共查询到20条相似文献,搜索用时 15 毫秒
1.
Yu-Jen Chen Kuen-Phon Wu Seho Kim Liliana Falzon Masayori Inouye Jean Baum 《Biomolecular NMR assignments》2008,2(2):131-133
Here we report the backbone chemical shifts of the DFP-inhibited mature subtilisin E, which was uniformly labeled by 13C, 15N with a supplement of excess calcium. 相似文献
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Wee Meng Tan Zhengtian Gu Ana Carolina Zeri Stanley J. Opella 《Journal of biomolecular NMR》1999,13(4):337-342
Triple-resonance solid-state NMR spectroscopy is demonstrated to sequentially assign the 13C and 15N amide backbone resonances of adjacent residues in an oriented protein sample. The observed 13C chemical shift frequency provides an orientational constraint complementary to those measured from the 1H and 15N amide resonances in double-resonance experiments. 相似文献
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Unfolded apomyoglobin in 8 M urea at pH 2.3 displays distinct regions with different backbone mobility, as monitored by NMR relaxation. These variations in backbone mobility can be correlated with intrinsic properties of the amino acids in the sequence. Clusters of small amino acids such as glycine and alanine show increased backbone mobility compared to the average. In contrast, local hydrophobic interactions that persist in urea denaturant cause some restriction of backbone motions on a picosecond to nanosecond time scale. The model derived from the behavior of apoMb in urea depends only on the most fundamental properties of the local amino acid sequence, and thus provides a feasible paradigm for the initiation of folding. 相似文献
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Jayneil R. Patel Yingqi Xu Claudia Capitini Fabrizio Chiti Alfonso De Simone 《Biomolecular NMR assignments》2018,12(2):273-277
The HypF protein is involved in the maturation and regulation of hydrogenases. The N-terminal domain of HypF (HypF-N) has served as a key model system to study the pathways of protein amyloid formation and the nature of the toxicity of pre-fibrilar protein oligomers. This domain can aggregate into two forms of oligomers having significantly different toxic effects when added to neuronal cultures. Here, NMR assignments of HypF-N backbone resonances are presented in its native state and under the conditions favouring the formation of toxic and non-toxic oligomers. The analyses of chemical shifts provide insights into the protein conformational state and the possible pathways leading to the formation of different types of oligomers. 相似文献
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Backbone and side-chain heteronuclear resonance assignments and hyperfine NMR shifts in horse cytochrome c 下载免费PDF全文
Liu W Rumbley J Englander SW Wand AJ 《Protein science : a publication of the Protein Society》2003,12(9):2104-2108
The [H26N, H33N] mutant of horse heart cytochrome c was expressed in E. coli during growth on isotopically enriched minimal media. Complete resonance assignments of both the diamagnetic reduced (spin zero) and paramagnetic oxidized (spin (1/2)) states of the protein were obtained using standard triple resonance and total correlation spectroscopy using the previously determined (1)H chemical shifts of the wild-type protein as a guide. The correspondence of chemical shifts between the wild type and the mutant protein is excellent, indicating that they have nearly identical structures. The expanded library of chemical shifts for both redox states in both proteins allowed the refinement of the electron spin g-tensor of the oxidized states. The g-tensors of the oxidized states of the wild-type and [H26N, H33N] mutant proteins are closely similar, indicating that the subtle details of the ligand fields are nearly identical. The refined g-tensors were then used to probe for redox-dependent structure change in the two proteins. 相似文献
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LmrA from Lactococcus lactis is a multidrug transporter and a member of the ATP binding cassette (ABC) transporter family. ABC transporters consist of
a transmembrane domain (TMD) and a nucleotide binding domain (NBD). The NBD contains the highly conserved signature motifs
of this transporter superfamily. In the case of LmrA, the TMD and the NBD are expressed as a single polypeptide. LmrA catalyzes
the extrusion of hydrophobic compounds including antibiotics from the cell membrane at the expense of ATP hydrolysis. ATP
binds to the NBD, where binding and hydrolysis induce conformational changes that lead to the extrusion of the substrate via
the TMD. Here, we report the 1H, 13C and 15N backbone chemical shift assignments of the isolated 263 amino acid containing NBD of LmrA in its ADP bound state. 相似文献
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Local structural preferences and dynamics restrictions in the urea-denatured state of SUMO-1: NMR characterization 下载免费PDF全文
We have investigated by multidimensional NMR the structural and dynamic characteristics of the urea-denatured state of activated SUMO-1, a 97-residue protein belonging to the growing family of ubiquitin-like proteins involved in post-translational modifications. Complete backbone amide and 15N resonance assignments were obtained in the denatured state by using HNN and HN(C)N experiments. These enabled other proton assignments from TOCSY-HSQC spectra. Secondary Halpha chemical shifts and 1H-1H NOE indicate that the protein chain in the denatured state has structural preferences in the broad beta-domain for many residues. Several of these are seen to populate the (phi,psi) space belonging to polyproline II structure. Although there is no evidence for any persistent structures, many contiguous stretches of three or more residues exhibit structural propensities suggesting possibilities of short-range transient structure formation. The hetero-nuclear 1H-15N NOEs are extremely weak for most residues, except for a few at the C-terminal, and the 15N relaxation rates show sequence-wise variation. Some of the regions of slow motions coincide with those of structural preferences and these are interspersed by highly flexible residues. The implications of these observations for the early folding events starting from the urea-denatured state of activated SUMO-1 have been discussed. 相似文献
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An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure ("template") for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange rates, TOCSY) and has high accuracy when the template is close to the target protein's structure (less than 2 A backbone RMSD). However, a close template may not always be available. We extend the circle of convergence of NVR for distant templates by using an ensemble of structures. This ensemble corresponds to the low-frequency perturbations of the given template and is obtained using normal mode analysis (NMA). Our algorithm assigns resonances and sparse NOEs using each of the structures in the ensemble separately, and aggregates the results using a voting scheme based on maximum bipartite matching. Experimental results on human ubiquitin, using four distant template structures show an increase in the assignment accuracy. Our algorithm also improves the robustness of NVR with respect to structural noise. We provide a confidence measure for each assignment using the percentage of the structures that agree on that assignment. We use this measure to assign a subset of the peaks with even higher accuracy. We further validate our algorithm on data for two additional proteins with NVR. We then show the general applicability of our approach by applying our NMA ensemble-based voting scheme to another SBA tool, MARS. For three test proteins with corresponding templates, including the 370-residue maltose binding protein, we increase the number of reliable assignments made by MARS. Finally, we show that our voting scheme is sound and optimal, by proving that it is a maximum likelihood estimator of the correct assignments. 相似文献
12.
We have developed a graphics based algorithm for semi-automated protein NMR assignments. Using the basic sequential triple resonance assignment strategy, the method is inspired by the Boolean operators as it applies "AND"-, "OR"- and "NOT"-like operations on planes pulled out of the classical three-dimensional spectra to obtain its functionality. The method's strength lies in the continuous graphical presentation of the spectra, allowing both a semi-automatic peaklist construction and sequential assignment. We demonstrate here its general use for the case of a folded protein with a well-dispersed spectrum, but equally for a natively unfolded protein where spectral resolution is minimal. 相似文献
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Chih-Ta Henry Chien Liang-Wei Wang Yu-Nan Liu Ban-Dar Hsu Ping-Chiang Lyu Shang-Te Danny Hsu 《Biomolecular NMR assignments》2014,8(2):287-289
Many knotted proteins have been discovered recently, but the folding process of which remains elusive. HP0242 is a hypothetical protein from Helicobacter pylori, which is a model system for studying the folding pathway of a knotted protein. In this study, we report the 1H, 13C, and 15N chemical shift assignments of HP0242. The results will enable us to further investigate HP0242 by NMR experiments. 相似文献
15.
Nese Sari Kathryn E. Fisher Philip N. Bryan John Orban 《Biomolecular NMR assignments》2007,1(2):209-211
Main chain assignments are described for a 266-residue subtilisin mutant, Sbt70, in its 35 kDa complex with an N-terminal
prodomain. The assignments provide the basis for understanding how the prodomain assists folding of subtilisin at a residue-specific
level. 相似文献
16.
YibK is a 160 residue homodimeric protein belonging to the SPOUT class of methyltransferases. Proteins in this group all display a unique topological feature; the backbone polypeptide chain folds to form a deep trefoil knot. Such knotted structures were completely unpredicted, it being thought impossible for a protein to fold efficiently in this way. However, they are becoming more common and there are now a growing number of examples in the Protein Data Bank. These intriguing knotted structures represent a new and significant challenge in the field of protein folding. Here, we present an initial characterisation of the folding of YibK, one of the smallest knotted proteins to be identified. This is the first detailed folding study on a knotted protein to be reported. We have established conditions under which the protein can be denatured reversibly in vitro using urea, thereby showing that molecular chaperones are not required for the efficient folding of this protein. A series of equilibrium unfolding experiments were performed over a 400-fold range of protein concentration. Both secondary and tertiary structural probes show a single, protein concentration-dependent unfolding transition, and data are most consistent with a three-state equilibrium denaturation model involving a monomeric intermediate. Thermodynamic parameters obtained from the fit of the data to this model indicate that the intermediate is a stable species with appreciable secondary and tertiary structure; whether the topological knot remains in the intermediate state is still to be shown. Together, these results demonstrate that, despite its complex knotted structure, YibK is able to fold efficiently and behaves remarkably similarly to other dimeric proteins under equilibrium conditions. 相似文献
17.
Annika Wagner Erika Diehl R. Luise Krauth-Siegel Ute A. Hellmich 《Biomolecular NMR assignments》2017,11(2):193-196
Tryparedoxin (Tpx) is a pivotal protein in the redox-metabolism of trypanosomatid parasites. Tpx has previously been identified as a potential target for drug development in the fight against human African sleeping sickness caused by Trypanosoma brucei. Tpx belongs to the thioredoxin superfamily and acts as an oxidoreductase in the parasite’s cytoplasm. It contains a WCPPC active site motif, which enables the protein to undergo thiol-disulfide exchange. To promote future protein-drug interaction analyses, we report the 1H, 13C and 15N backbone chemical shift assignments for both the oxidized and reduced states of Tpx. The redox state of the protein has a significant impact on the chemical shifts of the residues at the active site of the protein, especially on the two redox active site cysteines. The NMR assignments presented here will be a prerequisite for investigating drug binding to Tpx in molecular detail and to drive further drug optimization. 相似文献
18.
The single domain protein, interleukin-1beta, is representative of a distinct class of proteins characterized by their beta-trefoil topology. Each subdomain of this structural class is composed of a beta beta beta loop beta (betabetabetaLbeta) motif comprised of approximately 50 residues and gives the protein a pseudo- 3-fold axis of symmetry. A common feature of proteins in this topological family appears to be that they are slow folders, which reach the native state on the order of tens to 100s of seconds. Sequence analysis of interleukin-1beta indicates that three phenylalanine residues located at positions 42, 101, and 146 are well conserved, separated by approximately 50 residues in the primary sequence, located in similar positions in the pseudo-symmetric units of the trefoil, and are juxtaposed to one another in conformational space. These residues surround the hydrophobic cavity and "pin" the hairpin triplet cap to the core beta-barrel. To determine if cap-barrel interactions are involved in maintaining the structural stability and cooperativity or in controlling the slow formation of the native state, we performed a series of mutational studies. The results indicate that interleukin-1beta tolerates large increases in side-chain volume at these three topologically conserved sites with little effect on stability, while the kinetics show significant differences in both the unfolding and refolding rates. Taken together, our results indicate that these conserved core residues are essential contacts in the transition-state ensemble for folding. 相似文献
19.
Wood K Paz A Dijkstra K Scheek RM Otten R Silman I Sussman JL Mulder FA 《Biomolecular NMR assignments》2012,6(1):15-18
Neuroligins act as heterophilic adhesion molecules at neuronal synapses. Their cytoplasmic domains interact with synaptic
scaffolding proteins, and have been shown to be intrinsically disordered. Here we report the backbone and side chain 1H, 13C and 15N resonance assignments for the cytoplasmic domain of human neuroligin 3. 相似文献
20.
Jan Philip Wurm Anatoli Lioutikov Peter Kötter Karl-Dieter Entian Jens Wöhnert 《Biomolecular NMR assignments》2014,8(2):345-348
The Saccharomyces cerevisiae Nop6 protein is involved in the maturation of the small ribosomal subunit. It contains a central RNA binding domain and a predicted C-terminal coiled-coil domain. Here we report the almost complete (>90 %) 1H,13C,15N backbone and side chain NMR assignment of a 15 kDa Nop6 construct comprising the RNA binding and coiled-coil domains. 相似文献