共查询到20条相似文献，搜索用时 15 毫秒
1.
Ravi Raghav Sonani Mahima Sharma Gagan Deep Gupta Vinay Kumar Datta Madamwar 《Acta Crystallographica. Section F, Structural Biology Communications》2015,71(8):998-1004
The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting‐drop vapour‐diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus‐2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit‐cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular‐replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular‐sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher‐order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. 相似文献
2.
Wojciech Strzalka Takuji Oyama Kazuo Tori Kosuke Morikawa 《Protein science : a publication of the Protein Society》2009,18(5):1072-1080
The proliferating cell nuclear antigen (PCNA) is well recognized as one of the essential cellular components of the DNA replication machinery in all eukaryotic organisms. Despite their prominent importance, very little biochemical and structural information about plant PCNAs is available, in comparison with that obtained from other eukaryotic organisms. We have determined the atomic resolution crystal structures of the two distinct Arabidopsis thaliana PCNAs (AtPCNA), both complexed with the C‐terminal segment of human p21. Both AtPCNAs form homotrimeric ring structures, which are essentially identical to each other, including the major contacts with the p21 peptide. The structure of the amino‐terminal half of the p21 peptide, containing the typical PIP box sequence, is remarkably similar to those observed in the previously reported crystal structures of the human and archaeal PCNA‐PIP box complexes. Meanwhile, the carboxy‐terminal halves of the p21 peptide in the plant PCNA complexes are bound to the protein in a unique manner, most probably because of crystal packing effects. A surface plasmon resonance analysis revealed high affinity between each AtPCNA and the C‐terminal fragment of human p21. This result strongly suggests that the interaction is functionally significant, although no plant homologs of p21 have been identified yet. We also discovered that AtPCNA1 and AtPCNA2 form heterotrimers, implying that hetero‐PCNA rings may play critical roles in cellular signal transduction, particularly in DNA repair. 相似文献
3.
The X-ray crystallographic structure of a thioredoxin from Thermus thermophilus was solved to 1.8 A resolution by molecular replacement. The crystals' space group was C2 with cell dimensions of a = 40.91, b = 95.44, c = 56.68 A, beta =91.41 degrees, with two molecules in the asymmetric unit. Unlike the reported thioredoxin structures, the biological unit of T. thermophilus thioredoxin is a dimer both in solution and in the crystal. The fold conforms to the \"thioredoxin fold\" that is common over a class of nine protein families including thioredoxin; however, the folded portion of this protein is much more compact than other thioredoxins previously solved by X-ray crystallography being reduced by one alpha-helix and one beta-strand. As with other thioredoxins, the active site is highly conserved even though the variation in sequence can be quite large. The T. thermophilus thioredoxin has some variability at the active site, especially compared with previously solved structures from bacterial sources. 相似文献
4.
Constantinos D. Antoniadis Emiliana D'Oria Panagiotis G. Karamertzanis Derek A. Tocher Alastair J. Florence Sarah L. Price Alan G. Jones 《Chirality》2010,22(4):447-455
Following the computation of a lattice energy landscape which predicted that there should be more stable, denser forms of (R)‐1‐phenylethylammonium‐(S)‐2‐phenylbutyrate, crystallizations from a range of solvents were performed to search for other polymorphs and investigate the possibility that the known P41 structure could be a hydrate. Extensive crystallization experiments from a wide range of solvents gave fine needles or microcrystalline samples. A redetermination of the P41 structure by powder X‐ray diffraction located all protons, and in conjunction with other experimental and computational evidence showed that the structure was anhydrous. Evidence for two additional forms was found as mixtures with form I. These include an orthorhombic form, possibly a Z′ = 3 polymorph, and another as yet unidentified form obtained as a minor component from dichloromethane solution. However, both these forms appear to be metastable with respect to form I (P41), which is therefore probably the most thermodynamically stable form that can be crystallized from solution under ambient conditions. This determination of the solid state behavior of the less readily crystallized member of the diastereomeric salt system (R)‐1‐phenylethylammonium‐(R/S)‐2‐phenylbutyrate provides a challenge to the theoretical modeling to explain its ideal resolution behavior. Chirality 2010. © 2009 Wiley‐Liss, Inc. 相似文献
5.
Ajay D Parkhe Sharon J Cooper Edward D.T Atkins Maurille J Fournier Thomas L Mason David A Tirrell 《International journal of biological macromolecules》1998,23(4):251-258
The crystal structure and texture of the monodisperse periodic polypeptide [(AG)3EG(GA)3EG]10 (poly(±AG)3EG; A=alanine, G=glycine, E=glutamic acid) were analyzed by X-ray diffraction, Fourier transform infrared spectroscopy, and electron microscopy. Structure determination was aided by comparison with the recently described structure for the related periodic polypeptide [(AG)3EG]36 by Krejchi et al. (Macromolecules 1997;30:5012). Texture-oriented samples of poly(±AG)3EG were obtained by crystallization of the polymer from aqueous formic acid solution. The evidence supports an antiparallel (ap) β-sheet protein structure and the X-ray diffraction signals index on an orthorhombic unit cell with parameters: a=0.950 nm (hydrogen-bond direction), b=1.052 nm (apβ-sheet stacking direction), c=6.95 nm (chain direction). The absence of the (010) diffraction signal, a prominent signal in the poly(AG)3EG diffraction pattern, implies that the apβ-sheets are ‘apolar', i.e. both surfaces are equally populated with alanyl methyl groups. Selective line broadening of wide-angle diffraction signals with ℓ≠0 gives an estimated crystal size of 4 nm in the chain direction. This observation, coupled with the appearance of low-angle particle interference peaks, indicates a crystal thickness considerably less than the chain length and suggests an adjacent-re-entry chain-folded lamellar structure incorporating the apβ-sheet architecture. The polypeptide folds through γ-turns, in-phase with the pseudo-octapeptide repeat; the glutamic acid residues occur on the lamellar surfaces. These results and those from the crystalline lamellae of poly(AG)3EG suggest that β-turns are not compatible with these repetitively stacked apβ-sheet structures. This implies that intersheet interactions of alanyl methyl groups and glycyl -protons are not sufficiently strong to dictate the folding geometry in these structures. 相似文献
6.
L. Zhang M. R. Liu Y. C. Yao I. K. Bostrom Y. D. Wang A. Q. Chen J. X. Li S. H. Gu C. N. Ji 《Acta Crystallographica. Section F, Structural Biology Communications》2020,76(9):406-413
Glyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is a key enzyme in the glycolytic pathway that catalyzes the conversion of d ‐glyceraldehyde 3‐phosphate to 1,3‐diphosphoglycerate. Here, the full‐length GAPDH type 1 from Escherichia coli (EcGAPDH1) was cloned and overexpressed, and the protein was purified. Biochemical analyses found that the optimum reaction temperature and pH of EcGAPDH1 were 55°C and 10.0, respectively. The protein has a certain amount of thermostability. Crystals of EcGAPDH1 were obtained using the sitting‐drop vapor‐diffusion technique and X‐ray diffraction data were collected to 1.88 Å resolution. Characterization of the crystals showed that they belonged to space group P41212, with unit‐cell parameters a = b = 89.651, c = 341.007 Å, α = β = γ = 90°. The structure of EcGAPDH1 contains four subunits, each of which includes an N‐terminal NAD+‐binding domain and a C‐terminal catalytic domain. Analysis of the NAD+‐bound form showed some differences between the structures of EcGAPDH1 and human GAPDH. As EcGAPDH1 shares 100% identity with GAPDH from Shigella sonnei, its structure may help in finding a drug for the treatment of shigellosis. 相似文献
7.
Jabeen T Singh N Singh RK Jasti J Sharma S Kaur P Srinivasan A Singh TP 《Proteins》2006,62(2):329-337
The crystal structure of the phospholipase A2 (PLA2) heterodimer from Naja naja sagittifera reveals the presence of a new PLA2-like protein with eight disulphide bridges. The heterodimer is formed between a commonly observed group I PLA2 having seven characteristic disulfide bonds and a novel PLA2-like protein (Cys-PLA2) containing two extra cysteines at two highly conserved sites (positions 32 and 49) of structural and functional importance. The crystals of the heterodimer belong to tetragonal space group P41212 with cell dimensions, a = b = 77.7 A and c = 68.4 A corresponding to a solvent content of 33%, which is one of the lowest values observed so far in the PLA2 crystals. The structure has been solved with molecular replacement method and refined to a final R value of 21.6% [Rfree = 25.6%]. The electron density revealed the presence of cysteines 32 and 49 that are covalently linked to give rise to an eighth disulphide bridge in the PLA2-like monomer. A non-protein high-quality electron density was also observed at the substrate-binding site in the PLA2-like protein that has been interpreted as N-acetylglucosamine. The overall tertiary folds of the two monomers are similar having all features of PLA2-type folding. A zinc ion is detected at the interface of the heterodimer with fivefold coordination while another zinc ion was found on the surface of Cys-PLA2 with sixfold coordination. The conformations of the calcium-binding loops of both monomers are significantly different from each other as well as from those in other group I PLA2s. The N-acetylglucosamine molecule is favorably placed in the substrate-binding site of Cys-PLA2 and forms five hydrogen bonds and several van der Waals interactions with protein atoms, thus indicating a strong affinity. It also provides clue of the possible mechanism of sugar recognition by PLA2 and PLA2-like proteins. The formation of heterodimer seems to have been induced by zinc ion. 相似文献
8.
《Acta Crystallographica. Section F, Structural Biology Communications》2017,73(10):574-578
A microfluidic platform was used to address the problems of obtaining diffraction‐quality crystals and crystal handling during transfer to the X‐ray diffractometer. Crystallization conditions of a protein of pharmaceutical interest were optimized and X‐ray data were collected both in situ and ex situ . 相似文献
9.
10.
Das A Fu ZQ Tempel W Liu ZJ Chang J Chen L Lee D Zhou W Xu H Shaw N Rose JP Ljungdahl LG Wang BC 《Proteins》2007,67(1):167-176
The strict anaerobic, thermophilic bacterium Moorella thermoacetica metabolizes C1 compounds for example CO(2)/H(2), CO, formate, and methanol into acetate via the Wood/Ljungdahl pathway. Some of the key steps in this pathway include the metabolism of the C1 compounds into the methyl group of methylenetetrahydrofolate (MTHF) and the transfer of the methyl group from MTHF to the methyl group of acetyl-CoA catalyzed by methyltransferase, corrinoid protein and CO dehydrogenase/acetyl CoA synthase. Recently, we reported the crystallization of a 25 kDa methanol-induced corrinoid protein from M. thermoacetica (Zhou et al., Acta Crystallogr F 2005; 61:537-540). In this study we analyzed the crystal structure of the 25 kDa protein and provide genetic and biochemical evidences supporting its role in the methanol metabolism of M. thermoacetia. The 25 kDa protein was encoded by orf1948 of contig 303 in the M. thermoacetica genome. It resembles similarity to MtaC the corrinoid protein of the methanol:CoM methyltransferase system of methane producing archaea. The latter enzyme system also contains two additional enzymes MtaA and MtaB. Homologs of MtaA and MtaB were found to be encoded by orf2632 of contig 303 and orf1949 of contig 309, respectively, in the M. thermoacetica genome. The orf1948 and orf1949 were co-transcribed from a single polycistronic operon. Metal analysis and spectroscopic data confirmed the presence of cobalt and the corrinoid in the purified 25 kDa protein. High resolution X-ray crystal structure of the purified 25 kDa protein revealed corrinoid as methylcobalamin with the imidazole of histidine as the alpha-axial ligand replacing benziimidazole, suggesting base-off configuration for the corrinoid. Methanol significantly activated the expression of the 25 kDa protein. Cyanide and nitrate inhibited methanol metabolism and suppressed the level of the 25 kDa protein. The results suggest a role of the 25 kDa protein in the methanol metabolism of M. thermoacetica. 相似文献
11.
Operando X‐ray diffraction (XRD) and X‐ray absorption spectroscopy (XAS) studies of Ge anodes are carried out to understand the effect of cycling rate on Ge phase transformation during charge/discharge process and to relate that effect to capacity. It is discovered that the formation of crystalline Li15Ge4 (c‐Li15Ge4) during lithiation is suppressed beyond a certain cycling rate. A very stable and reversible high capacity of ≈1800 mAh g?1 can be attained up to 100 cycles at a slow C‐rate of C/21 when there is complete conversion of Ge anode into c‐Li15Ge4. When the C‐rate is increased to ≈C/10, the lithiation reaction is more heterogeneous and a relatively high capacity of ≈1000 mAh g?1 is achieved with poorer electrochemical reversibility. An increase in C‐rate to C/5 and higher reduces the capacity (≈500 mAh g?1) due to an impeded transformation from amorphous LixGe to c‐Li15Ge4, and yet improves the electrochemical reversibility. A proposed mechanism is presented to explain the C‐rate dependent phase transformations and the relationship of these to capacity fading. The operando XRD and XAS results provide new insights into the relationship between structural changes in Ge and battery capacity, which are important for guiding better design of high‐capacity anodes. 相似文献
12.
Juan Sanchez‐Weatherby Matthew W. Bowler Julien Huet Alexandre Gobbo Franck Felisaz Bernard Lavault Raphael Moya Jan Kadlec Raimond B. G. Ravelli Florent Cipriani 《Acta Crystallographica. Section D, Structural Biology》2009,65(12):1237-1246
Dehydration of protein crystals is rarely used, despite being a post‐crystallization method that is useful for the improvement of crystal diffraction properties, as it is difficult to reproduce and monitor. A novel device for hydration control of macromolecular crystals in a standard data‐collection environment has been developed. The device delivers an air stream of precise relative humidity that can be used to alter the amount of water in macromolecular crystals. The device can be rapidly installed and is fully compatible with most standard synchrotron X‐ray beamlines. Samples are mounted in cryoloops and the progress of dehydration can be monitored both optically and by the acquisition of diffraction images. Once the optimal hydration level has been obtained, cryocooling is easy to achieve by hand or by using a sample changer. The device has been thoroughly tested on several ESRF beamlines and is available to users. 相似文献
13.
Ha S Walker D Shi Y Walker S 《Protein science : a publication of the Protein Society》2000,9(6):1045-1052
The 1.9 A X-ray structure of a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis is reported. This enzyme, MurG, contains two alpha/beta open sheet domains separated by a deep cleft. Structural analysis suggests that the C-terminal domain contains the UDP-GlcNAc binding site while the N-terminal domain contains the acceptor binding site and likely membrane association site. Combined with sequence data from other MurG homologs, this structure provides insight into the residues that are important in substrate binding and catalysis. We have also noted that a conserved region found in many UDP-sugar transferases maps to a beta/alpha/beta/alpha supersecondary structural motif in the donor binding region of MurG, an observation that may be helpful in glycosyltransferase structure prediction. The identification of a conserved structural motif involved in donor binding in different UDP-sugar transferases also suggests that it may be possible to identify--and perhaps alter--the residues that help determine donor specificity. 相似文献
14.
Sterling Cornaby Doletha M. E. Szebenyi Detlef‐M. Smilgies David J. Schuller Richard Gillilan Quan Hao Donald H. Bilderback 《Acta Crystallographica. Section D, Structural Biology》2010,66(1):2-11
Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Laue technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a `pink' beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single‐shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used. 相似文献
15.
Benjamin L. Williams Jonathan D. Major Leon Bowen Wytze Keuning Mariadriana Creatore Ken Durose 《Liver Transplantation》2015,5(21)
This work presents the first systematic comparison of the effects of a range of chlorides (CdCl2, MgCl2, NaCl, and NH4Cl) on the microstructure and chemical composition of CdTe/CdS/ZnO/SnO2 solar cells, providing valuable insight to the ubiquitous Cl‐activation process. Using X‐ray diffraction, it is shown that CdCl2 induces the greatest extent of recrystallization (standard deviation of texture coefficients, σ, reduces from 0.93 for as‐grown CdTe to 0.43) and minimizing stress (from 178 MPa for as‐grown material to zero). MgCl2 treatment also yields significant randomization of the CdTe texture (σ = 0.55) but NaCl treatment does not (σ = 1.10). A strong correlation between the extent of metallurgical changes induced by the chloride treatment (and consequently, device efficiency) and the dissociation energy of the cationCl bond is shown, thereby accounting for the ineffectiveness of NaCl (bond energy = 4.3 eV). From this, a mechanism for Cl activation is postulated. By X‐ray photoelectron spectroscopy it is also shown that the Te/Cd ratio at the back surface, and the Cl content at the CdTe–CdS interface, are both higher following CdCl2‐ and MgCl2 treatments (Te/Cd = 1.3–1.4, and 1–2 at% Cl) than following NaCl treatment (Te/Cd = 1.1, and 0 at% Cl). 相似文献
16.
17.
Glutaraldehyde has been used for several decades as an effective crosslinking agent for many applications including sample fixation for microscopy, enzyme and cell immobilization, and stabilization of protein crystals. Despite of its common use as a crosslinking agent, the mechanism and chemistry involved in glutaraldehyde crosslinking reaction is not yet fully understood. Here we describe feasibility study and results obtained from a new approach to investigate the process of protein crystals stabilization by glutaraldehyde crosslinking. It involves exposure of a model protein crystal (Lysozyme) to glutaraldehyde in alkaline or acidic pH for different incubation periods and reaction arrest by medium exchange with crystallization medium to remove unbound glutaraldehyde. The crystals were subsequently incubated in diluted buffer affecting dissolution of un-crosslinked crystals. Samples from the resulting solution were subjected to protein composition analysis by gel electrophoresis and mass spectroscopy while crosslinked, dissolution resistant crystals were subjected to high resolution X-ray structural analysis. Data from gel electrophoresis indicated that the crosslinking process starts at specific preferable crosslinking site by lysozyme dimer formation, for both acidic and alkaline pH values. These dimer formations were followed by trimer and tetramer formations leading eventually to dissolution resistant crystals. The crosslinking initiation site and the end products obtained from glutaraldehyde crosslinking in both pH ranges resulted from reactions between lysine residues of neighboring protein molecules and the polymeric form of glutaraldehyde. Reaction rate was much faster at alkaline pH. Different reaction end products, indicating different reaction mechanisms, were identified for crosslinking taking place under alkaline or acidic conditions. 相似文献
18.
Wall JS Gupta V Wilkerson M Schell M Loris R Adams P Solomon A Stevens F Dealwis C 《Journal of molecular recognition : JMR》2004,17(4):323-331
Primary (AL) amyloidosis results from the pathologic deposition of monoclonal light chains as amyloid fibrils. Studies of recombinant-derived variable region (VL) fragments of these proteins have shown an inverse relationship between thermodynamic stability and fibrillogenic potential. Further, ionic interactions within the VL domain were predicted to influence the kinetics of light chain fibrillogenicity, as evidenced from our analyses of a relatively stable Vlambda6 protein (Jto) with a long range electrostatic interaction between Asp and Arg side chains at position 29 and 68, respectively, and an unstable, highly fibrillogenic Vlambda6 protein (Wil) that had neutral amino acids at these locations. To test this hypothesis, we have generated two Jto-related mutants designed to disrupt the interaction between Asp 29 and Arg 68 (JtoD29A and JtoR68S). Although the thermodynamic stabilities of unfolding for these two molecules were identical, they exhibited very different kinetics of fibril formation: the rate of JtoD29A fibrillogenesis was slow and comparable to the parent molecule, whereas that of JtoR68S was significantly faster. High-resolution X-ray diffraction analyses of crystals prepared from the two mutants having the same space group and unit cell dimensions revealed no significant main-chain conformational changes. However, several notable side-chain alterations were observed in JtoR68S, as compared with JtoD29A, that resulted in the solvent exposure of a greater hydrophobic surface and modifications in the electrostatic potential surface. We posit that these differences contributed to the enhanced fibrillogenic potential of the Arg 68 mutant, since both Jto mutants lacked the intrachain ionic interaction and were equivalently unstable. The information gleaned from our studies has provided insight into structural parameters that in addition to overall thermodynamic stability, contribute to the fibril forming propensity of immunoglobulin light chains. 相似文献
19.
The present paper describes the synthesis of cerium‐doped barium magnesium aluminate phosphor by combustion method. The crystal structure of synthesized phosphor belongs to the P63/mmc space group and is related to the β‐alumina structure. The photoluminescence emission spectra exhibited a broad peak centered at 440 nm showing the Ce3+ emission. The thermoluminescence properties of phosphors under ultraviolet irradiation were investigated. The activation energy was calculated by Chen's empirical method. Fracto‐mechanoluminescence properties were also investigated. The phosphor showed mechanoluminescence (ML) properties without irradiation and the ML intensity increased linearly with the impact height of the moving piston. Therefore this compound may have a use as a damage sensor. Copyright © 2016 John Wiley & Sons, Ltd. 相似文献
20.
《Acta Crystallographica. Section D, Structural Biology》2018,74(5):411-421
Real macromolecular crystals can be non‐ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X‐ray synchrotron beam was used to collect a series of 18 separate data sets from non‐overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit‐cell variations between the members of the two groups. This categorization mapped the different data‐set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal‐mode molecular‐dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure‐factor data ultimately obtained in X‐ray diffraction experiments. 相似文献