Contact replacement for NMR resonance assignment

Motivation: Complementing its traditional role in structural studies of proteins, nuclear magnetic resonance (NMR) spectroscopy is playing an increasingly important role in functional studies. NMR dynamics experiments characterize motions involved in target recognition, ligand binding, etc., while NMR chemical shift perturbation experiments identify and localize protein–protein and protein–ligand interactions. The key bottleneck in these studies is to determine the backbone resonance assignment, which allows spectral peaks to be mapped to specific atoms. This article develops a novel approach to address that bottleneck, exploiting an available X-ray structure or homology model to assign the entire backbone from a set of relatively fast and cheap NMR experiments

Activation of the phosphosignaling protein CheY. I. Analysis of the phosphorylated conformation by 19F NMR and protein engineering

CheY, the 14-kDa response regulator protein of the Escherichia coli chemotaxis pathway, is activated by phosphorylation of Asp57. In order to probe the structural changes associated with activation, an approach which combines 19F NMR, protein engineering, and the known crystal structure of one conformer has been utilized. This first of two papers examines the effects of Mg(II) binding and phosphorylation on the conformation of CheY. The molecule was selectively labeled at its six phenylalanine positions by incorporation of 4-fluorophenylalanine, which yielded no significant effect on activity. One of these 19F probe positions monitored the vicinity of Lys109, which forms a salt bridge to Asp57 in the apoprotein and has been proposed to act as a structural "switch" in activation. 19F NMR chemical shift studies of the labeled protein revealed that the binding of the cofactor Mg(II) triggered local structural changes in the activation site, but did not perturb the probe of the Lys109 region. The structural changes associated with phosphorylation were then examined, utilizing acetyl phosphate to chemically generate phsopho-CheY during NMR acquisition. Phosphorylation triggered a long-range conformational change extending from the activation site to a cluster of 4 phenylalanine residues at the other end of the molecule. However, phosphorylation did not perturb the probe of Lys109. The observed phosphorylated conformer is proposed to be the first step in the activation of CheY; later steps appear to perturb Lys109, as evidenced in the following paper. Together these results may give insight into the activation of other prokaryotic response regulators

Automated protein structure calculation from NMR data

Current software is almost at the stage to permit completely automatic structure determination of small proteins of < 15 kDa, from NMR spectra to structure validation with minimal user interaction. This goal is welcome, as it makes structure calculation more objective and therefore more easily validated, without any loss in the quality of the structures generated. Moreover, it releases expert spectroscopists to carry out research that cannot be automated. It should not take much further effort to extend automation to ca 20 kDa. However, there are technological barriers to further automation, of which the biggest are identified as: routines for peak picking; adoption and sharing of a common framework for structure calculation, including the assembly of an automated and trusted package for structure validation; and sample preparation, particularly for larger proteins. These barriers should be the main target for development of methodology for protein structure determination, particularly by structural genomics consortia

Fluorine in silicate glasses: A multinuclear nuclear magnetic resonance study

Anhydrous nepheline, jadeite, and albite glasses doped with F as well as hydrous F-containing haplogranitic glasses were investigated using 19F combined rotation and multiple-pulse spectroscopy; 19F → 29Si cross-polarization/magic angle spinning (MAS); and high-power 19F decoupled 29Si, 23Na, and 27Al MAS nuclear magnetic resonance methods. Fluorine preferentially coordinates with Al to form octahedral AlF63− complexes in all glasses studied. In addition, F anions bridging two Al cations, units containing octahedral Al coordinated by both O and F, or tetrahedral Al-F complexes might be present. The presence of Si-F bonds cannot be entirely ruled out but appears unlikely on the basis of the 19F → 29Si CP/MAS spectra. There is no evidence for any significant coordination of F with alkalis in the glasses studied. 23Na spectra are identical for the samples and their F-free equivalents and the spectra do not change upon decoupling of 19F. The speciation of F in the hydrous and anhydrous glasses appears to be very similar. Over the range of F contents studied ( up to 5 wt.% ), there seems to be hardly any dependence of F speciation on the concentration of F in the samples. The spectroscopic results explain the decrease of the viscosity of silicate melts with increasing F content by removal of Al from bridging AlO4-units due to complexing with F, which causes depolymerization of the melt. The same mechanism can account for the shift of the eutectic point in the haplogranite system to more feldspar-rich compositions with increasing F content, and for the peraluminous composition of most F-rich granites. Liquid immiscibility in F-rich granitic melts might be caused by formation of (Na,K)3AlF6 units in the melt with little or no interaction with the silicate component. The presence of F in granitic melts might increase the solubility of high field strength cations by making nonbridging O atoms available which form complexes with these cations

Letter to the Editor: 1H, 15N, and 13C chemical shift assignments of the resuscitation promoting factor domain of Rv1009 from Mycobacterium tuberculosis

International audienceNo abstract availabl

Characterisation of the tetrahalophosphonium cations PBrnI4 − n+ (0 ≤ n ≤ 4) by 31P MAS NMR, IR and Raman spectroscopy and the crystal structures of PI4+AlCl4−, PI4+AlBr4− and PI4+GaI4−

The novel tetrahalophosphonium salts PBr4+AsF6−, PI4+AlCl4− and PI4+EBr4− (E = Al, Ga) have been synthesised. A variety of solid complexes containing PBr4+ (e.g. PBr4+AsF6−, PBr4+AlBr4− PBr4+GaBr4−), PI4+ (e.g. PI4+AlCl4−, PI4+AlBr4−, PI4+GaBr4−) or the mixed species PBrnI4 − n+ (0 ≤ n ≤ 4, containing AlBr4−, GaBr4−, AsF6− or SbF6−) have been studied by solid-state 31P MAS NMR and vibrational spectroscopy. The influence of the counter-ion on the chemical shift and the vibrational frequencies are discussed. The crystal structures of PI4+AlCl4−, PI4+AlBr4− and PI4+GaI4− are reported. Evidence for the existence of the hitherto unknown mixed bromoiodophosphonium cations PBr3I+, PBr2I2+ and PBrI3+ has been confirmed by spin–orbit corrected density functional calculations of isotropic 31P chemical shifts for PBrnI4 − n+

High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility

ERp27 (endoplasmic reticulum protein 27.7 kDa) is a homologue of PDI (protein disulfide-isomerase) localized to the endoplasmic reticulum. ERp27 is predicted to consist of two thioredoxinfold domains homologous with the non-catalytic b and b domains of PDI. The structure in solution of the N-terminal blike domain of ERp27 was solved using high-resolution NMR data. The structure confirms that it has the thioredoxin fold and that ERp27 is a member of the PDI family. 15N-NMR relaxation data were obtained and ModelFree analysis highlighted limited exchange contributions and slow internal motions, and indicated that the domain has an average order parameter S 2 of 0.79. Comparison of the single-domain structure determined in the present study with the equivalent domain within fulllength ERp27, determined independently by X-ray diffraction, indicated very close agreement. The domain interface inferred from NMR data in solution was much more extensive than that observed in the X-ray structure, suggesting that the domains flex independently and that crystallization selects one specific interdomain orientation. This led us to apply a new rapid method to simulate the flexibility of the full-length protein, establishing that the domains show considerable freedom to flex (tilt and twist) about the interdomain linker, consistent with the NMR data

Graph algorithms for NMR resonance assignment and cross-link experiment planning

The study of three-dimensional protein structures produces insights into protein function at the molecular level. Graphs provide a natural representation of protein structures and associated experimental data, and enable the development of graph algorithms to analyze the structures and data. This thesis develops such graph representations and algorithms for two novel applications: structure-based NMR resonance assignment and disulfide cross-link experiment planning for protein fold determination. The first application seeks to identify correspondences between spectral peaks in NMR data and backbone atoms in a structure (from x-ray crystallography or homology modeling), by computing correspondences between a contact graph representing the structure and an analogous but very noisy and ambiguous graph representing the data. The assignment then supports further NMR studies of protein dynamics and protein-ligand interactions. A hierarchical grow-and-match algorithm was developed for smaller assignment problems, ensuring completeness of assignment, while a random graph approach was developed for larger problems, provably determining unique matches in polynomial time with high probability. Test results show that our algorithms are robust to typical levels of structural variation, noise, and missings, and achieve very good overall assignment accuracy. The second application aims to rapidly determine the overall organization of secondary structure elements of a target protein by probing it with a set of planned disulfide cross-links. A set of informative pairs of secondary structure elements is selected from graphs representing topologies of predicted structure models. For each pair in this ``fingerprint\u27\u27, a set of informative disulfide probes is selected from graphs representing residue proximity in the models. Information-theoretic planning algorithms were developed to maximize information gain while minimizing experimental complexity, and Bayes error plan assessment frameworks were developed to characterize the probability of making correct decisions given experimental data. Evaluation of the approach on a number of structure prediction case studies shows that the optimized plans have low risk of error while testing only a very small portion of the quadratic number of possible cross-link candidates

Three-Dimensional Structure of the Complexin/SNARE Complex

During neurotransmitter release, the neuronal SNARE proteins synaptobrevin/VAMP, syntaxin, and SNAP-25 form a four-helix bundle, the SNARE complex, that pulls the synaptic vesicle and plasma membranes together possibly causing membrane fusion. Complexin binds tightly to the SNARE complex and is essential for efficient Ca2+-evoked neurotransmitter release. A combined X-ray and TROSY-based NMR study now reveals the atomic structure of the complexin/SNARE complex. Complexin binds in an antiparallel α-helical conformation to the groove between the synaptobrevin and syntaxin helices. This interaction stabilizes the interface between these two helices, which bears the repulsive forces between the apposed membranes. These results suggest that complexin stabilizes the fully assembled SNARE complex as a key step that enables the exquisitely high speed of Ca2+-evoked neurotransmitter release

NOEnet–Use of NOE networks for NMR resonance assignment of proteins with known 3D structure

Motivation: A prerequisite for any protein study by NMR is the assignment of the resonances from the 15N−1H HSQC spectrum to their corresponding atoms of the protein backbone. Usually, this assignment is obtained by analyzing triple resonance NMR experiments. An alternative assignment strategy exploits the information given by an already available 3D structure of the same or a homologous protein. Up to now, the algorithms that have been developed around the structure-based assignment strategy have the important drawbacks that they cannot guarantee a high assignment accuracy near to 100%