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Native Structure (native + structure)
Selected AbstractsReagentless Biosensor for Hydrogen Peroxide Based on the Immobilization of Hemoglobin in Platinum Nanoparticles Enhanced Poly(chloromethyl thiirane) Cross-linked Chitosan Hybrid FilmELECTROANALYSIS, Issue 12 2009Shanshan Jia Abstract An unmediated hydrogen peroxide (H2O2) biosensor was prepared by co-immobilizing hemoglobin (Hb) with platinum nanoparticles enhanced poly(chloromethyl thiirane) cross-linked chitosan (CCCS-PNs) hybrid film. CCCS could provide a biocompatible microenvironment for Hb and PNs could accelerate the electron transfer between Hb and the electrode. Spectroscopic analysis indicated that the immobilized Hb could maintain its native structure in the CCCS-PNs hybrid film. Entrapped Hb exhibited direct electrochemistry for its heme Fe(III)/Fe(II) redox couples at ,0.396,V in the CCCS-PNs hybrid film, as well as peroxidase-like activity to the reduction of hydrogen peroxide without the aid of an electron mediator. [source] Direct Electron Transfer and Electrocatalysis of Hemoglobin on Chitosan-TiO2 Nanorods-Glass Carbon ElectrodeELECTROANALYSIS, Issue 20 2008Xiaoling Xiao Abstract The direct electron transfer between hemoglobin (Hb) and the glassy carbon electrode (GC) can be readily achieved via a high biocompatible composite system based on biopolymer chitosan (CHT) and TiO2 nanorods (TiO2 -NRs). TiO2 -NRs greatly promote the electron transfer between Hb and GC, which contribute to the higher redox peaks. UV-vis spectra result indicated the Hb entrapped in the composite film well keep its native structure. The immobilized Hb remains its bioelectrocatalytical activity to the reduction of H2O2 with a lower detection limit. A novel, sensitive, reproducible and stable electrochemical biosensing platform of H2O2 based on Hb-TiO2 -CHT electrode is explored. [source] Direct Electrochemistry and Electrocatalysis of Myoglobin Immobilized on Gold Nanoparticles/Carbon Nanotubes Nanohybrid FilmELECTROANALYSIS, Issue 17 2008Wei Cao Abstract A novel nanohybrid material, constructed by gold nanoparticles (GNPs) and multiwalled carbon nanotubes (MWNTs), was designed for immobilization and biosensing of myoglobin (Mb). Morphology of the nanohybrid film was characterized by SEM. UV-vis spectroscopy demonstrated that Mb on the composite film could retain its native structure. Direct electrochemistry of Mb immobilized on the GNPs/MWNTs film was investigated. The immobilized Mb showed a couple of quasireversible and well-defined cyclic voltammetry peaks with a formal potential of about ,0.35,V (vs. Ag/AgCl) in pH,6.0 phosphate buffer solution (PBS) solution. Furthermore, the modified electrode also displayed good sensitivity, wide linear range and long-term stability to the detection of hydrogen peroxide. The experiment results demonstrated that the hybrid matrix provided a biocompatible microenvironment for protein and supplied a necessary pathway for its direct electron transfer. [source] Self-Assembled Graphene,Enzyme Hierarchical Nanostructures for Electrochemical BiosensingADVANCED FUNCTIONAL MATERIALS, Issue 19 2010Qiong Zeng Abstract The self-assembly of sodium dodecyl benzene sulphonate (SDBS) functionalized graphene sheets (GSs) and horseradish peroxidase (HRP) by electrostatic attraction into novel hierarchical nanostructures in aqueous solution is reported. Data from scanning electron microscopy, high-resolution transmission electron microscopy, and X-ray diffraction demonstrate that the HRP,GSs bionanocomposites feature ordered hierarchical nanostructures with well-dispersed HRP intercalated between the GSs. UV-vis and infrared spectra indicate the native structure of HRP is maintained after the assembly, implying good biocompatibility of SDBS-functionalized GSs. Furthermore, the HRP,GSs composites are utilized for the fabrication of enzyme electrodes (HRP,GSs electrodes). Electrochemical measurements reveal that the resulting HRP,GSs electrodes display high electrocatalytic activity to H2O2 with high sensitivity, wide linear range, low detection limit, and fast amperometric response. These desirable electrochemical performances are attributed to excellent biocompatibility and superb electron transport efficiency of GSs as well as high HRP loading and synergistic catalytic effect of the HRP,GSs bionanocomposites toward H2O2. As graphene can be readily non-covalently functionalized by "designer" aromatic molecules with different electrostatic properties, the proposed self-assembly strategy affords a facile and effective platform for the assembly of various biomolecules into hierarchically ordered bionanocomposites in biosensing and biocatalytic applications. [source] Full-length prion protein aggregates to amyloid fibrils and spherical particles by distinct pathwaysFEBS JOURNAL, Issue 9 2008Driss El Moustaine As limited structural information is available on prion protein (PrP) misfolding and aggregation, a causative link between the specific (supra)molecular structure of PrP and transmissible spongiform encephalopathies remains to be elucidated. In this study, high pressure was utilized, as an approach to perturb protein structure, to characterize different morphological and structural PrP aggregates. It was shown that full-length recombinant PrP undergoes ,-sheet aggregation on high-pressure-induced destabilization. By tuning the physicochemical conditions, the assembly process evolves through two distinct pathways leading to the irreversible formation of spherical particles or amyloid fibrils, respectively. When the PrP aggregation propensity is enhanced, high pressure induces the formation of a partially unfolded aggregated protein, AggHP, which relaxes at ambient pressure to form amorphous aggregates. The latter largely retain the native secondary structure. On prolonged incubation at high pressure, followed by depressurization, AggHP transforms to a monodisperse population of spherical particles of about 20 nm in diameter, characterized by an essentially ,-sheet secondary structure. When the PrP aggregation propensity is decreased, an oligomeric reaction intermediate, IHP, is formed under high pressure. After pressure release, IHP relaxes to the original native structure. However, on prolonged incubation at high pressure and subsequent depressurization, it transforms to amyloid fibrils. Structural evaluation, using optical spectroscopic methods, demonstrates that the conformation adopted by the subfibrillar oligomeric intermediate, IHP, constitutes a necessary prerequisite for the formation of amyloids. The use of high-pressure perturbation thus provides an insight into the molecular mechanism of the first stages of PrP misfolding into amyloids. [source] Exploring the primary electron acceptor (QA)-site of the bacterial reaction center from Rhodobacter sphaeroidesFEBS JOURNAL, Issue 4 2002Binding mode of vitamin K derivatives The functional replacement of the primary ubiquinone (QA) in the photosynthetic reaction center (RC) from Rhodobacter sphaeroides with synthetic vitamin K derivatives has provided a powerful tool to investigate the electron transfer mechanism. To investigate the binding mode of these quinones to the QA binding site we have determined the binding free energy and charge recombination rate from QA, to D+ (kAD) of 29 different 1,4-naphthoquinone derivatives with systematically altered structures. The most striking result was that none of the eight tested compounds carrying methyl groups in both positions 5 and 8 of the aromatic ring exhibited functional binding. To understand the binding properties of these quinones on a molecular level, the structures of the reaction center-naphthoquinone complexes were predicted with ligand docking calculations. All protein,ligand structures show hydrogen bonds between the carbonyl oxygens of the quinone and AlaM260 and HisM219 as found for the native ubiquinone-10 in the X-ray structure. The center-to-center distance between the naphthoquinones at QA and the native ubiquinone-10 at QB (the secondary electron acceptor) is essentially the same, compared to the native structure. A detailed analysis of the docking calculations reveals that 5,8-disubstitution prohibits binding due to steric clashes of the 5-methyl group with the backbone atoms of AlaM260 and AlaM249. The experimentally determined binding free energies were reproduced with an rmsd of ,,4 kJ·mol,1 in most cases providing a valuable tool for the design of new artificial electron acceptors and inhibitors. [source] Induced SER-Activity in Nanostructured Ag,Silica,Au Supports via Long-Range Plasmon CouplingADVANCED FUNCTIONAL MATERIALS, Issue 12 2010Jiu-Ju Feng Abstract A novel Ag,silica,Au hybrid device is developed that displays a long-range plasmon transfer of Ag to Au leading to enhanced Raman scattering of molecules largely separated from the optically excited Ag surface. A nanoscopically rough Ag surface is coated by a silica spacer of variable thickness from ,1 to 21,nm and a thin Au film of ,25,nm thickness. The outer Au surface is further functionalized by a self-assembled monolayer (SAM) for electrostatic binding of the heme protein cytochrome c (Cyt c) that serves as a Raman probe and model enzyme. High-quality surface-enhanced resonance Raman (SERR) spectra are obtained with 413,nm excitation, demonstrating that the enhancement results exclusively from excitation of Ag surface plasmons. The enhancement factor is estimated to be 2,×,104,8,×,103 for a separation of Cyt c from the Ag surface by 28,47,nm, corresponding to an attenuation of the enhancement by a factor of only 2,6 compared to Cyt c adsorbed directly on a SAM-coated Ag electrode. Upon immobilization of Cyt c on the functionalized Ag,silica,Au device, the native structure and redox properties are preserved as demonstrated by time- and potential-dependent SERR spectroscopy. [source] SKATE: A docking program that decouples systematic sampling from scoringJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2010Jianwen A. Feng Abstract SKATE is a docking prototype that decouples systematic sampling from scoring. This novel approach removes any interdependence between sampling and scoring functions to achieve better sampling and, thus, improves docking accuracy. SKATE systematically samples a ligand's conformational, rotational and translational degrees of freedom, as constrained by a receptor pocket, to find sterically allowed poses. Efficient systematic sampling is achieved by pruning the combinatorial tree using aggregate assembly, discriminant analysis, adaptive sampling, radial sampling, and clustering. Because systematic sampling is decoupled from scoring, the poses generated by SKATE can be ranked by any published, or in-house, scoring function. To test the performance of SKATE, ligands from the Asetex/CDCC set, the Surflex set, and the Vertex set, a total of 266 complexes, were redocked to their respective receptors. The results show that SKATE was able to sample poses within 2 Å RMSD of the native structure for 98, 95, and 98% of the cases in the Astex/CDCC, Surflex, and Vertex sets, respectively. Cross-docking accuracy of SKATE was also assessed by docking 10 ligands to thymidine kinase and 73 ligands to cyclin-dependent kinase. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Can a physics-based, all-atom potential find a protein's native structure among misfolded structures?JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2007Abstract Recent work has shown that physics-based, all-atom energy functions (AMBER, CHARMM, OPLS-AA) and local minimization, when used in scoring, are able to discriminate among native and decoy structures. Yet, there have been only few instances reported of the successful use of physics based potentials in the actual refinement of protein models from a starting conformation to one that ends in structures, which are closer to the native state. An energy function that has a global minimum energy in the protein's native state and a good correlation between energy and native-likeness should be able to drive model structures closer to their native structure during a conformational search. Here, the possible reasons for the discrepancy between the scoring and refinement results for the case of AMBER potential are examined. When the conformational search via molecular dynamics is driven by the AMBER potential for a large set of 150 nonhomologous proteins and their associated decoys, often the native minimum does not appear to be the lowest free energy state. Ways of correcting the potential function in order to make it more suitable for protein model refinement are proposed. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Conformational search of peptides and proteins: Monte Carlo minimization with an adaptive bias method applied to the heptapeptide deltorphinJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 4 2004S. Banu Ozkan Abstract The energy function of a protein consists of a tremendous number of minima. Locating the global energy minimum (GEM) structure, which corresponds approximately to the native structure, is a severe problem in global optimization. Recently we have proposed a conformational search technique based on the Monte Carlo minimization (MCM) method of Li and Scheraga, where trial dihedral angles are not selected at random within the range [,180°,180°] (as with MCM) but with biased probabilities depending on the increased structure-energy correlations as the GEM is approached during the search. This method, called the Monte Carlo minimization with an adaptive bias (MCMAB), was applied initially to the pentapeptide Leu-enkephalin. Here we study its properties further by applying it to the larger peptide with bulky side chains, deltorphin (H-Tyr-D-Met-Phe-His-Leu-Met-Asp-NH2). We find that on average the number of energy minimizations required by MCMAB to locate the GEM for the first time is smaller by a factor of approximately three than the number required by MCM,in accord with results obtained for Leu-enkephalin. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 565,572, 2004 [source] Systematic epitope analysis of the p26 EIAV core proteinJOURNAL OF MOLECULAR RECOGNITION, Issue 4 2007Adriana Soutullo Abstract The major core protein of equine infectious anemia virus (EIAV), p26, is one of the primary immunogenic structural proteins during a persistent infection of horses and is highly conserved among antigenically variants of viral isolates. In order to investigate its immune profile in more detail for a better diagnostic, an epitope mapping was carried out by means of two libraries of overlapping peptide fragments prepared by simultaneous and parallel SPPS on derivatized cellulose membranes (SPOT synthesis). Polyclonal equine sera from infected horses were used for the biological assay. Particularly two promising continuous epitopes (NAMRHL and MYACRD) were localized on the C-terminal extreme of p26, region 194,222. A cyclic synthetic fragment of 29 amino acid residues containing the identified epitopes was designed and studied. A significant conformational change towards a helical structure was observed when the peptide was cyclized by a bridge between Cys198 and Cys218. This observation correlated with an improvement of its ability to be recognized by specific antibodies in an EIA (Enzyme-linked Immunosorbent assay). These results suggest that the conformationally restricted synthetic antigen adequately mimics the native structure of this region of p26 core protein. Copyright © 2007 John Wiley & Sons, Ltd. [source] Sustained and Extended Release with Structural and Activity Recovery of Lysozyme from Complexes with Sodium (Sulfamate Carboxylate) Isoprene/Ethylene Oxide Block CopolymerMACROMOLECULAR BIOSCIENCE, Issue 2 2010Gao Gao Abstract The complexation of lysozyme and sodium (sulfamate carboxylate) isoprene/ethylene oxide (SCIEO) at pH,=,7.4 and the release of lysozyme from the complexes in the presence of NaCl were investigated. Through electrostatic and hydrophobic interactions, lysozyme and SCIEO form stable complex nanoparticles. The complexation partially disturbs the structure of lysozyme. Some of the hydrophobic residues of lysozyme are exposed to bind with SCIEO. The complexation leads to loss of most of the lysozyme activity. In the presence of NaCl, lysozyme can be released from the complexes. The released lysozyme molecules recover their native structure and activity completely. In the condition of physiological pH and ionic strength, a sustained and extended release of lysozyme was achieved. [source] Core glycan in the yeast multicopper ferroxidase, Fet3p: A case study of N-linked glycosylation, protein maturation, and stabilityPROTEIN SCIENCE, Issue 9 2010Lynn Ziegler Abstract Glycosylation is essential to the maintenance of protein quality in the vesicular protein trafficking pathway in eukaryotic cells. Using the yeast multicopper oxidase, Fet3p, the hypothesis is tested that core glycosylation suppresses Fet3p nascent chain aggregation during synthesis into the endoplasmic reticulum (ER). Fet3p has 11 crystallographically mapped N-linked core glycan units. Assembly of four of these units is specifically required for localization of Fet3p to the plasma membrane (PM). Fet3 protein lacking any one of these glycan units is found in an intracellular high-molecular mass species resolvable by blue native gel electrophoresis. Individually, the remaining glycan moieties are not required for ER exit; however, serial deletion of these by N , A substitution correlates with these desglycan species failure to exit the ER. Desglycan Fet3 proteins that localize to the PM are wild type in function indicating that the missing carbohydrate is not required for native structure and biologic activity. This native function includes the interaction with the iron permease, Ftr1p, and wild type high-affinity iron uptake activity. The four essential sequons are found within relatively nonpolar regions located in surface recesses and are strongly conserved among fungal Fet3 proteins. The remaining N-linked sites are found in more surface exposed, less nonpolar environments, and their conservation is weak or absent. The data indicate that in Fet3p the N-linked glycan has little effect on the enzyme's molecular activity but is critical to its cellular activity by maximizing the protein's exit from the ER and assembly into a functional iron uptake complex. [source] How well can the accuracy of comparative protein structure models be predicted?PROTEIN SCIENCE, Issue 11 2008David Eramian Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the C, root-mean-squared deviation (RMSD) and native overlap (NO3.5Å) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model-specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3.5Å errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71. [source] Detecting equilibrium cytochrome c folding intermediates by electrospray ionisation mass spectrometry: Two partially folded forms populate the molten-globule statePROTEIN SCIENCE, Issue 3 2002Rita Grandori Abstract Nanoelectrospray ionization mass spectrometry (nano-ESI-MS) is applied to the characterization of ferric cytochromec (cytc) conformational states under different solvent conditions. The methanol-induced molten-globule state in the pH range 2.6,3.0 is found to be populated by two distinct, partially folded conformers IA and IB. The more compact intermediate IB resembles that induced by glycerol in acid-unfolded cytc. The less compact one, IA, also can be induced by destabilization of the native structure by trifluoroethanol. IA and IB can be detected, in the absence of additives, around the midpoint of the acid-induced unfolding transition, providing direct evidence for involvement of equilibrium folding intermediates in cytc conformational transitions at low pH. This study shows that mass spectrometry can contribute to the characterization of molten-globule states of proteins by detection of distinct, although poorly populated, conformations involved in a dynamic equilibrium. [source] The role of strand 1 of the C ,-sheet in the structure and function of ,1 -antitrypsinPROTEIN SCIENCE, Issue 12 2001Stephen P. Bottomley Abstract Serpins inhibit cognate serine proteases involved in a number of important processes including blood coagulation and inflammation. Consequently, loss of serpin function or stability results in a number of disease states. Many of the naturally occurring mutations leading to disease are located within strand 1 of the C ,-sheet of the serpin. To ascertain the structural and functional importance of each residue in this strand, which constitutes the so-called distal hinge of the reactive center loop of the serpin, an alanine scanning study was carried out on recombinant ,1 -antitrypsin Pittsburgh mutant (P1 = Arg). Mutation of the P10, position had no effect on its inhibitory properties towards thrombin. Mutations to residues P7, and P9, caused these serpins to have an increased tendency to act as substrates rather than inhibitors, while mutations at P6, and P8, positions caused the serpin to behave almost entirely as a substrate. Mutations at the P6, and P8, residues of the C ,-sheet, which are buried in the hydrophobic core in the native structure, caused the serpin to become highly unstable and polymerize much more readily. Thus, P6, and P8, mutants of ,1 -antitrypsin had melting temperatures 14 degrees lower than wild-type ,1 -antitrypsin. These results indicate the importance of maintaining the anchoring of the distal hinge to both the inhibitory mechanism and stability of serpins, the inhibitory mechanism being particularly sensitive to any perturbations in this region. The results of this study allow more informed analysis of the effects of mutations found at these positions in disease-associated serpin variants. [source] Free energy determinants of tertiary structure and the evaluation of protein modelsPROTEIN SCIENCE, Issue 11 2000Donald Petrey Abstract We develop a protocol for estimating the free energy difference between different conformations of the same polypeptide chain. The conformational free energy evaluation combines the CHARMM force field with a continuum treatment of the solvent. In almost all cases studied, experimentally determined structures are predicted to be more stable than misfolded "decoys." This is due in part to the fact that the Coulomb energy of the native protein is consistently lower than that of the decoys. The solvation free energy generally favors the decoys, although the total electrostatic free energy (sum of Coulomb and solvation terms) favors the native structure. The behavior of the solvation free energy is somewhat counterintuitive and, surprisingly, is not correlated with differences in the burial of polar area between native structures and decoys. Rather, the effect is due to a more favorable charge distribution in the native protein, which, as is discussed, will tend to decrease its interaction with the solvent. Our results thus suggest, in keeping with a number of recent studies, that electrostatic interactions may play an important role in determining the native topology of a folded protein. On this basis, a simplified scoring function is derived that combines a Coulomb term with a hydrophobic contact term. This function performs as well as the more complete free energy evaluation in distinguishing the native structure from misfolded decoys. Its computational efficiency suggests that it can be used in protein structure prediction applications, and that it provides a physically well-defined alternative to statistically derived scoring functions. [source] Synthesis and NMR solution structure of an ,-helical hairpin stapled with two disulfide bridgesPROTEIN SCIENCE, Issue 5 2000Philippe Barthe Abstract Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of ,-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38-amino acid peptide, ,2p8, encompassing the ,-helical hairpin present in the structure of p8MTCP1, as an ,-helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three-dimensional structure of this peptide has been solved using homonuclear two-dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of ,2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65 ± 0.25 and 1.51 ± 0.21 Å, respectively. Excised from its protein context, the ,-hairpin keeps its native structure: an ,-helical coiled-coil, similar to that found in superhelical structures, with two helices spanning residues 4-16 and 25,36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent-exposed surface available for mutation. This ,-helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries. [source] Affinity cleavage at the divalent metal site of porcine NAD-specific isocitrate dehydrogenasePROTEIN SCIENCE, Issue 1 2000Yu-Chu Huang Abstract A divalent metal ion, such as Mn2+, is required for the catalytic reaction and allosteric regulation of pig heart NAD-dependent isocitrate dehydrogenase. The enzyme is irreversibly inactivated and cleaved by Fe2+ in the presence of O2 and ascorbate at pH 7.0. Mn2+ prevents both inactivation and cleavage. Nucleotide ligands, such as NAD, NADPH, and ADP, neither prevent nor promote inactivation or cleavage of the enzyme by Fe2+. The NAD-specific isocitrate dehydrogenase is composed of three distinct subunits in the ratio 2,:1 ,:1 ,. The results indicate that the oxidative inactivation and cleavage are specific and involve the 40 kDa , subunit of the enzyme. A pair of major peptides is generated during Fe2+ inactivation: 29.5 + 10.5 kDa, as determined by SDS-PAGE. Amino-terminal sequencing reveals that these peptides arise by cleavage of the Val262-His263 bond of the , subunit. No fragments are produced when enzyme is incubated with Fe2+ and ascorbate under denaturing conditions in the presence of 6 M urea, indicating that the native structure is required for the specific cleavage. These results suggest that His263 of the , subunit may be a ligand of the divalent metal ion needed for the reaction catalyzed by isocitrate dehydrogenase. Isocitrate enhances the inactivation of enzyme caused by Fe2+ in the presence of oxygen, but prevents the cleavage, suggesting that inactivation occurs by a different mechanism when metal ion is bound to the enzyme in the presence of isocitrate: oxidation of cysteine may be responsible for the rapid inactivation in this case. Affinity cleavage caused by Fe2+ implicates , as the catalytic subunit of the multisubunit porcine NAD-dependent isocitrate dehydrogenase. [source] Travelling wave ion mobility mass spectrometry studies of protein structure: biological significance and comparison with X-ray crystallography and nuclear magnetic resonance spectroscopy measurementsRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 20 2008Charlotte A. Scarff The three-dimensional conformation of a protein is central to its biological function. The characterisation of aspects of three-dimensional protein structure by mass spectrometry is an area of much interest as the gas-phase conformation, in many instances, can be related to that of the solution phase. Travelling wave ion mobility mass spectrometry (TWIMS) was used to investigate the biological significance of gas-phase protein structure. Protein standards were analysed by TWIMS under denaturing and near-physiological solvent conditions and cross-sections estimated for the charge states observed. Estimates of collision cross-sections were obtained with reference to known standards with published cross-sections. Estimated cross-sections were compared with values from published X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy structures. The cross-section measured by ion mobility mass spectrometry varies with charge state, allowing the unfolding transition of proteins in the gas phase to be studied. Cross-sections estimated experimentally for proteins studied, for charge states most indicative of native structure, are in good agreement with measurements calculated from published X-ray and NMR structures. The relative stability of gas-phase structures has been investigated, for the proteins studied, based on their change in cross-section with increase in charge. These results illustrate that the TWIMS approach can provide data on three-dimensional protein structures of biological relevance. Copyright © 2008 John Wiley & Sons, Ltd. [source] Structure of native laccase from Trametes hirsuta at 1.8,Å resolutionACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2009Konstantin M. Polyakov This paper describes the structural analysis of the native form of laccase from Trametes hirsuta at 1.8,Å resolution. This structure provides a basis for the elucidation of the mechanism of catalytic action of these ubiquitous proteins. The 1.8,Å resolution native structure provided a good level of structural detail compared with many previously reported laccase structures. A brief comparison with the active sites of other laccases is given. [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] Structure of BthA-I complexed with p -bromophenacyl bromide: possible correlations with lack of pharmacological activityACTA CRYSTALLOGRAPHICA SECTION D, Issue 12 2005Angelo J. Magro The crystal structure of an acidic phospholipase A2 isolated from Bothrops jararacussu venom (BthA-I) chemically modified with p -bromophenacyl bromide (BPB) has been determined at 1.85,Å resolution. The catalytic, platelet-aggregation inhibition, anticoagulant and hypotensive activities of BthA-I are abolished by ligand binding. Electron-density maps permitted unambiguous identification of inhibitor covalently bound to His48 in the substrate-binding cleft. The BthA-I,BPB complex contains three structural regions that are modified after inhibitor binding: the Ca2+ -binding loop, ,-wing and C-terminal regions. Comparison of BthA-I,BPB with two other BPB-inhibited PLA2 structures suggests that in the absence of Na+ ions at the Ca2+ -binding loop, this loop and other regions of the PLA2s undergo structural changes. The BthA-I,BPB structure reveals a novel oligomeric conformation. This conformation is more energetically and conformationally stable than the native structure and the abolition of pharmacological activities by the ligand may be related to the oligomeric structural changes. A residue of the `pancreatic' loop (Lys69), which is usually attributed as providing the anticoagulant effect, is in the dimeric interface of BthA-I,BPB, leading to a new hypothesis regarding the abolition of this activity by BPB. [source] Escherichia coli MltA: MAD phasing and refinement of a tetartohedrally twinned protein crystal structureACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2005Thomas R. M. Barends Crystals were grown of a mutant form of the bacterial cell-wall maintenance protein MltA that diffracted to 2.15,Å resolution. When phasing with molecular replacement using the native structure failed, selenium MAD was used to obtain initial phases. However, after MAD phasing the crystals were found to be tetartohedrally twinned, hampering correct space-group determination and refinement. A refinement protocol was designed to take tetartohedral twinning into account and was successfully applied to refine the structure. The refinement protocol is described and the reasons for the failure of molecular replacement and the success of MAD are discussed in terms of the effects of the tetartohedral twinning. [source] Structure of pyrR (Rv1379) from Mycobacterium tuberculosis: a persistence gene and protein drug targetACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Katherine A. Kantardjieff The Mycobacterium tuberculosis pyrR gene (Rv1379) encodes a protein that regulates the expression of pyrimidine-nucleotide biosynthesis (pyr) genes in a UMP-dependent manner. Because pyrimidine biosynthesis is an essential step in the progression of TB, the gene product pyrR is an attractive antitubercular drug target. The 1.9,Å native structure of Mtb pyrR determined by the TB Structural Genomics Consortium facilities in trigonal space group P3121 is reported, with unit-cell parameters a = 66.64, c = 154.72,Å at 120,K and two molecules in the asymmetric unit. The three-dimensional structure and residual uracil phosphoribosyltransferase activity point to a common PRTase ancestor for pyrR. However, while PRPP- and UMP-binding sites have been retained in Mtb pyrR, a distinct dimer interaction among subunits creates a deep positively charged cleft capable of binding pyr mRNA. In silico screening of pyrimidine-nucleoside analogs has revealed a number of potential lead compounds that, if bound to Mtb pyrR, could facilitate transcriptional attenuation, particularly cyclopentenyl nucleosides. [source] Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Kazuaki Harata A triclinic crystal of hen egg-white lysozyme obtained from a D2O solution at 313,K was transformed into a new triclinic crystal by slow release of solvent under a temperature-regulated nitrogen-gas stream. The progress of the transition was monitored by X-ray diffraction. The transition started with the appearance of strong diffuse streaks. The diffraction spots gradually fused and faded with the emergence of diffraction from the new lattice; the scattering power of the crystal fell to a resolution of 1.5,Å from the initial 0.9,Å resolution. At the end of the transition, the diffuse streaks disappeared and the scattering power recovered to 1.1,Å resolution. The transformed crystal contained two independent molecules and the solvent content had decreased to 18% from the 32% solvent content of the native crystal. The structure was determined at 1.1,Å resolution and compared with the native structure refined at the same resolution. The backbone structures of the two molecules in the transformed crystal were superimposed on the native structure with root-mean-square deviations of 0.71 and 0.96,Å. A prominent structural difference was observed in the loop region of residues Ser60,Leu75. In the native crystal, a water molecule located at the centre of this helical loop forms hydrogen bonds to main-chain peptide groups. In the transformed crystal, this water molecule is replaced by a sodium ion with octahedral coordination that involves water molecules and a nitrate ion. The peptide group connecting Arg73 and Asn74 is rotated by 180° so that the CO group of Arg73 can coordinate to the sodium ion. The change in the X-ray diffraction pattern during the phase transition suggests that the transition proceeds at the microcrystal level. A mechanism is proposed for the crystal transformation. [source] Soft energy function and generic evolutionary method for discriminating native from nonnative protein conformationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2008Yi-yuan Chiu Abstract We have developed a soft energy function, termed GEMSCORE, for the protein structure prediction, which is one of emergent issues in the computational biology. The GEMSORE consists of the van der Waals, the hydrogen-bonding potential and the solvent potential with 12 parameters which are optimized by using a generic evolutionary method. The GEMSCORE is able to successfully identify 86 native proteins among 96 target proteins on six decoy sets from more 70,000 near-native structures. For these six benchmark datasets, the predictive performance of the GEMSCORE, based on native structure ranking and Z -scores, was superior to eight other energy functions. Our method is based solely on a simple and linear function and thus is considerably faster than other methods that rely on the additional complex calculations. In addition, the GEMSCORE recognized 17 and 2 native structures as the first and the second rank, respectively, among 21 targets in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction). These results suggest that the GEMSCORE is fast and performs well to discriminate between native and nonnative structures from thousands of protein structure candidates. We believe that GEMSCORE is robust and should be a useful energy function for the protein structure prediction. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 [source] MOPED: Method for optimizing physical energy parameters using decoysJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2003Chaok Seok Abstract We present a method called MOPED for optimizing energetic and structural parameters in computational models, including all-atom energy functions, when native structures and decoys are given. The present method goes beyond previous approaches in treating energy functions that are nonlinear in the parameters and continuous in the degrees of freedom. We illustrate the method by improving solvation parameters in the energy function EEF1, which consists of the CHARMM19 polar hydrogen force field augmented by a Gaussian solvation term. Although the published parameters for EEF1 correctly discriminate the native from decoys in the decoy sets of Levitt et al., they fail on several of the more difficult decoy sets of Baker et al. MOPED successfully finds improved parameters that allow EEF1 to discriminate native from decoy structures on all protein structures that do not have metals or prosthetic groups. © 2002 Wiley Periodicals, Inc. J Comput Chem 24: 89,97, 2003 [source] Loopholes and missing links in protein modelingPROTEIN SCIENCE, Issue 9 2007Karen A. Rossi Abstract This paper provides an unbiased comparison of four commercially available programs for loop sampling, Prime, Modeler, ICM, and Sybyl, each of which uses a different modeling protocol. The study assesses the quality of results and examines the relative strengths and weaknesses of each method. The set of loops to be modeled varied in length from 4,12 amino acids. The approaches used for loop modeling can be classified into two methodologies: ab initio loop generation (Modeler and Prime) and database searches (Sybyl and ICM). Comparison of the modeled loops to the native structures was used to determine the accuracy of each method. All of the protocols returned similar results for short loop lengths (four to six residues), but as loop length increased, the quality of the results varied among the programs. Prime generated loops with RMSDs <2.5 Å for loops up to 10 residues, while the other three methods met the 2.5 Å criteria at seven-residue loops. Additionally, the ability of the software to utilize disulfide bonds and X-ray crystal packing influenced the quality of the results. In the final analysis, the top-ranking loop from each program was rarely the loop with the lowest RMSD with respect to the native template, revealing a weakness in all programs to correctly rank the modeled loops. [source] Cofactor effects on the protein folding reaction: Acceleration of ,-lactalbumin refolding by metal ionsPROTEIN SCIENCE, Issue 4 2006Natalia A. Bushmarina Abstract About 30% of proteins require cofactors for their proper folding. The effects of cofactors on the folding reaction have been investigated with ,-lactalbumin as a model protein and metal ions as cofactors. Metal ions accelerate the refolding of ,-lactalbumin by lessening the energy barrier between the molten globule state and the transition state, mainly by decreasing the difference of entropy between the two states. These effects are linked to metal ion binding to the protein in the native state. Hence, relationships between the metal affinities for the intermediate states and those for the native state are observed. Some residual specificity for the calcium ion is still observed in the molten globule state, this specificity getting closer in the transition state to that of the native state. The comparison between kinetic and steady-state data in association with the , value method indicates the binding of the metal ions on the unfolded state of ,-lactalbumin. Altogether, these results provide insight into cofactor effects on protein folding. They also suggest new possibilities to investigate the presence of residual native structures in the unfolded state of protein and the effects of such structures on the protein folding reaction and on protein stability. [source] | |||||||||||||