract The aim of the present study was to incorporate a model water-insoluble photosensitizer, curcumin, in novel alginate foams, further to evaluate the suitability of the curcumin loaded foams in antimicrobial photodynamic therapy of infected wounds. Six foam formulations were prepared and characterized with respect to physical characteristics, in vitro release and storage- and photo-stability of curcumin. One formulation was sterilized (,-sterilization). The foams contained hydroxypropyl-,-cyclodextrins or hydroxypropyl-,-cyclodextrins as solubilizers of curcumin. A reference foam without cyclodextrins was prepared with PEG 400 as the solubilizer. At a curcumin load of 0.153% (w/w), the water insoluble photosensitizer was uniformly distributed in the hydrophilic foams matrix. All foams were easy to handle, flexible and hydrated rapidly in a model physiological fluid. Release of curcumin in its monomeric form was demonstrated in vitro and found to be dependent on the type and amount of cyclodextrins in the formulation. Curcumin was stable during storage, but susceptible to photodegradation in the foams, especially when the formulations contain PEG 400 or hydroxypropyl-,-cyclodextrins. Curcumin did not degrade after ,-sterilization, however a decrease in the in vitro release rate of curcumin and changes in the foams physical characteristics were detected. © 2010 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 99:3499,3513, 2010 [source] Glycoprotein (GP) VI dimer as a major collagen-binding site of native platelets: direct evidence obtained with dimeric GPVI-specific FabsJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 8 2009S. M. JUNG Summary.,Background: The platelet collagen receptor glycoprotein (GP) VI is suggested to exist as a dimer on the platelet surface, but no direct proof of the functional importance of dimer formation has been provided. Objectives: To obtain direct evidence for GPVI dimers on the platelet membrane and their functional importance, Fab antibodies were developed that bind to GPVI dimer (GPVI-Fc2) but not to GPVI monomer (GPVIex) through a phage display method. Results: Ssix Fabs were found: B,F, only reactive with GPVI-Fc2, and A, mainly reactive with GPVI-Fc2, with some reactivity towards GPVIex; each Fab (Fab-dHLX-MH) forms a bivalent dimer (b-Fab) by dimerizing the dHLX domains from two Fab molecules. Fab F was subcloned to a monovalent format by deleting its dHLX domain. All b-Fabs induced platelet aggregation, but the monomeric form of Fab F (m-Fab-F) specifically inhibited collagen-induced aggregation. All b-Fabs and m-Fab-F inhibited GPVI-Fc2 binding to fibrous collagen. Immunoblotting showed that b-Fab-F and m-Fab-F bound weakly to GPVI-Fc2. Adding the anti-GPVI monoclonal antibody 204-11 increased the Bmax of m-Fab-F binding to GPVI-Fc2, suggesting that 204-11 binds to GPVI-Fc2 molecules not already in the appropriate conformation to recognize the Fab, converting them to a conformation reactive to the Fab. Conclusions: GPVI forms a specific structure by dimerization that is necessary for the binding of this receptor to collagen fibrils. The binding of m-Fab-F to platelets directly demonstrates that GPVI is present as a functionally relevant dimer on the platelet surface. [source] Effect of GroEL on Thermal Aggregation of Glycogen Phosphorylase b from Rabbit Skeletal MuscleMACROMOLECULAR BIOSCIENCE, Issue 7 2010Tatyana B. Eronina Abstract The suppression of the thermal aggregation of glycogen phosphorylase b (Phb) from rabbit skeletal muscle by the chaperonin GroEL is studied using dynamic light scattering. It is shown that the decrease in the rate of Phb aggregation under the action of GroEL is due to the transition of the aggregation process from the kinetic regime, wherein the rate of aggregation is limited by diffusion of the interacting particles, to a regime where the sticking probability for the colliding particles becomes lower than one (reaction-limited cluster-cluster aggregation). The analytical-ultracentrifugation data show that elevated temperatures induce dissociation of the dimeric Phb. The formation of a complex between the denatured monomeric form of Phb and the dissociated forms of GroEL is detected during heating at 46,°C. [source] NMR,spectroscopic investigation of o-nitrosobenzoic acidMAGNETIC RESONANCE IN CHEMISTRY, Issue 12 2008Klaus Schaper Abstract The synthesis of o -nitrosobenzoic acid 2 has been known for more than 100 years, and the photochemical preparation from o -nitrobenzaldehyde 1 became a textbook example for [1,5]-hydrogen shifts. However, neither the 1H,NMR spectra nor the 13C{1H},NMR of this compound have been reported so far. This fact can most likely be attributed to the monomer,dimer equilibrium of the nitrosobenzoic acid, which leads to rather complex, concentration-dependent NMR spectra. In this paper, we report a thorough investigation of these spectra. In the 13C-{1H}-NMR spectra, all 21 lines could be assigned to the monomeric form, the E -dimer, and the Z -dimer. Copyright © 2008 John Wiley & Sons, Ltd. [source] A chloroplast transgenic approach to hyper-express and purify Human Serum Albumin, a protein highly susceptible to proteolytic degradationPLANT BIOTECHNOLOGY JOURNAL, Issue 2 2003Alicia Fernández-San Millán Summary Human Serum Albumin (HSA) accounts for 60% of the total protein in blood serum and it is the most widely used intravenous protein in a number of human therapies. HSA, however, is currently extracted only from blood because of a lack of commercially feasible recombinant expression systems. HSA is highly susceptible to proteolytic degradation in recombinant systems and is expensive to purify. Expression of HSA in transgenic chloroplasts using Shine-Dalgarno sequence (SD), which usually facilitates hyper-expression of transgenes, resulted only in 0.02% HSA in total protein (tp). Modification of HSA regulatory sequences using chloroplast untranslated regions (UTRs) resulted in hyper-expression of HSA (up to 11.1% tp), compensating for excessive proteolytic degradation. This is the highest expression of a pharmaceutical protein in transgenic plants and 500-fold greater than previous reports on HSA expression in transgenic leaves. Electron micrographs of immunogold labelled transgenic chloroplasts revealed HSA inclusion bodies, which provided a simple method for purification from other cellular proteins. HSA inclusion bodies could be readily solubilized to obtain a monomeric form using appropriate reagents. The regulatory elements used in this study should serve as a model system for enhancing expression of foreign proteins that are highly susceptible to proteolytic degradation and provide advantages in purification, when inclusion bodies are formed. [source] Multiple crystal structures of actin dimers and their implications for interactions in the actin filamentACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2008Michael R. Sawaya The structure of actin in its monomeric form is known at high resolution, while the structure of filamentous F-actin is only understood at considerably lower resolution. Knowing precisely how the monomers of actin fit together would lead to a deeper understanding of the dynamic behavior of the actin filament. Here, a series of crystal structures of actin dimers are reported which were prepared by cross-linking in either the longitudinal or the lateral direction in the filament state. Laterally cross-linked dimers, comprised of monomers belonging to different protofilaments, are found to adopt configurations in crystals that are not related to the native structure of filamentous actin. In contrast, multiple structures of longitudinal dimers consistently reveal the same interface between monomers within a single protofilament. The reappearance of the same longitudinal interface in multiple crystal structures adds weight to arguments that the interface visualized is similar to that in actin filaments. Highly conserved atomic interactions involving residues 199,205 and 287,291 are highlighted. [source] Chaperone-like activities of different molecular forms of ,-casein.BIOPOLYMERS, Issue 8 2009Importance of polarity of N-terminal hydrophilic domain Abstract As a member of intrinsically unstructured protein family, ,-casein (,-CN) contains relatively high amount of prolyl residues, adopts noncompact and flexible structure and exhibits chaperone-like activity in vitro. Like many chaperones, native ,-CN does not contain cysteinyl residues and exhibits strong tendencies for self-association. The chaperone-like activities of three recombinant ,-CNs wild type (WT) ,-CN, C4 ,-CN (with cysteinyl residue in position 4) and C208 ,-CN (with cysteinyl residue in position 208), expressed and purified from E. coli, which, consequently, lack the phosphorylated residues, were examined and compared with that of native ,-CN using insulin and alcohol dehydrogenase as target/substrate proteins. The dimers (,-CND) of C4-,-CN and C208 ,-CN were also studied and their chaperone-like activities were compared with those of their monomeric forms. Lacking phosphorylation, WT ,-CN, C208 ,-CN, C4 ,-CN and C4 ,-CND exhibited significantly lower chaperone-like activities than native ,-CN. Dimerization of C208 ,-CN with two distal hydrophilic domains considerably improved its chaperone-like activity in comparison with its monomeric form. The obtained results demonstrate the significant role played by the polar contributions of phosphorylated residues and N-terminal hydrophilic domain as important functional elements in enhancing the chaperone-like activity of native ,-CN. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 623,632, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Recombinant human elastin polypeptides self-assemble into biomaterials with elastin-like propertiesBIOPOLYMERS, Issue 4 2003Catherine M. Bellingham Abstract Processes involving self-assembly of monomeric units into organized polymeric arrays are currently the subject of much attention, particularly in the areas of nanotechnology and biomaterials. One biological example of a protein polymer with potential for self-organization is elastin. Elastin is the extracellular matrix protein that imparts the properties of extensibility and elastic recoil to large arteries, lung parenchyma, and other tissues. Tropoelastin, the ,70 kDa soluble monomeric form of elastin, is highly nonpolar in character, consisting essentially of 34 alternating hydrophobic and crosslinking domains. Crosslinking domains contain the lysine residues destined to form the covalent intermolecular crosslinks that stabilize the polymer. We and others have suggested that the hydrophobic domains are sites of interactions that contribute to juxtaposition of lysine residues in preparation for crosslink formation. Here, using recombinant polypeptides based on sequences in human elastin, we demonstrate that as few as three hydrophobic domains flanking two crosslinking domains are sufficient to support a self-assembly process that aligns lysines for zero-length crosslinking, resulting in formation of the crosslinks of native elastin. This process allows fabrication of a polymeric matrix with solubility and mechanical properties similar to those of native elastin. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 445,455, 2003 [source] Surface-enhanced Raman and steady fluorescence study of interaction between antitumoral drug 9-aminoacridine and trypsin-like protease related to metastasis processes, guanidinobenzoataseBIOPOLYMERS, Issue 2 2001Adrian Murza Abstract Fluorescence spectroscopy and surface-enhanced Raman spectroscopy (SERS) were applied to study the interaction of the antitumoral drug 9-aminoacridine (9AA) with a trypsin-like protease guanidinobenzoatase (GB) extracted from a mouse Erlich tumor. As a consequence of this interaction, a strong 9AA exciplex emission was detected in the emission fluorescence spectra at certain drug and enzyme concentrations. A SERS study was accomplished on silver colloids at several excitation wavelengths in order to obtain more information about the interaction mechanism. The results derived from Raman spectroscopy indicated that 9AA in the amino monomeric form may interact with the enzyme by means of two different bonds: an ionic bond with a negatively charged amino acid and a ring stacking interaction with an aromatic residue placed in the catalytic site of GB. This interaction mechanism was responsible for a strong exciplex emission detected at a longer wavelength than the expected value of the normal fluorescence emission. Moreover, the GB concentration dependence of the interaction suggested that the drug was sensitive to the quaternary structure of the enzyme. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 85,94, 2001 [source] Crystallization and preliminary crystallographic analysis of decameric and monomeric forms of C49S mutant thioredoxin-dependent AhpC from Helicobacter pyloriACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2008Supangat Cys49Ser mutant Helicobacter pylori alkyl hydroperoxide reductase (C49S HpAhpC) was purified under reducing conditions in monomeric and decameric forms. The monomeric form was crystallized by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.25,Å resolution and belonged to space group C2, with unit-cell parameters a = 245.8, b = 140.7, c = 189.5,Å, , = 127°, and contained 20 molecules in the asymmetric unit. A crystal of the decameric form was obtained by the microbatch crystallization method and diffracted to 2.8,Å resolution. It belonged to space group C222, with unit-cell parameters a = 257.5, b = 417.5, c = 95.6,Å. The structure of the monomeric form of C49S HpAhpC has been solved by the molecular-replacement method. [source] Sugar Recovery and Fermentability of Hemicellulose Hydrolysates from Steam-Exploded Softwoods Containing BarkBIOTECHNOLOGY PROGRESS, Issue 5 2001Abdel Boussaid The hemicellulose sugar recovery and ethanol production obtained from SO2 -catalyzed steam explosion of a mixed white fir (70%) and ponderosa pine (30%) feedstock containing bark (9% dry weight/dry weight) was assessed. More than 90% of the available hemicellulose sugars could be recovered in the hydrolysate obtained after steam explosion at 195 °C, 2.38 min, and 3.91% SO2, with 59% of the original hemicellulose sugars detected in a monomeric form. Despite this high sugar recovery, this hydrolysate showed low ethanol yield (64% of theoretical yield) when fermented with a spent sulfite liquor-adapted strain of Saccharomyces cerevisiae. In contrast, most hydrolysates prepared at higher steam explosion severity showed comparable or higher ethanol yields. Furthermore, the hydrolysates prepared from bark-free feedstock showed better fermentability (87% of theoretical yield) despite containing higher concentration of known inhibitors. The ethanol yield from the hydrolysate prepared from a bark-containing wood sample could be improved to 81% by an extra stage acid hydrolysis (121 °C for 1 h in 3% sulfuric acid). This extra stage acid hydrolysis and steam explosion at higher severity conditions seem to improve the fermentability of the hydrolysates by transforming certain inhibitory compounds present in the hydrolysates prepared from the bark-containing feedstock and thus lowering their inhibitory effect on the yeast used for the ethanol fermentation. [source] Selective Detection of Phosphotyrosine in the Presence of Various Phosphate-Containing Biomolecules with the Aid of a Terbium(III) ComplexCHEMBIOCHEM, Issue 11 2009Hiroki Akiba Finding phosphotyrosine: Phosphotyrosine (either in its monomeric form or as a component of oligopeptides) was selectively detected by using luminescence in the presence of a specialized terbium(III) complex, without any signals from nonphosphorylated tyrosine, phosphoserine, phosphothreonine, nucleotides, or nucleic acids. Tyrosine phosphorylation could clearly be distinguished even in the presence of single-stranded RNA. [source] Effects of the G376E and G157D mutations on the stability of yeast enolase , a model for human muscle enolase deficiencyFEBS JOURNAL, Issue 1 2008Songping Zhao The first known human enolase deficiency was reported in 2001 [Comi GP, Fortunato F, Lucchiari S, Bordoni A, Prelle A, Jann S, Keller A, Ciscato P, Galbiati S, Chiveri L et al. (2001) Ann Neurol50, 202,207]. The subject had inherited two mutated genes for ,-enolase. These mutations changed glycine 156 to aspartate and glycine 374 to glutamate. In order to study the effects of these changes on the structure and stability of enolase, we have introduced the corresponding changes (G157D and G376E) into yeast enolase. The two variants are correctly folded. They are less stable than wild-type enolase with respect to thermal denaturation, and both have increased Kd values for subunit dissociation. At 37 °C, in the presence of salt, both are partially dissociated and are extensively cleaved by trypsin. Under the same conditions, wild-type enolase is fully dimeric and is only slightly cleaved by trypsin. However, wild-type enolase is also extensively cleaved if it is partially dissociated. The identification of the cleavage sites and spectral studies of enolase have revealed some of the structural differences between the dimeric and monomeric forms of this enzyme. [source] NEMO oligomerization in the dynamic assembly of the I,B kinase core complexFEBS JOURNAL, Issue 10 2007Elisabeth Fontan NF-,B essential modulator (NEMO) plays an essential role in the nuclear factor ,B (NF-,B) pathway as a modulator of the two other subunits of the I,B kinase (IKK) complex, i.e. the protein kinases, IKK, and IKK,. Previous reports all envision the IKK complex to be a static entity. Using glycerol-gradient ultracentrifugation, we observed stimulus-dependent dynamic IKK complex assembly. In wild-type fibroblasts, the kinases and a portion of cellular NEMO associate in a 350-kDa high-molecular-mass complex. In response to constitutive NF-,B stimulation by Tax, we observed NEMO recruitment and oligomerization to a shifted high-molecular-mass complex of 440 kDa which displayed increased IKK activity. This stimulus-dependent oligomerization of NEMO was also observed using fluorescence resonance energy transfer after a transient pulse with interleukin-1,. In addition, fully activated, dimeric kinases not bound to NEMO were detected in these Tax-activated fibroblasts. By glycerol gradient ultracentrifugation, we also showed that: (a) in fibroblasts deficient in IKK, and IKK,, NEMO predominantly exists as a monomer; (b) in NEMO-deficient fibroblasts, IKK, dimers are present that are less stable than IKK, dimers. Intriguingly, in resting Rat-1 fibroblasts, 160-kDa IKK,,NEMO and IKK,,NEMO heterocomplexes were observed as well as a significant proportion of NEMO monomer. These results suggest that most NEMO molecules do not form a tripartite IKK complex with an IKK,,IKK, heterodimer as previously reported in the literature but, instead, NEMO is able to form a complex with the monomeric forms of IKK, and IKK,. [source] Visualization of the interaction between archaeal DNA polymerase and uracil-containing DNA by atomic force microscopyGENES TO CELLS, Issue 1 2006Yasuo Asami Deamination of cytosine to uracil is a hydrolytic reaction that is greatly accelerated at high temperatures. The resulting uracil pairs with adenine during DNA replication, thereby inducing G:C to A:T transitions in the progeny. Interestingly, B-family DNA polymerases from hyperthermophilic Archaea recognize the presence of uracil in DNA and stall DNA synthesis. To better understand the recognition mechanism, the binding modes of DNA polymerase B1 of Sulfolobus solfataricus (Pol B1) to uracil-containing DNA were examined by gel mobility shift assays and atomic force microscopy. Although PolB1 per se specifically binds to uracil-containing single-stranded DNA, the binding efficiency was substantially enhanced by the initiation of DNA synthesis. Analysis by the atomic force microscopy showed a number of double-stranded DNA (dsDNA) in the products of DNA synthesis. The generation of ds DNA was significantly inhibited, however, by the presence of template uracil, and intermediates where monomeric forms of Pol B1 appeared to bind to uracil-containing DNA were observed. These results suggest that Pol B1 more efficiently recognizes uracil in DNA during DNA synthesis rather than during random diffusion in solution, and that single molecules of Pol B1 bind to template uracil and stall DNA synthesis. [source] Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plantsTHE PLANT JOURNAL, Issue 6 2007G. Gómez Summary Viroids, small non-coding pathogenic RNAs, are able to induce RNA silencing, a phenomenon that has been associated with the pathogenesis and evolution of these small RNAs. It has been recently suggested that viroids may resist this plant defense mechanism. However, the simultaneous degradation of non-replicating full-length viroid RNA, and the resistance of mature forms of viroids to RNA silencing, have not been experimentally demonstrated. Transgenic Nicotiana benthamiana plants expressing a dimeric form of Hop stunt viroid (HSVd) that have the capability to cleave and circularize this viroid RNA were used to address this question. A reporter construct, consisting of a full-length HSVd RNA fused to GFP-mRNA, was agroinfiltrated in these plants and its expression was suppressed. Interestingly, both circular and linear HSVd molecules were stable and able to traffic through grafts in these restrictive conditions, indicating that the mature forms of HSVd are able, in some way, to resist the RNA-silencing mechanism. The observation that a full-length HSVd RNA fused to GFP-mRNA, but not circular and/or linear viroid forms, was fully susceptible to RNA degradation strongly suggests that structures adopted by the free mature monomer protect the pathogenesis-associated forms of the viroid from RNA silencing. [source] Chaperone-like activities of different molecular forms of ,-casein.BIOPOLYMERS, Issue 8 2009Importance of polarity of N-terminal hydrophilic domain Abstract As a member of intrinsically unstructured protein family, ,-casein (,-CN) contains relatively high amount of prolyl residues, adopts noncompact and flexible structure and exhibits chaperone-like activity in vitro. Like many chaperones, native ,-CN does not contain cysteinyl residues and exhibits strong tendencies for self-association. The chaperone-like activities of three recombinant ,-CNs wild type (WT) ,-CN, C4 ,-CN (with cysteinyl residue in position 4) and C208 ,-CN (with cysteinyl residue in position 208), expressed and purified from E. coli, which, consequently, lack the phosphorylated residues, were examined and compared with that of native ,-CN using insulin and alcohol dehydrogenase as target/substrate proteins. The dimers (,-CND) of C4-,-CN and C208 ,-CN were also studied and their chaperone-like activities were compared with those of their monomeric forms. Lacking phosphorylation, WT ,-CN, C208 ,-CN, C4 ,-CN and C4 ,-CND exhibited significantly lower chaperone-like activities than native ,-CN. Dimerization of C208 ,-CN with two distal hydrophilic domains considerably improved its chaperone-like activity in comparison with its monomeric form. The obtained results demonstrate the significant role played by the polar contributions of phosphorylated residues and N-terminal hydrophilic domain as important functional elements in enhancing the chaperone-like activity of native ,-CN. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 623,632, 2009. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Crystallization and preliminary crystallographic analysis of decameric and monomeric forms of C49S mutant thioredoxin-dependent AhpC from Helicobacter pyloriACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 5 2008Supangat Cys49Ser mutant Helicobacter pylori alkyl hydroperoxide reductase (C49S HpAhpC) was purified under reducing conditions in monomeric and decameric forms. The monomeric form was crystallized by the hanging-drop vapour-diffusion method. The crystals diffracted to 2.25,Å resolution and belonged to space group C2, with unit-cell parameters a = 245.8, b = 140.7, c = 189.5,Å, , = 127°, and contained 20 molecules in the asymmetric unit. A crystal of the decameric form was obtained by the microbatch crystallization method and diffracted to 2.8,Å resolution. It belonged to space group C222, with unit-cell parameters a = 257.5, b = 417.5, c = 95.6,Å. The structure of the monomeric form of C49S HpAhpC has been solved by the molecular-replacement method. [source] | ||||||||||||||||||||||||||||