共查询到20条相似文献，搜索用时 15 毫秒
1.
P Therese Lang Ho-Leung Ng James S Fraser Jacob E Corn Nathaniel Echols Mark Sales James M Holton Tom Alber 《Protein science : a publication of the Protein Society》2010,19(7):1420-1431
Although proteins populate large structural ensembles, X-ray diffraction data are traditionally interpreted using a single model. To search for evidence of alternate conformers, we developed a program, Ringer, which systematically samples electron density around the dihedral angles of protein side chains. In a diverse set of 402 structures, Ringer identified weak, nonrandom electron-density features that suggest of the presence of hidden, lowly populated conformations for >18% of uniquely modeled residues. Although these peaks occur at electron-density levels traditionally regarded as noise, statistically significant (P < 10−5) enrichment of peaks at successive rotameric χ angles validates the assignment of these features as unmodeled conformations. Weak electron density corresponding to alternate rotamers also was detected in an accurate electron density map free of model bias. Ringer analysis of the high-resolution structures of free and peptide-bound calmodulin identified shifts in ensembles and connected the alternate conformations to ligand recognition. These results show that the signal in high-resolution electron density maps extends below the traditional 1 σ cutoff, and crystalline proteins are more polymorphic than current crystallographic models. Ringer provides an objective, systematic method to identify previously undiscovered alternate conformations that can mediate protein folding and function. 相似文献
2.
Voronov-Goldman M Lamed R Noach I Borovok I Kwiat M Rosenheck S Shimon LJ Bayer EA Frolow F 《Proteins》2011,79(1):50-60
3.
R. L. Dunbrack Jr F. E. Cohen 《Protein science : a publication of the Protein Society》1997,6(8):1661-1681
We present a Bayesian statistical analysis of the conformations of side chains in proteins from the Protein Data Bank. This is an extension of the backbone-dependent rotamer library, and includes rotamer populations and average chi angles for a full range of phi, psi values. The Bayesian analysis used here provides a rigorous statistical method for taking account of varying amounts of data. Bayesian statistics requires the assumption of a prior distribution for parameters over their range of possible values. This prior distribution can be derived from previous data or from pooling some of the present data. The prior distribution is combined with the data to form the posterior distribution, which is a compromise between the prior distribution and the data. For the chi 2, chi 3, and chi 4 rotamer prior distributions, we assume that the probability of each rotamer type is dependent only on the previous chi rotamer in the chain. For the backbone-dependence of the chi 1 rotamers, we derive prior distributions from the product of the phi-dependent and psi-dependent probabilities. Molecular mechanics calculations with the CHARMM22 potential show a strong similarity with the experimental distributions, indicating that proteins attain their lowest energy rotamers with respect to local backbone-side-chain interactions. The new library is suitable for use in homology modeling, protein folding simulations, and the refinement of X-ray and NMR structures. 相似文献
4.
Akifumi Higashiura Takeshi Kurakane Makoto Matsuda Mamoru Suzuki Koji Inaka Masaru Sato Tomoyuki Kobayashi Tetsuo Tanaka Hiroaki Tanaka Kazuko Fujiwara Atsushi Nakagawa 《Acta Crystallographica. Section D, Structural Biology》2010,66(6):698-708
Recent technical improvements in macromolecular X‐ray crystallography have significantly improved the resolution limit of protein structures. However, examples of high‐resolution structure determination are still limited. In this study, the X‐ray crystal structure of bovine H‐protein, a component of the glycine cleavage system, was determined at 0.88 Å resolution. This is the first ultrahigh‐resolution structure of an H‐protein. The data were collected using synchrotron radiation. Because of limitations of the hardware, especially the dynamic range of the CCD detector, three data sets (high‐, medium‐ and low‐resolution data sets) were measured in order to obtain a complete set of data. To improve the quality of the merged data, the reference data set was optimized for merging and the merged data were assessed by comparing merging statistics and R factors against the final model and the number of visualized H atoms. In addition, the advantages of merging three data sets were evaluated. The omission of low‐resolution reflections had an adverse effect on visualization of H atoms in hydrogen‐omit maps. Visualization of hydrogen electron density is a good indicator for assessing the quality of high‐resolution X‐ray diffraction data. 相似文献
5.
Karin E. van Straaten Claudio F. Gonzalez Ricardo B. Valladares Xiaohui Xu Alexei V. Savchenko David A. R. Sanders 《Protein science : a publication of the Protein Society》2009,18(10):2196-2202
The structure of the Atu1476 protein from Agrobacterium tumefaciens was determined at 2 Å resolution. The crystal structure and biochemical characterization of this enzyme support the conclusion that this protein is an S-formylglutathione hydrolase (AtuSFGH). The three-dimensional structure of AtuSFGH contains the α/β hydrolase fold topology and exists as a homo-dimer. Contacts between the two monomers in the dimer are formed both by hydrogen bonds and salt bridges. Biochemical characterization reveals that AtuSFGH hydrolyzes C—O bonds with high affinity toward short to medium chain esters, unlike the other known SFGHs which have greater affinity toward shorter chained esters. A potential role for Cys54 in regulation of enzyme activity through S-glutathionylation is also proposed. 相似文献
6.
Mostafa H. Ahmed Vishal N. Koparde Martin K. Safo J. Neel Scarsdale Glen E. Kellogg 《Proteins》2015,83(6):1118-1136
Sidechain rotamer libraries are obtained through exhaustive statistical analysis of existing crystallographic structures of proteins and have been applied in multiple aspects of structural biology, for example, crystallography of relatively low‐resolution structures, in homology model building and in biomolecular NMR. Little is known, however, about the driving forces that lead to the preference or suitability of one rotamer over another. Construction of 3D hydropathic interaction maps for nearly 30,000 tyrosines reveals the environment around each, in terms of hydrophobic (π–π stacking, etc.) and polar (hydrogen bonding, etc.) interactions. After partitioning the tyrosines into backbone‐dependent (?, ψ) bins, a map similarity metric based on the correlation coefficient was applied to each map‐map pair to build matrices suitable for clustering with k‐means. The first bin (?200° ≤ ? < –155°; ?205° ≤ ψ < –160°), representing 631 tyrosines, reduced to 14 unique hydropathic environments, with most diversity arising from favorable hydrophobic interactions with many different residue partner types. Polar interactions for tyrosine include surprisingly ubiquitous hydrogen bonding with the phenolic OH and a handful of unique environments surrounding the tyrosine backbone. The memberships of all but one of the 14 environments are dominated (>50%) by a single χ1/χ2 rotamer. The last environment has weak or no interactions with the tyrosine ring and its χ1/χ2 rotamer is indeterminate, which is consistent with it being composed of mostly surface residues. Each tyrosine residue attempts to fulfill its hydropathic valence and thus, structural water molecules are seen in a variety of roles throughout protein structure. Proteins 2015; 83:1118–1136. © 2015 Wiley Periodicals, Inc. 相似文献
7.
John H. Beale 《Acta Crystallographica. Section D, Structural Biology》2020,76(5):400-405
The number of new X‐ray crystallography‐based submissions to the Protein Data Bank appears to be at the beginning of a decline, perhaps signalling an end to the era of the dominance of X‐ray crystallography within structural biology. This letter, from the viewpoint of a young structural biologist, applies the Copernican method to the life expectancy of crystallography and asks whether the technique is still the mainstay of structural biology. A study of the rate of Protein Data Bank depositions allows a more nuanced analysis of the fortunes of macromolecular X‐ray crystallography and shows that cryo‐electron microscopy might now be outcompeting crystallography for new labour and talent, perhaps heralding a change in the landscape of the field. 相似文献
8.
The 2.1-A resolution crystal structure of the MATalpha2 homeodomain bound to DNA reveals the unexpected presence of two nonspecifically bound alpha2 homeodomains, in addition to the two alpha2 homeodomains bound to canonical alpha2 binding sites. One of the extra homeodomains makes few base-specific contacts, while the other extra homeodomain binds to DNA in a previously unobserved manner. This unusually bound homeodomain is rotated on the DNA, making possible major groove contacts by side-chains that normally do not contact the DNA. This alternate docking may represent one way in which homeodomains sample nonspecific DNA sequences. 相似文献
9.
We determined the three-dimensional (3D) crystal structure of protein TM841, a protein product from a hypothetical open-reading frame in the genome of the hyperthermophile bacterium Thermotoga maritima, to 2.0 A resolution. The protein belongs to a large protein family, DegV or COG1307 of unknown function. The 35 kDa protein consists of two separate domains, with low-level structural resemblance to domains from other proteins with known 3D structures. These structural homologies, however, provided no clues for the function of TM841. But the electron density maps revealed clear density for a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that TM841 has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism. 相似文献
10.
Sarah Triest Alexandre Wohlknig Els Pardon Jan Steyaert 《Acta Crystallographica. Section F, Structural Biology Communications》2014,70(11):1504-1507
GPCR–G‐protein complexes are one of the most important components of cell‐signalling cascades. Extracellular signals are sensed by membrane‐associated G‐protein‐coupled receptors (GPCRs) and transduced via G proteins towards intracellular effector molecules. Structural studies of these transient complexes are crucial to understand the molecular details of these interactions. Although a nucleotide‐free GPCR–G‐protein complex is stable, it is not an ideal sample for crystallization owing to the intrinsic mobility of the Gαs α‐helical domain (AHD). To stabilize GPCR–G‐protein complexes in a nucleotide‐free form, nanobodies were selected that target the flexible GαsAHD. One of these nanobodies, CA9177, was co‐crystallized with the GαsAHD. Initial crystals were obtained using the sitting‐drop method in a sparse‐matrix screen and further optimized. The crystals diffracted to 1.59 Å resolution and belonged to the monoclinic space group P21, with unit‐cell parameters a = 44.07, b = 52.55, c = 52.66 Å, α = 90.00, β = 107.89, γ = 90.00°. The structure of this specific nanobody reveals its binding epitope on GαsAHD and will help to determine whether this nanobody could be used as crystallization chaperone for GPCR–G‐protein complexes. 相似文献
11.
Jin Zhang Katsuhide Mizuno Yuki Murata Hideaki Koide Midori Murakami Kunio Ihara Tsutomu Kouyama 《Proteins》2013,81(9):1585-1592
Deltarhodopsin, a new member of the microbial rhodopsin family, functions as a light‐driven proton pump. Here, we report the three‐dimensional structure of deltarhodopsin (dR3) from Haloterrigena thermotolerans at 2.7 Å resolution. A crystal belonging to space group R32 (a, b = 111.71 Å, c = 198.25 Å) was obtained by the membrane fusion method. In this crystal, dR3 forms a trimeric structure as observed for bacteriorhodopsin (bR). Structural comparison of dR with bR showed that the inner part (the proton release and uptake pathways) is highly conserved. Meanwhile, residues in the protein–protein contact region are largely altered so that the diameter of the trimeric structure at the cytoplasmic side is noticeably larger in dR3. Unlike bR, dR3 possesses a helical segment at the C‐terminal region that fills the space between the AB and EF loops. A significant difference is also seen in the FG loop, which is one residue longer in dR3. Another peculiar property of dR3 is a highly crowded distribution of positively charged residues on the cytoplasmic surface, which may be relevant to a specific interaction with some cytoplasmic component.Proteins 2013; © 2013 Wiley Periodicals, Inc. 相似文献
12.
13.
Russell A. Judge Kerry Swift Carlos Gonzlez 《Acta Crystallographica. Section D, Structural Biology》2005,61(1):60-66
Intrinsic ultraviolet fluorescence has been investigated as a rapid non‐invasive method for identifying and distinguishing protein crystals. An epi‐fluorescence microscope, which provides for excitation and viewing of fluorescence from above the sample, and a straight‐through geometry, which provides excitation from above and views fluorescence from underneath the sample, were tested with protein and non‐protein crystal samples. In both systems the protein crystals were observed to fluoresce brightly, providing a high contrast against background solution fluorescence, thus enabling protein crystals to be identified and distinguished from non‐protein crystals. 相似文献
14.
15.
Anna S. Gardberg Alexis Rae Del Castillo Kevin L. Weiss Flora Meilleur Matthew P. Blakeley Dean A. A. Myles 《Acta Crystallographica. Section D, Structural Biology》2010,66(5):558-567
The locations of H atoms in biological structures can be difficult to determine using X‐ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 Å resolution neutron diffraction studies of fully perdeuterated and selectively CH3‐protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D‐rubredoxin and HD‐rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 Å resolution X‐ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the σ level at the D‐atom coordinate in simulated‐annealing composite D‐OMIT maps. It is shown that 1.65 Å resolution RT neutron data for perdeuterated rubredoxin are ∼8 times more likely overall to provide high‐confidence positions for D atoms than 1.1 Å resolution X‐ray data at 100 K or RT. At or above the 1.0σ level, the joint X‐ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D‐atom positions for D‐rubredoxin and HD‐rubredoxin, respectively. The X‐ray‐only 1.1 Å resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D‐atom positions above the 1.0σ level for D‐rubredoxin and HD‐rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron‐density maps, permitting the location of more D atoms than electron‐density maps from models refined against X‐ray data only. 相似文献
16.
SF3a is an evolutionarily conserved heterotrimeric complex essential for pre-mRNA splicing. It functions in spliceosome assembly within the mature U2 snRNP (small nuclear ribonucleoprotein particle), and its displacement from the spliceosome initiates the first step of the splicing reaction. We have identified a core domain of the yeast SF3a complex required for complex assembly and determined its crystal structure. The structure shows a bifurcated assembly of three subunits, Prp9, Prp11 and Prp21, with Prp9 interacting with Prp21 via a bidentate-binding mode, and Prp21 wrapping around Prp11. Structure-guided biochemical analysis also shows that Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA. These findings provide mechanistic insights into the assembly of U2 snRNP. 相似文献
17.
Brian P. Ziemba Emma J. Murphy Hannah T. Edlin David N. M. Jones 《Protein science : a publication of the Protein Society》2013,22(1):11-21
Anopheles gambiae mosquitoes that transmit malaria are attracted to humans by the odor molecules that emanate from skin and sweat. Odorant binding proteins (OBPs) are the first component of the olfactory apparatus to interact with odorant molecules, and so present potential targets for preventing transmission of malaria by disrupting the normal olfactory responses of the insect. AgamOBP20 is one of a limited subset of OBPs that it is preferentially expressed in female mosquitoes and its expression is regulated by blood feeding and by the day/night light cycles that correlate with blood‐feeding behavior. Analysis of AgamOBP20 in solution reveals that the apo‐protein exhibits significant conformational heterogeneity but the binding of odorant molecules results in a significant conformational change, which is accompanied by a reduction in the conformational flexibility present in the protein. Crystal structures of the free and bound states reveal a novel pathway for entrance and exit of odorant molecules into the central‐binding pocket, and that the conformational changes associated with ligand binding are a result of rigid body domain motions in α‐helices 1, 4, and 5, which act as lids to the binding pocket. These structures provide new insights into the specific residues involved in the conformational adaptation to different odorants and have important implications in the selection and development of reagents targeted at disrupting normal OBP function. 相似文献
18.
The artificial lipocalin FluA with novel specificity toward fluorescein was derived via combinatorial engineering from the bilin-binding protein, BBP by exchange of 16 amino acids in the ligand pocket. Here, we describe the crystal structure of FluA at 2.0 A resolution in the space group P2(1) with two protein-ligand complexes in the asymmetric unit. In both molecules, the characteristic beta-barrel architecture with the attached alpha-helix is well preserved. In contrast, the four loops at one end of the beta-barrel that form the entrance to the binding site exhibit large conformational deviations from the wild-type protein, which can be attributed to the sidechain replacements. Specificity for the new ligand is furnished by hydrophobic packing, charged sidechain environment, and hydrogen bonds with its hydroxyl groups. Unexpectedly, fluorescein is bound in a much deeper cavity than biliverdin IX(gamma) in the natural lipocalin. Triggered by the substituted residues, unmutated sidechains at the bottom of the binding site adopt conformations that are quite different from those observed in the BBP, illustrating that not only the loop region but also the hydrophobic interior of the beta-barrel can be reshaped for molecular recognition. Particularly, Trp 129 participates in a tight stacking interaction with the xanthenolone moiety, which may explain the ultrafast electron transfer that occurs on light excitation of the bound fluorescein. These structural findings support our concept of using lipocalins as a scaffold for the engineering of so-called \"anticalins\" directed against prescribed targets as an alternative to recombinant antibody fragments. 相似文献
19.
Samantha Perez-Miller Qin Zou Milos V Novotny Thomas D Hurley 《Protein science : a publication of the Protein Society》2010,19(8):1469-1479
In mice, the major urinary proteins (MUP) play a key role in pheromonal communication by binding and transporting semiochemicals. MUP‐IV is the only isoform known to be expressed in the vomeronasal mucosa. In comparison with the MUP isoforms that are abundantly excreted in the urine, MUP‐IV is highly specific for the male mouse pheromone 2‐sec‐butyl‐4,5‐dihydrothiazole (SBT). To examine the structural basis of this ligand preference, we determined the X‐ray crystal structure of MUP‐IV bound to three mouse pheromones: SBT, 2,5‐dimethylpyrazine, and 2‐heptanone. We also obtained the structure of MUP‐IV with 2‐ethylhexanol bound in the cavity. These four structures show that relative to the major excreted MUP isoforms, three amino acid substitutions within the binding calyx impact ligand coordination. The F103 for A along with F54 for L result in a smaller cavity, potentially creating a more closely packed environment for the ligand. The E118 for G substitution introduces a charged group into a hydrophobic environment. The sidechain of E118 is observed to hydrogen bond to polar groups on all four ligands with nearly the same geometry as seen for the water‐mediated hydrogen bond network in the MUP‐I and MUP‐II crystal structures. These differences in cavity size and interactions between the protein and ligand are likely to contribute to the observed specificity of MUP‐IV. 相似文献
20.
In a crystallography experiment, a crystal is irradiated with X-rays whose diffracted waves are collected and measured. The reconstruction of the structure of the molecule in the crystal requires knowledge of the phase of the diffracted waves, information that is lost in the passage from the three-dimensional structure of the molecule to its diffraction pattern. It can be recovered using experimental methods such as heavy-atom isomorphous replacement and anomalous scattering or by molecular replacement, which relies on the availability of an atomic model of the target structure. This can be the structure of the target protein itself, if a previous structure determination is available, or a computational model or, in some cases, the structure of a homologous protein. It is not straightforward to predict beforehand whether or not a computational model will work in a molecular replacement experiment, although some rules of thumb exist. The consensus is that even minor differences in the quality of the model, which are rather difficult to estimate a priori, can have a significant effect on the outcome of the procedure. We describe here a method for quickly assessing whether a protein structure can be solved by molecular replacement. The procedure consists in submitting the sequence of the target protein to a selected list of freely available structure prediction servers, cluster the resulting models, select the representative structures of each cluster and use them as search models in an automatic phasing procedure. We tested the procedure using the structure factors of newly released proteins of known structure downloaded from the Protein Data Bank as soon as they were made available. Using our automatic procedure we were able to obtain an interpretable electron density map in more than half the cases. 相似文献