RESUMO
SAXSMoW (SAXS Molecular Weight) is an online platform widely used over the past few years for determination of molecular weights of proteins in dilute solutions. The scattering intensity retrieved from small-angle X-ray scattering (SAXS) raw data is the sole input to SAXSMoW for determination of molecular weights of proteins in liquid. The current updated SAXSMoW version 3.0 determines the linear dependence of the true protein volume on their apparent protein volume, based on SAXS curves calculated for 67,000 protein structures selected from the Protein Data Bank. SAXSMoW 3.0 was tested against 43 experimental SAXS scattering curves from proteins with known molecular weights. Our results demonstrate that most of the molecular weights determined for the nonglycosylated and also for the glycosylated proteins are in good agreement with their expected molecular weights. Additionally, the average discrepancies between the calculated molecular weights and their nominal values for glycosylated proteins are similar to those for nonglycosylated ones.
Assuntos
Bases de Dados de Proteínas , Simulação de Dinâmica Molecular , Proteínas/química , Espalhamento a Baixo Ângulo , Software , Difração de Raios X , Peso MolecularRESUMO
Knowledge of molecular weight, oligomeric states, and quaternary arrangements of proteins in solution is fundamental for understanding their molecular functions and activities. We describe here a program SAXSMoW 2.0 for robust and quick determination of molecular weight and oligomeric state of proteins in dilute solution, starting from a single experimental small-angle scattering intensity curve, I(q), measured on a relative scale. The first version of this calculator has been widely used during the last decade and applied to analyze experimental SAXS data of many proteins and protein complexes. SAXSMoW 2.0 exhibits new features which allow for the direct input of experimental intensity curves and also automatic modes for quick determinations of the radius of gyration, volume, and molecular weight. The new program was extensively tested by applying it to many experimental SAXS curves downloaded from the open databases, corresponding to proteins with different shapes and molecular weights ranging from ~10 kDa up to about ~500 kDa and different shapes from globular to elongated. These tests reveal that the use of SAXSMoW 2.0 allows for determinations of molecular weights of proteins in dilute solution with a median discrepancy of about 12% for globular proteins. In case of elongated molecules, discrepancy value can be significantly higher. Our tests show discrepancies of approximately 21% for the proteins with molecular shape aspect ratios up to 18.
Assuntos
Proteínas/química , Espalhamento a Baixo Ângulo , Software , Difração de Raios X , Peso MolecularRESUMO
Biomedical magnetic colloids commonly used in magnetic hyperthermia experiments often display a bidisperse structure, i.e., are composed of stable nanoclusters coexisting with well-dispersed nanoparticles. However, the influence of nanoclusters in the optimization of colloids for heat dissipation is usually excluded. In this work, bidisperse colloids are used to analyze the effect of nanoclustering and long-range magnetic dipolar interaction on the magnetic hyperthermia efficiency. Two kinds of colloids, composed of magnetite cores with mean sizes of around 10 and 18 nm, coated with oleic acid and dispersed in hexane, and coated with meso-2,3-dimercaptosuccinic acid and dispersed in water, were analyzed. Small-angle X-ray scattering was applied to thoroughly characterize nanoparticle structuring. We proved that the magnetic hyperthermia performances of nanoclusters and single nanoparticles are distinctive. Nanoclustering acts to reduce the specific heating efficiency whereas a peak against concentration appears for the well-dispersed component. Our experiments show that the heating efficiency of a magnetic colloid can increase or decrease when dipolar interactions increase and that the colloid concentration, i.e., dipolar interaction, can be used to improve magnetic hyperthermia. We have proven that the power dissipated by an ensemble of dispersed magnetic nanoparticles becomes a nonextensive property as a direct consequence of the long-range nature of dipolar interactions. This knowledge is a key point in selecting the correct dose that has to be injected to achieve the desired outcome in intracellular magnetic hyperthermia therapy.
RESUMO
We report a synthetic approach for the production of ultra-small (0.6 nm) gold nanoparticles soluble in water with a precise control of the nanoparticle size. Our synthetic approach utilizes a pH-depending Au-cysteine polymer as a quencher for the AuNPs grown. The method extends the synthetic capabilities of nanoparticles with sizes down to 1 nm. In addition to the strict pH control, the existence of free -SH groups present in the mixture of reaction has been observed as a key requirement for the synthesis of small nanoparticles in mild conditions. UV-Vis, SAXS, XANES, EXAFS and HR-TEM, has been used to determinate the particle size, characterization of the gold precursor and gold-cysteine interaction.
Assuntos
Cisteína/química , Ouro/química , Nanopartículas Metálicas/química , Polímeros/química , Concentração de Íons de Hidrogênio , Microscopia Eletrônica de Transmissão , Tamanho da PartículaRESUMO
Polyvinylpyrollidone (PVP)-capped platinum nanoparticles (NPs) are found to change shape from spherical to flat when deposited on mesoporous silica substrates (SBA-15). Transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), and extended X-ray absorption fine structure (EXAFS) analyses are used in these studies. The SAXS results indicate that, after deposition, the 2 nm NPs have an average gyration radius 22% larger than in solution, while the EXAFS measurements indicate a decrease in first neighbor co-ordination number from 9.3 to 7.4. The deformation of these small capped NPs is attributed to interactions with the surface of the SBA-15 support, as evidenced by X-ray absorption near-edge structure (XANES).
RESUMO
ZrO(2)-10, 12 and 14 mol% Sc(2)O(3) nanopowders were prepared by using a nitrate-lysine gel-combustion synthesis. These materials were studied by synchrotron X-ray powder diffraction (SXPD) and Raman spectroscopy after calcination at different temperatures from 650 to 1200 degrees C, which led to samples with different average crystallite sizes, up to about 100 nm. The results from SXPD and Raman analyses indicate that, depending on Sc(2)O(3) content, the metastable t''-form of the tetragonal phase or the cubic phase are fully retained at room temperature in nanocrystalline powders, provided an average crystallite sizes lower than approximately 30 nm. By contrast, powders with larger average crystallite sizes exhibit the stable rhombohedral, beta and gamma, phases and do not retain or very partially retain the metastable t'' and cubic ones.
RESUMO
Interleukin-22 (IL-22) is a class 2 cytokine whose primary structure is similar to that of interleukin 10 (IL-10) and interferon-gamma (IFN-gamma). IL-22 induction during acute phase immune response indicates its involvement in mechanisms of inflammation. Structurally different from IL-10 and a number of other members of IL-10 family, which form intertwined inseparable V-shaped dimers of two identical polypeptide chains, a single polypeptide chain of IL-22 folds on itself in a relatively globular structure. Here we present evidence, based on native gel electrophoresis, glutaraldehyde cross-linking, dynamic light scattering, and small angle x-ray scattering experiments, that human IL-22 forms dimers and tetramers in solution under protein concentrations assessable by these experiments. Unexpectedly, low-resolution molecular shape of IL-22 dimers is strikingly similar to that of IL-10 and other intertwined cytokine dimeric forms. Furthermore, we determine an ab initio molecular shape of the IL-22/IL-22R1 complex which reveals the V-shaped IL-22 dimer interacting with two cognate IL-22R1 molecules. Based on this collective evidence, we argue that dimerization might be a common mechanism of all class 2 cytokines for the molecular recognition with their respective membrane receptor. We also speculate that the IL-22 tetramer formation could represent a way to store the cytokine in nonactive form at high concentrations that could be readily converted into functionally active monomers and dimers upon interaction with the cognate cellular receptors.
Assuntos
Interleucinas/química , Receptores de Interleucina/química , Sequência de Aminoácidos , Reagentes de Ligações Cruzadas/química , Citocinas/química , Citocinas/metabolismo , Dimerização , Eletroforese , Glutaral/química , Humanos , Interleucina-10/química , Interleucina-10/metabolismo , Interleucinas/metabolismo , Dados de Sequência Molecular , Receptores de Superfície Celular/química , Receptores de Superfície Celular/metabolismo , Receptores de Interleucina/metabolismo , Espalhamento de Radiação , Espalhamento a Baixo Ângulo , Difração de Raios X , Interleucina 22RESUMO
The thyroid hormone receptor (TR) D-domain links the ligand-binding domain (LBD, EF-domain) to the DNA-binding domain (DBD, C-domain), but its structure, and even its existence as a functional unit, are controversial. The D domain is poorly conserved throughout the nuclear receptor family and was originally proposed to comprise an unfolded hinge that facilitates rotation between the LBD and the DBD. Previous TR LBD structures, however, have indicated that the true unstructured region is three to six amino acid residues long and that the D-domain N terminus folds into a short amphipathic alpha-helix (H0) contiguous with the DBD and that the C terminus of the D-domain comprises H1 and H2 of the LBD. Here, we solve structures of TR-LBDs in different crystal forms and show that the N terminus of the TRalpha D-domain can adopt two structures; it can either fold into an amphipathic helix that resembles TRbeta H0 or form an unstructured loop. H0 formation requires contacts with the AF-2 coactivator-binding groove of the neighboring TR LBD, which binds H0 sequences that resemble coactivator LXXLL motifs. Structural analysis of a liganded TR LBD with small angle X-ray scattering (SAXS) suggests that AF-2/H0 interactions mediate dimerization of this protein in solution. We propose that the TR D-domain has the potential to form functionally important extensions of the DBD and LBD or unfold to permit TRs to adapt to different DNA response elements. We also show that mutations of the D domain LXXLL-like motif indeed selectively inhibit TR interactions with an inverted palindromic response element (F2) in vitro and TR activity at this response element in cell-based transfection experiments.
Assuntos
Receptores alfa dos Hormônios Tireóideos/química , Receptores alfa dos Hormônios Tireóideos/metabolismo , Receptores beta dos Hormônios Tireóideos/química , Receptores beta dos Hormônios Tireóideos/metabolismo , Motivos de Aminoácidos , DNA/metabolismo , Dimerização , Células HeLa , Humanos , Ligantes , Modelos Moleculares , Ligação Proteica , Dobramento de Proteína , Estrutura Terciária de Proteína , Elementos de Resposta/genética , Soluções , Relação Estrutura-Atividade , Tri-Iodotironina/metabolismo , Células Tumorais Cultivadas , Difração de Raios XRESUMO
The enzyme beta-xylosidase from Trichoderma reesei, a member of glycosil hydrolase family 3 (GH3), is a glycoside hydrolase which acts at the glycosidic linkages of 1,4-beta-xylooligosaccharides and that also exhibits alpha-l-arabinofuranosidase activity on 4-nitrophenyl alpha-l-arabinofuranoside. In this work, we show that the enzyme forms monomers in solution and derive the low-resolution molecular envelope of the beta-xylosidase from small-angle X-ray scattering (SAXS) data using the ab initio simulated annealing algorithm. The radius of gyration and the maximum dimension of the beta-xylosidase are 30.3 +/- 0.2 and 90 +/- 5 A, respectively. In contrast to the fold of the only two structurally characterized members of GH3, the barley beta-d-glucan exohydrolase and beta-hexosaminidase from Vibrio cholerae, which have respectively two or one distinct domains, the shape of the beta-xylosidase indicates the presence of three distinct structural modules. Domain recognition algorithms were used to show that the C-terminal part of the amino acid sequence of the protein forms the third domain. Circular dichroism spectroscopy and secondary structure prediction programs demonstrate that this additional domain adopts a predominantly beta conformation.
Assuntos
Trichoderma/enzimologia , Xilosidases/química , Algoritmos , Dicroísmo Circular , Modelos Moleculares , Conformação Proteica , Estrutura Secundária de Proteína , Espalhamento de Radiação , Soluções , Raios XRESUMO
Proteins that belong to the heat shock protein (Hsp) 40 family assist Hsp70 in many cellular functions and are important for maintaining cell viability. A knowledge of the structural and functional characteristics of the Hsp40 family is therefore essential for understanding the role of the Hsp70 chaperone system in cells. In this work, we used small angle x-ray scattering and analytical ultracentrifugation to study two representatives of human Hsp40, namely, DjA1 (Hdj2/dj2/HSDJ/Rdj1) from subfamily A and DjB4 (Hlj1/DnaJW) from subfamily B, and to determine their quaternary structure. We also constructed low resolution models for the structure of DjA1-(1-332), a C-terminal-deleted mutant of DjA1 in which dimer formation is prevented. Our results, together with the current structural information of the Hsp40 C-terminal and J-domains, were used to generate models of the internal structural organization of DjA1 and DjB4. The characteristics of these models indicated that DjA1 and DjB4 were both dimers, but with substantial differences in their quaternary structures: whereas DjA1 consisted of a compact dimer in which the N and C termini of the two monomers faced each other, DjB4 formed a dimer in which only the C termini of the two monomers were in contact. The two proteins also differed in their ability to bind unfolded luciferase. Overall, our results indicate that these representatives of subfamilies A and B of human Hsp40 have different quaternary structures and chaperone functions.
Assuntos
Proteínas de Choque Térmico/química , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Sequência de Aminoácidos , Cristalografia por Raios X , Dimerização , Proteínas de Choque Térmico HSP40 , Proteínas de Choque Térmico HSP70/química , Proteínas de Choque Térmico/genética , Proteínas de Choque Térmico/isolamento & purificação , Humanos , Modelos Moleculares , Chaperonas Moleculares/química , Chaperonas Moleculares/genética , Chaperonas Moleculares/isolamento & purificação , Dados de Sequência Molecular , Dobramento de Proteína , Alinhamento de Sequência , SoluçõesRESUMO
The mass density of proteins is a relevant basic biophysical quantity. It is also a useful input parameter, for example, for three-dimensional structure determination by protein crystallography and studies of protein oligomers in solution by analytic ultracentrifugation. We have performed a critical analysis of published, theoretical, and experimental investigations about this issue and concluded that the average density of proteins is not a constant as often assumed. For proteins with a molecular weight below 20 kDa, the average density exhibits a positive deviation that increases for decreasing molecular weight. A simple molecular-weight-depending function is proposed that provides a more accurate estimate of the average protein density.
Assuntos
Proteínas/química , Biologia Computacional/métodos , Cristalografia , Peso Molecular , Conformação Proteica , UltracentrifugaçãoRESUMO
Irradiation of teeth with lasers using specific wavelengths and energy densities produces surface melting. This effect has been already applied to different procedures such as caries prevention and hypersensitivity reduction. The aim of this study is to characterize the crystalline structure of bovine enamel after holmium laser irradiation. A holmium laser (Ho:YLF) with emission wavelength of 2065 nm was used. Enamel tissues were irradiated in ablative regime and their structures before and after irradiation were analyzed using the powder X-ray diffraction technique. The X-ray diffraction patterns of non-irradiated enamel correspond to carbonated hydroxyapatite and those produced by irradiated samples indicate the existence of a mixture of two crystalline phases: hydroxyapatite and tetracalcium phosphate. The structural characteristics of holmium irradiated enamel were compared with those of the same tissue irradiated with other lasers.
Assuntos
Esmalte Dentário/efeitos da radiação , Lasers , Animais , Fosfatos de Cálcio/análise , Bovinos , Cristalização , Esmalte Dentário/química , Durapatita/análise , Difração de Raios XRESUMO
The alpha zein, the maize storage prolamin, is a mixture of several homologous polypeptides that shows two bands in SDS-PAGE, called Z19 and Z22. The conformation studies carried out by several authors in this mixture are conflicting. To elucidate these inconsistencies, we analyzed the conformation of the Z19 fraction, extracted from BR451 maize variety by Fourier transform infrared spectroscopy, nuclear magnetic resonance, and small-angle X-ray scattering. The infrared results show that Z19 has 46% of alpha helix and 22% of beta sheet. The fast N-H to N-D exchange measured by (1)H NMR spectroscopy showed that Z19 is not a compact structure. The scattering measurements indicated an extended structure with 12 by 130 A. With these data, we have modeled the Z19 structure as a hairpin, composed of helical, sheet, turns, and secondary structures, folded back on itself.
Assuntos
Conformação Proteica , Zea mays/química , Zeína/química , Espectroscopia de Ressonância Magnética , Espalhamento de Radiação , Espectroscopia de Infravermelho com Transformada de Fourier , Raios XRESUMO
The co-chaperone GrpE is essential for the activities of the Hsp70 system, which assists protein folding. GrpE is present in several organisms, and characterization of homologous GrpEs is important for developing structure-function relationships. Cloning, producing, and conformational studies of the recombinant human mitochondrial GrpE are reported here. Circular dichroism measurements demonstrate that the purified protein is folded. Thermal unfolding of human GrpE measured both by circular dichroism and differential scanning calorimetry differs from that of prokaryotic GrpE. Analytical ultracentrifugation data indicate that human GrpE is a dimer, and the sedimentation coefficient agrees with an elongated shape model. Small angle x-ray scattering analysis shows that the protein possesses an elongated shape in solution and demonstrates that its envelope, determined by an ab initio method, is similar to the high resolution envelope of Escherichia coli GrpE bound to DnaK obtained from single crystal x-ray diffraction. However, in these conditions, the E. coli GrpE dimer is asymmetric because the monomer that binds DnaK adopts an open conformation. It is of considerable importance for structural GrpE research to answer the question of whether the GrpE dimer is only asymmetric while bound to DnaK or also as a free dimer in solution. The low resolution structure of human GrpE presented here suggests that GrpE is a symmetric dimer when not bound to DnaK. This information is important for understanding the conformational changes GrpE undergoes on binding to DnaK.
Assuntos
Proteínas de Choque Térmico/química , Mitocôndrias/química , Chaperonas Moleculares , Sequência de Aminoácidos , Sequência de Bases , Varredura Diferencial de Calorimetria , Dicroísmo Circular , Clonagem Molecular , Simulação por Computador , Primers do DNA , Dimerização , Humanos , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Conformação Proteica , Dobramento de Proteína , Proteínas Recombinantes/química , Alinhamento de Sequência , Homologia de Sequência de Aminoácidos , Soluções , Termodinâmica , Difração de Raios XRESUMO
The binding of MgATP and fructose-6-phosphate to phosphofructokinase-2 from Escherichia coli induces conformational changes that result in significant differences in the x-ray-scattering profiles compared with the unligated form of the enzyme. When fructose- 6-phosphate binds to the active site of the enzyme, the pair distribution function exhibits lower values at higher distances, indicating a more compact structure. Upon binding of MgATP to the allosteric site of the enzyme, the intensity at lower angles increases as a consequence of tetramer formation, but differences along higher angles also suggest changes at the tertiary structure level. We have used homology modeling to build the native dimeric form of phosphofructokinase-2 and fitted the experimental scattering curves by using rigid body movements of the domains in the model, similar to those observed in known homologous structures. The best fit with the experimental data of the unbound protein was achieved with open conformations of the domains in the model, whereas domain closure improves the agreement with the scattering of the enzyme-fructose-6-phosphate complex. Using the same approach, we utilized the scattering curve of the phosphofructokinase-2-MgATP complex to model the arrangement and conformation of dimers in the tetramer. We observed that, along with tetramerization, binding of MgATP to the allosteric site induces domain closure. Additionally, we used the scattering data to restore the low resolution structure of phosphofructokinase-2 (free and bound forms) by an ab initio procedure. Based on these findings, a proposal is made to account for the inhibitory effect of MgATP on the enzymatic activity.
Assuntos
Escherichia coli/enzimologia , Fosfofrutoquinase-2/química , Estrutura Quaternária de Proteína , Ligantes , Modelos Moleculares , Fosfofrutoquinase-2/isolamento & purificação , Fosfofrutoquinase-2/metabolismo , Conformação Proteica , Estrutura Secundária de Proteína , Soluções , Difração de Raios XRESUMO
A molecular envelope of the beta-mannosidase from Trichoderma reesei has been obtained by combined use of solution small-angle X-ray scattering (SAXS) and protein crystallography. Crystallographic data at 4 A resolution have been used to enhance informational content of the SAXS data and to obtain an independent, more detailed protein shape. The phased molecular replacement technique using a low resolution SAXS model, building, and refinement of a free atom model has been employed successfully. The SAXS and crystallographic free atom models exhibit a similar globular form and were used to assess available crystallographic models of glycosyl hydrolases. The structure of the beta-galactosidase, a member of a family 2, clan GHA glycosyl hydrolases, shows an excellent fit to the experimental molecular envelope and distance distribution function of the beta-mannosidase, indicating gross similarities in their three-dimensional structures. The secondary structure of beta-mannosidase quantified by circular dichroism measurements is in a good agreement with that of beta-galactosidase. We show that a comparison of distance distribution functions in combination with 1D and 2D sequence alignment techniques was able to restrict the number of possible structurally homologous proteins. The method could be applied as a general method in structural genomics and related fields once protein solution scattering data are available.