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Protein Molecules (protein + molecule)
Selected AbstractsAzotobacter vinelandii Metal Storage Protein: "Classical" Inorganic Chemistry Involved in Mo/W Uptake and Release ProcessesCHEMBIOCHEM, Issue 4 2008Jörg Schemberg Dr. Abstract The release of Mo (as molybdate) from the Mo storage protein (MoSto), which is unique among all existing metalloproteins, is strongly influenced by temperature and pH value; other factors (incubation time, protein concentration, degree of purity) have minor, though significant effects. A detailed pH titration at 12,°C revealed that three different steps can be distinguished for the Mo-release process. A proportion of ,15,% at pH 6.8,7.0, an additional 25,% at pH 7.2,7.5 and ca. 50,% (up to 90,% in total) at pH 7.6,7.8. This triphasic process supports the assumption of the presence of different types of molybdenum-oxide-based clusters that exhibit different pH lability. The complete release of Mo was achieved by increasing the temperature to 30,°C and the pH value to >7.5. The Mo-release process does not require ATP; on the contrary, ATP prevents, or at least reduces the degree of metal release, depending on the concentration of the nucleotide. From this point of view, the intracellular ATP concentration is suggested to play,in addition to the pH value,an indirect but crucial role in controlling the extent of Mo release in the cell. The binding of molybdenum to the apoprotein (reconstitution process) was confirmed to be directly dependent on the presence of a nucleotide (preferably ATP) and MgCl2. Maximal reincorporation of Mo required 1 mM ATP, which could partly be replaced by GTP. When the storage protein was purified in the presence of ATP and MgCl2 (1 mM each), the final preparation contained 80 Mo atoms per protein molecule. Maximal metal loading (110,115 atoms/MoSto molecule) was only achieved, if Mo was first completely released from the native protein and subsequently (re-) bound under optimal reconstitution conditions: 1 h incubation at pH 6.5 and 12,°C in the presence of ATP, MgCl2 and excess molybdate. A corresponding tungsten-containing storage protein ("WSto") could not only be synthesized in vivo by growing cells, but could also be constructed in vitro by a metalate,ion exchange procedure by using the isolated MoSto protein. The high W content of the isolated cell-made WSto (,110 atoms/protein molecule) and the relatively low amount of tungstate that was released from the protein under optimal "release conditions", demonstrates that the W-oxide-based clusters are more stable inside the protein cavity than the Mo-oxide analogues, as expected from the corresponding findings in polyoxometalate chemistry. The optimized isolation of the W-loaded protein form allowed us to get single crystals, and to determine the crystal X-ray structure. This proved that the protein contains remarkably different types of polyoxotungstates, the formation of which is templated in an unprecedented process by the different protein pockets. (Angew. Chem. Int. Ed.2007, 46, 2408,2413). [source] Protein crystal nucleation: Recent notionsCRYSTAL RESEARCH AND TECHNOLOGY, Issue 1 2007Christo N. Nanev Abstract The nucleation of protein crystals is reconsidered taking into account the specificity of the protein molecules. In contrast to the homogeneous surface properties of small molecules, the protein molecule surface is highly inhomogeneous. Over their surfaces proteins exhibit high anisotropic distribution of patches, which are able to form crystalline bonds, the crystallization patch representing only a small fraction of the total surface of the protein molecule. Therefore, an appropriate spatial orientation of the colliding protein molecules is required in order to create a crystalline cluster. This scenario decreases considerably the success ratio of the attempt frequency for crystal nucleation. On the other hand a heterogeneous nucleation of (protein) crystals may be accelerated due to the arrival on some support of under-critical clusters that are formed in bulk solution; when arriving there they may acquire the property of critical nuclei. Thus, a plausible explanation of important peculiarities of protein crystal nucleation, as inferred from the experimental data, is suggested. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] High epitope density in a single protein molecule significantly enhances antigenicity as well as immunogenicity: a novel strategy for modern vaccine development and a preliminary investigation about B,cell discrimination of monomeric proteinsEUROPEAN JOURNAL OF IMMUNOLOGY, Issue 2 2005Wanli Liu Abstract Although early studies have shown a close correlation between epitope density and epitope-specific humoral immune responses, few attempts have been made to quantitatively compare the antigenic and immunogenic differences between protein molecules bearing low or high degrees of epitope density, nor have studies quantitatively investigated the mechanism of B,cell discrimination of monomeric antigens. In this study, we prepared glutathione S-transferase (GST) fusion proteins bearing various copies of the M2e epitope from the influenza virus M2,protein [GST-(M2e)8, GST-(M2e)4 and GST-(M2e)1], which were used to detect and compare the real-time kinetic binding with M2e-specific mAb by surface plasma resonance. Our data show clearly that fusion proteins bearing higher M2e epitope density resulted in higher average avidity for M2e-specific mAb. Furthermore, it was observed that fusion proteins bearing high M2e epitope density could induce polyclonal antibodies (pAb) with enhanced an average affinity constant (KA) for M2e epitope peptide compared to fusion proteins bearing low epitope density. The average KA of pAb induced by GST-(M2e)8 (3.08 × 108,M,1 or 9.96 × 108,M,1) was up to two orders of magnitude greater than the average KA of pAb induced by GST-(M2e)1 (2.00 × 106,M,1 or 3.43 × 106,M,1). Thus, the data presented here demonstrate that high epitope density in a single protein molecule significantly enhances antigenicity and immunogenicity. These findings enrich our knowledge of how epitope density might relate to the recognition, activation and antibody production processes of epitope-specific immature B,cells. [source] Effect of mutations in the ,5,,7 loop on the structure and properties of human small heat shock protein HSP22 (HspB8, H11)FEBS JOURNAL, Issue 21 2007Alexei S. Kasakov The human genome encodes ten different small heat shock proteins, each of which contains the so-called ,-crystallin domain consisting of 80,100 residues and located in the C-terminal part of the molecule. The ,-crystallin domain consists of six or seven ,-strands connected by different size loops and combined in two ,-sheets. Mutations in the loop connecting the ,5 and ,7 strands and conservative residues of ,7 in ,A-, ,B-crystallin and HSP27 correlate with the development of different congenital diseases. To understand the role of this part of molecule in the structure and function of small heat shock proteins, we mutated two highly conservative residues (K137 and K141) of human HSP22 and investigated the properties of the K137E and K137,141E mutants. These mutations lead to a decrease in intrinsic Trp fluorescence and the double mutation decreased fluorescence resonance energy transfer from Trp to bis-ANS bound to HSP22. Mutations K137E and especially K137,141E lead to an increase in unordered structure in HSP22 and increased susceptibility to trypsinolysis. Both mutations decreased the probability of dissociation of small oligomers of HSP22, and mutation K137E increased the probability of HSP22 crosslinking. The wild-type HSP22 possessed higher chaperone-like activity than their mutants when insulin or rhodanase were used as the model substrates. Because conservative Lys residues located in the ,5,,7 loop and in the ,7 strand appear to play an important role in the structure and properties of HSP22, mutations in this part of the small heat shock protein molecule might have a deleterious effect and often correlate with the development of different congenital diseases. [source] Probing the unfolding region of ribonuclease A by site-directed mutagenesisFEBS JOURNAL, Issue 20 2004Jens Köditz Ribonuclease A contains two exposed loop regions, around Ala20 and Asn34. Only the loop around Ala20 is sufficiently flexible even under native conditions to allow cleavage by nonspecific proteases. In contrast, the loop around Asn34 (together with the adjacent ,-sheet around Thr45) is the first region of the ribonuclease A molecule that becomes susceptible to thermolysin and trypsin under unfolding conditions. This second region therefore has been suggested to be involved in early steps of unfolding and was designated as the unfolding region of the ribonuclease A molecule. Consequently, modifications in this region should have a great impact on the unfolding and, thus, on the thermodynamic stability. Also, if the Ala20 loop contributes to the stability of the ribonuclease A molecule, rigidification of this flexible region should stabilize the entire protein molecule. We substituted several residues in both regions without any dramatic effects on the native conformation and catalytic activity. As a result of their remarkably differing stability, the variants fell into two groups carrying the mutations: (a) A20P, S21P, A20P/S21P, S21L, or N34D; (b) L35S, L35A, F46Y, K31A/R33S, L35S/F46Y, L35A/F46Y, or K31A/R33S/F46Y. The first group showed a thermodynamic and kinetic stability similar to wild-type ribonuclease A, whereas both stabilities of the variants in the second group were greatly decreased, suggesting that the decrease in ,G can be mainly attributed to an increased unfolding rate. Although rigidification of the Ala20 loop by introduction of proline did not result in stabilization, disturbance of the network of hydrogen bonds and hydrophobic interactions that interlock the proposed unfolding region dramatically destabilized the ribonuclease A molecule. [source] Pressure-exploration of the 33-kDa protein from the spinach photosystem II particleFEBS JOURNAL, Issue 9 2001Kangcheng Ruan The 33-kDa protein isolated from the spinach photosystem II particle is an ideal model to explore high-pressure protein-unfolding. The protein has a very low free energy as previously reported by chemical unfolding studies, suggesting that it must be easy to modulate its unfolding transition by rather mild pressure. Moreover, the protein molecule consists of only one tryptophan residue (Trp241) and eight tyrosine residues, which can be conveniently used to probe the protein conformation and structural changes under pressure using either fluorescence spectroscopy or fourth derivative UV absorbance spectroscopy. The different experimental methods used in the present study indicate that at 20 °C and pH 6, the 33-kDa protein shows a reversible two-state unfolding transition from atmospheric pressure to about 180 MPa. This value is much lower than those found for the unfolding of most proteins studied so far. The unfolding transition induces a large red shift of the maximum fluorescence emission of 34 nm (from 316 nm to 350 nm). The change in standard free energy (,Go) and in volume (,V) for the transition at pH 6.0 and 20 °C are ,14.6 kJ·mol,1 and ,120 mL·mol,1, respectively, in which the ,Go value is consistent with that obtained by chemical denaturation. We found that pressure-induced protein unfolding is promoted by elevated temperatures, which seem largely attributed to the decrease in the absolute value of ,Go (only a minor variation was observed for the ,V value). However, the promotion of the unfolding by alkaline pH seems mainly related to the increase in ,V without any significant changes in ,Go. It was also found that NaCl significantly protects the protein from pressure-induced unfolding. In the presence of 1 m NaCl, the pressure needed to induce the half-unfold of the protein is shifted to a higher value (shift of 75 MPa) in comparison with that observed without NaCl. Interestingly, in the presence of NaCl, the value of ,V is significantly reduced whilst that of ,Go remains as before. The unfolding-refolding kinetics of the protein has also been studied by pressure-jump, in which it was revealed that both reactions are a two-state transition process with a relatively slow relaxation time of about 102 s. [source] A novel NADPH-dependent oxidoreductase with a unique domain structure in the hyperthermophilic Archaeon, Thermococcus litoralisFEMS MICROBIOLOGY LETTERS, Issue 1 2008András Tóth Abstract Thermococcus litoralis, a hyperthermophilic Archaeon, is able to reduce elemental sulfur during fermentative growth. An unusual gene cluster (nsoABCD) was identified in this organism. In silico analysis suggested that three of the genes (nsoABC) probably originated from Eubacteria and one gene (nsoD) from Archaea. The putative NsoA and NsoB are similar to NuoE- and NuoF-type electron transfer proteins, respectively. NsoC has a unique domain structure and contains a GltD domain, characteristic of glutamate synthase small subunits, which seems to be integrated into a NuoG-type sequence. Flavin and NAD(P)H binding sites and conserved cysteines forming iron,sulfur clusters binding motifs were identified in the protein sequences deduced. The purified recombinant NsoC contains one FAD cofactor per protein molecule and catalyzes the reduction of polysulfide with NADPH as an electron donor and it also reduces oxygen. It was concluded that the Nso complex is a new type of NADPH-oxidizing enzyme using sulfur and/or oxygen as an electron acceptor. [source] Antibody response against NY-ESO-1 in CHP-NY-ESO-1 vaccinated patientsINTERNATIONAL JOURNAL OF CANCER, Issue 10 2007Ryohei Kawabata Abstract NY-ESO-1 specific humoral responses are frequently observed in patients with various types of NY-ESO-1 antigen expressing tumors. In a large proportion of NY-ESO-1 antibody-positive patients of NY-ESO-1-specific CD8 T-cells can also be detected suggesting that monitoring of the NY-ESO-1 specific humoral immune response may be a relevant and more practical surrogate for estimating the overall immune response against NY-ESO-1 in clinical vaccine studies. We have immunized 9 cancer patients with full length NY-ESO-1 protein formulated with cholesterol-bearing hydrophobized pullulan (CHP-NY-ESO-1) and investigated the humoral immune responses against NY-ESO-1. Seven patients were NY-ESO-1 antibody-negative and 2 patients were positive prior to vaccination. Vaccination with CHP-NY-ESO-1 resulted in the induction or increase of NY-ESO-1 antibody responses in all 9 patients immunized. Epitope analysis revealed 5 regions in the NY-ESO-1 protein molecule that were recognized by antibodies induced after vaccination. The 5 regions were also recognized by antibodies present in nonvaccinated, NY-ESO-1 antibody-positive cancer patients. A peptide spanning amino acids 91,108 was recognized in 6 out of 9 vaccinated patients and in 8 out of 9 nonvaccinated, sero-positive patients, being the most dominant antigenic epitope in NY-ESO-1 for antibody recognition in cancer patients. In conclusion, we showed that CHP-NY-ESO-1 protein vaccination had a potent activity for inducing humoral immune responses against NY-ESO-1 antigen in cancer patients. The antigenic epitopes recognized by antibodies in the vaccinated patients were similar to those recognized in cancer patients with spontaneous humoral immunity against NY-ESO-1. © 2007 Wiley-Liss, Inc. [source] Quantitative Determination of Surface Concentration of Human Apolipoprotein H with Capillary ElectrophoresisIUBMB LIFE, Issue 5 2000Shao-xiong Wang Abstract The phospholipid monolayer at an air/water interface is widely used to mimic the biological membrane. The dynamic process of the protein or peptide interacting with lipid molecules can be reflected in the change in surface pressure of the monolayer. But the conventional method used to measure the surface pressure change gives results that cannot easily be correlated with the contribution of a single protein molecule. Previously, measuring the surface concentration of the protein molecules at the air/water interface has required the protein to be labeled with radioactivity or fluorescence. Here, a new method using capillary electrophoresis is introduced to measure the surface concentration of the protein. The results show at least two advantages of the new method: The numerical results of protein concentration can be obtained in a more precise and rapid way; and there is no need to label the protein sample or to build a special monolayer setup. [source] Use of Cr K, radiation to enhance the signal from anomalous scatterers including sulfurJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 3-2 2000Witek Kwiatkowski The anomalous signals from scatterers such as sulfur (S) and arsenic (As) were compared in diffraction data sets collected from an X-ray source with three different targets, Au, Cu and Cr, on a multi-target rotating anode. HIV-1 integrase crystals served as the test case for this study. The crystalline specimen of HIV-1 integrase contains in each protein molecule two As atoms, each covalently bound to a cysteine S atom, and two additional S atoms derived from methionine. It was found that the Cr K, radiation gave the clearest peaks in anomalous difference Fourier maps, although the signal-to-noise ratios of the anomalous signal for the Cu K, and Cr K, data were similar but better than that for Au L,. This result was in spite of the fourfold higher flux from the Cu anode versus the Cr anode. For all three X-ray wavelengths, anomalous difference Fourier maps calculated with bias-removed phases derived from the known atomic model revealed clear peaks at the two As sites. However, only in the map calculated using the Cr K, data were both peaks of the expected ellipsoidal shape, enveloping the As atom and the adjacent S atom. None of the S sites was apparent in difference maps calculated using the Au L, data. The ability to enhance the S-derived anomalous signal using Cr K, radiation has particularly useful applications in the structure determination of proteins, for example in resolving ambiguities in the chain tracing of a protein with numerous disulfide bonds and in assigning amino acid identities. Additionally, anomalous difference Patterson maps calculated from the Cr K, data were sufficiently clear to identify the As-related peaks. These results form the groundwork for in-house phase determination with the multi-wavelength anomalous diffraction method. [source] Electrostatic-induced interfacial assembly of enzymes with nanosheets: Controlled orientation and optimized activityAICHE JOURNAL, Issue 10 2010Zhe An Abstract In this work, an electrostatic-induced interfacial assembly of porcine pancreatic lipase (PPL) with the nanosheets of layered double hydroxide (LDHNSs) is designed to rationally control the orientation of bound PPL. The PPL orientation in the bidimensional confinement spacing alters relying on the PPL loading, with the majority of active sites facing the LDH layer at low PPL loading and facing the adjacent protein molecule at high PPL loading. The biocatalytic activity of the bound PPL significantly depends on its orientation. Remarkable enhancement of the bio-activity has been observed when the PPL/LDHNSs mass ratio is less than 9, and a maximum activity is met with at PPL/LDHNSs = 0.5. In addition, the thermal stability of PPL-LDHNSs bioactivity has been obviously improved in comparison with soluble PPL. © 2010 American Institute of Chemical Engineers AIChE J, 2010 [source] Effect of buffer cations and of H3O+ on the charge states of native proteins.JOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 6 2003Significance to determinations of stability constants of protein complexes Abstract The progressive reduction of charge in charge states of non-denatured proteins (lysozyme, ubiquitin, and cytochrome c), observed with nanospray in the positive ion mode, when the buffer salt ammonium acetate is replaced by ethylammonium acetates (EtNH3Ac, Et2NH2Ac and Et3NHAc) is rationalized on the basis of the charge residue model (CRM). The charge states of the multiply protonated protein are shown to be controlled by the increasing gas-phase basicities, GB(B), of the bases(B) NH3, EtNH2, Et2NH and Et3N. Charge states derived from evaluated apparent gas-phase basicities GBapp of the basic side-chains of the protein and the known GB(B) of the above bases are found to be in agreement with the experimentally observed charge states. This is a requirement of the CRM, because in this model the small positive ions (the buffer cations in the present case) at the surface of the electrospray droplets are the excess ions that provide the charge of the final small droplet that contains the protein molecule and on evaporation of the solvent transfer the charge to the protein. The observed charge states in the absence of buffer salts, i.e. pure water, are attributed to excess H3O+ ions produced by the electrolysis process that attends electrospray. A proposed extended mechanism provides predictions of factors that determine the sensitivity for detection of the multiply protonated proteins. Consideration of restraints imposed by the CRM lead to some simple predictions for conditions that should be present to obtain accurate determinations by electrospray and nanospray of stability constants for the protein,complex equilibrium in aqueous solution. Copyright © 2003 John Wiley & Sons, Ltd. [source] Amino terminal interaction in the prion protein identified using fusion to green fluorescent proteinJOURNAL OF NEUROCHEMISTRY, Issue 5 2003Yongxiu Yao Abstract In contrast to the well-characterized carboxyl domain, the amino terminal half of the mature cellular prion protein has no defined structure. Here, following fusion of mouse prion protein fragments to green fluorescence protein as a reporter of protein stability, we report extreme variability in fluorescence level that is dependent on the prion fragment expressed. In particular, exposure of the extreme amino terminus in the context of a truncated prion protein molecule led to rapid degradation, whereas the loss of only six amino terminal residues rescued high level fluorescence. Study of the precise endpoints and residue identity associated with high fluorescence suggested a domain within the amino terminal half of the molecule defined by a long-range intramolecular interaction between 23KKRPKP28 and 143DWED146 and dependent upon the anti-parallel ,-sheet ending at residue 169 and normally associated with the structurally defined carboxyl terminal domain. This previously unreported interaction may be significant for understanding prion bioactivity and for structural studies aimed at the complete prion structure. [source] Formulation considerations for proteins susceptible to asparagine deamidation and aspartate isomerizationJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2006Aditya A. Wakankar Abstract The asparagine (Asn) deamidation and aspartate (Asp) isomerization reactions are nonenzymatic intra-molecular reactions occurring in peptides and proteins that are a source of major stability concern in the formulation of these biomolecules. The mechanisms for the deamidation and isomerization reactions are similar since they both proceed through an intra-molecular cyclic imide (Asu) intermediate. The formation of the Asu intermediate, which involves the attack by nitrogen of the peptide backbone on the carbonyl carbon of the Asn or the Asp side chain, is the rate-limiting step in both the deamidation and the isomerization reactions at physiological pH. In this article, the influence of factors such as formulation conditions, protein primary sequence, and protein structure on the reactivity of Asn and Asp residues in proteins are reviewed. The importance of formulation conditions such as pH and solvent dielectric in influencing deamidation and isomerization reaction rates is addressed. Formulation strategies that could improve the stability of proteins to deamidation and isomerization reactions are described. The review is intended to provide information to formulation scientists, based on protein sequence and structure, to predict potential degradative sites on a protein molecule and to enable formulation scientists to set appropriate formulation conditions to minimize reactivity of Asn and Asp residues in protein therapeutics. © 2006 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 95:2321,2336, 2006 [source] Features of the secondary structure of a protein molecule from powder diffraction dataACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Sebastian Basso Protein powder diffraction is shown to be suitable for obtaining de novo solutions to the phase problem at low resolution via phasing methods such as the isomorphous replacement method. Two heavy-atom derivatives (a gadolinium derivative and a holmium derivative) of the tetragonal form of hen egg-white lysozyme were crystallized at room temperature. Using synchrotron radiation, high-quality powder patterns were collected in which pH-induced anisotropic lattice-parameter changes were exploited in order to reduce the challenging and powder-specific problem of overlapping reflections. The phasing power of two heavy-atom derivatives in a multiple isomorphous replacement analysis enabled molecular structural information to be obtained up to approximately 5.3,Å resolution. At such a resolution, features of the secondary structure of the lysozyme molecule can be accurately located using programs dedicated to that effect. In addition, the quoted resolution is sufficient to determine the correct hand of the heavy-atom substructure which leads to an electron-density map representing the protein molecule of proper chirality. [source] Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5ACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2010Jeyaraman Jeyakanthan Asymmetric diadenosine tetraphosphate (Ap4A) hydrolases degrade the metabolite Ap4A back into ATP and AMP. The three-dimensional crystal structure of Ap4A hydrolase (16,kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95,Å resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an ,,,-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap4A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule. [source] On the routine use of soft X-rays in macromolecular crystallography.ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2007Part IV. 23 different crystal forms of 19 different biological macromolecules were examined with respect to their anomalously scattering substructures using diffraction data collected at a wavelength of 2.0,Å (6.2,keV). In more than 90% of the cases the substructure was found to contain more than just the protein S atoms. The data presented suggest that chloride, sulfate, phosphate or metal ions from the buffer or even from the purification protocol are frequently bound to the protein molecule and that these ions are often overlooked, especially if they are not bound at full occupancy. Thus, in order to fully describe the macromolecule under study, it seems desirable that any structure determination be complemented with a long-wavelength data set. [source] Away from the edge II: in-house Se-SAS phasing with chromium radiationACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2005Hao Xu Recently, the demands of high-throughput macromolecular crystallography have driven continuous improvements in phasing methods, data-collection protocols and many other technologies. Single-wavelength anomalous scattering (SAS) phasing with chromium X-ray radiation opens a new possibility for phasing a protein with data collected in-house and has led to several successful examples of de novo structure solution using only weak anomalous scatterers such as sulfur. To further reduce data-collection time and make SAS phasing more robust, it is natural to combine selenomethionine-derivatized protein (SeMet protein) with Cr,K, radiation to take advantage of the larger anomalous scattering signal from selenium ( = 2.28 e,) compared with sulfur ( = 1.14 e,). As reported herein, the crystal structure of a putative chorismate mutase from Clostridium thermocellum was determined using Se-SAS with Cr,K, radiation. Each protein molecule contains eight selenomethionine residues in 148 amino-acid residues, providing a calculated Bijvoet ratio of about 3.5% at the Cr,K, wavelength. A single data set to 2.2,Å resolution with approximately ninefold redundancy was collected using an imaging-plate detector coupled with a Cr source. Structure solution, refinement and deposition to the Protein Data Bank were performed within 9,h of the availability of the scaled diffraction data. The procedure used here is applicable to many other proteins and promises to become a routine pathway for in-house high-throughput crystallography. [source] A molecular viewer for the analysis of TLS rigid-body motion in macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Jay Painter TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement. [source] Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanicsACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2005Ning Yu A novel method is proposed in which combined restraints derived from linear-scaling semiempirical quantum-mechanical (QM) calculations and X-ray diffraction data are combined to refine crystal structures of proteins. Its performance has been tested on a small protein molecule, bovine pancreatic trypsin inhibitor (BPTI). The refinement involves minimization of the sum of a geometric energy function and an X-ray target function based on either the least-squares residual or the maximum-likelihood formalism. For comparison, similar refinement runs have also been performed using energy restraints derived from the force field available in the Crystallography & NMR System (CNS) program. The QM refinements were carried out with weights that were varied by several orders of magnitude and the optimal weights were identified by observing the trend in the final free R values, QM heats of formation and coordinate root-mean-square deviations (r.m.s.d.s) from the crystal structure. It is found that the QM weights are typically smaller but generally on the same scale as the molecular-mechanics (MM) weights for the respective X-ray target functions. The crystallographic R, free R, real-space R values and correlation coefficients based on the structures refined with the energy restraints derived from our QM calculations and Engh and Huber parameters are comparable, suggesting that the QM restraints are capable of maintaining reasonable stereochemistry to a similar degree as the force-field parameters. A detailed inspection of the structures refined with the QM and MM energy restraints reveals that one of the common differences between them and the crystal structure is that the strained bond angles in the crystal structure are corrected after energetically restrained refinements. Systematic differences in certain bond lengths between the QM-refined structures and the statistical averages of experimental structures have also been observed and discussed. [source] Crystallization and preliminary X-ray diffraction analysis of homing endonuclease I- Tsp061IACTA CRYSTALLOGRAPHICA SECTION D, Issue 11 2004Takahito Imagawa Two crystal forms, rhombohedral and hexagonal, of a homing endonuclease from Thermoproteus sp. IC-061 (I- Tsp0611) were obtained by the hanging-drop and sitting-drop method, respectively. The hexagonal crystals belong to space group P6322, with unit-cell parameters a = b = 111.4, c = 97.6,Å, and diffract to 3.2,Å resolution on beamline BL44 at SPring-8 (Harima, Japan). The rhombohedral crystals belong to space group R32, with unit-cell parameters a = b = 95.4, c = 192.9,Å, and diffract to 2.7,Å resolution using a Cu,K, rotating-anode generator with an R-AXIS VII detector. The crystal asymmetric unit contained one protein molecule and the solvent contents of the two crystal forms were estimated to be 68.3 and 67.6% by volume, respectively. [source] Cloning, purification, crystallization and preliminary crystallographic studies of Bradyrhizobium fucosyltransferase NodZACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2004Krzysztof Brzezinski The ,-1,6-fucosyltransferase NodZ from Bradyrhizobium sp. WM9 (Lupinus), composed of 325 amino acids with a molecular weight of 37,kDa, has been cloned, expressed and purified. Protein crystals suitable for X-ray diffraction were obtained under optimized crystallization conditions using ammonium dihydrogen phosphate as a precipitant. The crystals are hexagonal and belong to space group P6122 or P6522, with unit-cell parameters a = 125.5, c = 95.6,Å, and contain 56.8% solvent and a single protein molecule in the asymmetric unit. Native data were collected to 2.85,Å using synchrotron radiation and cryogenic conditions. The native crystals were soaked in a mother-liquor solution containing 2.5,mM [Ta6Br12]2+ cluster for derivatization and SAD data were collected to 3.4,Å at the tantalum LIII absorption peak. [source] Ping-pong cross-validation in real space: a method for increasing the phasing power of a partial model without risk of model biasACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2003John F. Hunt Experimental phases could only be obtained to 4.4,Å resolution for crystals of the SecA translocation ATPase. Density modification of these phases exploiting the 65% solvent content of the crystal produced a map from which an approximate backbone model could be built for 80% of the structure. Combining the phases inferred from this partial model with the MIR phases and repeating the density modification produced an improved map from which a more complete backbone model could be built. However, this procedure converged before yielding a map, that allowed unambiguous sequence assignment for the majority of the protein molecule. In order to avoid the likely model bias associated with a speculative attempt at sequence assignment, a real-space cross-validation procedure was employed to facilitate completion of the crystal structure based on partial model phasing. The protein was partitioned into two disjoint sets of residues. Models in which the side chains were built for residues in one of the two sets were used for phase combination and density modification in order to produce improved electron density for interpretation of residues in the other set that had not been included in the model. Residues in the two sets were therefore omitted from the model in alternation except at sites where the side chain could be identified definitively based on phasing with the other set. This ping-pong cross-validation procedure allowed partial model phasing to be used to complete the crystal structure of SecA without being impeded by model bias. These results show that the structure of a large protein molecule can be solved with exclusively low-resolution experimental phase information based on intensive use of partial model phasing and density modification. Real-space cross-validation can be applied to reduce the risk of model bias associated with partial model phasing, streamlining this approach and expanding its range of applicability. [source] Crystallization of agglutinin from the seeds of Abrus precatoriusACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2000Kaliyamoorthy Panneerselvam Agglutinin protein purified from the seeds of Abrus precatorius has a high antitumour activity and was crystallized at room temperature with polyethylene glycol 8000 as the precipitant. The agglutinin crystal diffracted to 3.45,Å and belongs to one of two possible tetragonal space groups, P41212 or P43212, with unit-cell parameters a = b = 141.91, c = 105.63,Å. The asymmetric unit contains a heterotetrameric protein molecule of molecular weight 134,kDa and has a solvent content of approximately 38%. [source] Cloning, purification, crystallization and preliminary crystallographic analysis of the tandem tudor domain of Sgf29 from Saccharomyces cerevisiaeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 8 2010Jing Li The protein Sgf29 has been identified as a subunit of the SAGA (Spt,Ada,Gcn5 acetyltransferase) histone acetyltransferase complex in Saccharomyces cerevisiae, which is conserved from yeast to humans. The tandem tudor domain at the C-terminus of Sgf29 was crystallized using the hanging-drop vapour-diffusion method and the crystals diffracted to 1.92,Å resolution. The crystals belonged to space group P212121, with unit-cell parameters a = 49.76, b = 95.10, c = 114.43,Å, and are estimated to contain one protein molecule per asymmetric unit. [source] Crystallization and preliminary X-ray diffraction studies of hyperthermophilic archaeal Rieske-type ferredoxin (ARF) from Sulfolobus solfataricus P1ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2010Asako Kounosu The hyperthermophilic archaeal Rieske-type [2Fe,2S] ferredoxin (ARF) from Sulfolobus solfataricus P1 contains a low-potential Rieske-type [2Fe,2S] cluster that has served as a tractable model for ligand-substitution studies on this protein family. Recombinant ARF harbouring a pET30a vector-derived N-terminal extension region plus a hexahistidine tag has been heterologously overproduced in Escherichia coli, purified and crystallized by the hanging-drop vapour-diffusion method using 0.05,M sodium acetate, 0.05,M HEPES, 2,M ammonium sulfate pH 5.5. The crystals diffracted to 1.85,Å resolution and belonged to the tetragonal space group P43212, with unit-cell parameters a = 60.72, c = 83.31,Å. The asymmetric unit contains one protein molecule. [source] Structure of a putative ,-phosphoglucomutase (TM1254) from Thermotoga maritimaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2009Richard W. Strange The structure of TM1254, a putative ,-phosphoglucomutase from T. maritima, was determined to 1.74,Å resolution in a high-throughput structural genomics programme. Diffraction data were obtained from crystals belonging to space group P22121, with unit-cell parameters a = 48.16, b = 66.70, c = 83.80,Å, and were refined to an R factor of 19.2%. The asymmetric unit contained one protein molecule which is comprised of two domains. Structural homologues were found from protein databases that confirmed a strong resemblance between TM1254 and members of the haloacid dehalogenase (HAD) hydrolase family. [source] Preliminary structural characterization of human SOUL, a haem-binding proteinACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Filipe Freire Human SOUL (hSOUL) is a 23,kDa haem-binding protein that was first identified as the PP23 protein isolated from human full-term placentas. Here, the overexpression, purification and crystallization of hSOUL are reported. The crystals belonged to space group P6422, with unit-cell parameters a = b = 145, c = 60,Å and one protein molecule in the asymmetric unit. X-ray diffraction data were collected to 3.5,Å resolution at the ESRF. A preliminary model of the three-dimensional structure of hSOUL was obtained by molecular replacement using the structures of murine p22HBP (PDB codes 2gov and 2hva), obtained by solution NMR, as search models. [source] Purification, crystallization and preliminary X-ray analysis of cytochrome P450 219A1 from Novosphingobium aromaticivorans DSM 12444ACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2009Chuan Hong Cytochrome P450 enzymes catalyze a variety of reactions and are widely distributed in living organisms. In recent studies, the first members of five new families of cytochrome P450 enzymes have been identified, including cytochrome P450 219A1 (CYP219A1) from Novosphingobium aromaticivorans DSM 12444. It has also been reported that isolongifolen-9-one (C15H22O), a sesquiterpenoid ketone derivative, is a potential substrate for CYP219A1, inducing a ,95% shift of the haem spin state to high spin upon binding. The CYP219A1 protein has been crystallized and single crystals have been studied by X-ray crystallography. Diffraction data were collected to 2.4,Å resolution. The crystals belonged to space group P6, with unit-cell parameters a = 93.1, b = 93.1, c = 98.0,Å. Preliminary X-ray diffraction data analysis revealed that the asymmetric unit contained one protein molecule. [source] The ribbon of hydrogen bonds and the pseudomolecule in the three-dimensional structure of globular proteins.BIOPOLYMERS, Issue 5 2002Abstract The model of the three-dimensional structure of globular proteins, which is based on a ribbon of hydrogen bonds along the whole of the backbone, is now applied to the comparison between monomeric bovine pancreatic ribonuclease A and dimeric bovine seminal ribonuclease. Some waters are involved in the hydrogen bonding of the ribbon, and the protein molecule plus these waters forms a pseudomolecule. The conformations of the three backbones are essentially identical and the three ribbons of hydrogen bonds are conserved with greater than 90% accuracy. We suggest that the conservation of the backbone conformations of the two molecules is a consequence of the conservation of the ribbons of hydrogen bonds. There are 16 simple mutations between the two molecules, of which 15 involve only side-chain groups with no more than one hydrogen bond to the backbone. Such mutations are not sufficient to change the ribbon of hydrogen bonds and hence there is no change in the backbone conformation. Generalizing this result, we suggest that the conservation of the ribbon is the reason why single point mutations rarely change the conformation of the backbone of the globular proteins. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 347,353, 2002 [source] | |||||||||||||||||||||||||||||||||||||||||||