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Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the implementation of a set of novel ¹H-detected 5D experiments, (HACA)CON(CACO)NCO(CA)HA, BT-(H)NCO(CAN)CONNH and BT-HN(COCAN)CONNH, optimized for the study of highly flexible IDPs that exploit the best resolved correlations, those involving the carbonyl and nitrogen nuclei of neighboring amino acids, to achieve sequence-specific resonance assignment. Together with the analogous recently proposed pulse schemes based on ¹³C detection, they form a complete set of experiments for sequence-specific assignment of highly flexible IDPs. Depending on the particular sample conditions (concentration, lifetime, pH, temperature, etc.), these experiments present certain advantages and disadvantages that will be discussed. Needless to say, that the availability of a variety of complementary experiments will be important for accurate determination of resonance frequencies in complex IDPs.

A large number of proteins carry out their function in highly flexible and disordered states, lacking a well-defined 3D structure. These proteins, referred to as intrinsically disordered proteins (IDPs), are now in the spotlight of modern structural biology. Nuclear magnetic resonance (NMR) spectroscopy represents a unique tool for accessing atomic resolution information on IDPs in complex environments as whole cells, provided that the methods are optimized to their peculiar properties and to the characteristics of in-cell experiments. We describe procedures for the preparation of in-cell NMR samples, as well as for the setup of NMR experiments and their application to in-cell studies, using human α-synuclein overexpressed in Escherichia coli as an example. The expressed protein is labeled with (13)C and (15)N stable isotopes to enable the direct recording of (13)C-detected NMR experiments optimized for the properties of IDPs. The entire procedure covers 24 h, including cell transformation, cell growth overnight, setup of the spectrometer and NMR experiment recording.

Intrinsically disordered proteins (IDPs) are characterized by highly flexible solvent exposed backbones and can sample many different conformations. These properties confer them functional advantages, complementary to those of folded proteins, which need to be characterized to expand our view of how protein structural and dynamic features affect function beyond the static picture of a single well defined 3D structure that has influenced so much our way of thinking. NMR spectroscopy provides a unique tool for the atomic resolution characterization of highly flexible macromolecules in general and of IDPs in particular. The peculiar properties of IDPs however have profound effects on spectroscopic parameters. It is thus worth thinking about these aspects to make the best use of the great potential of NMR spectroscopy to contribute to this fascinating field of research. In particular, after many years of dealing with exclusively heteronuclear NMR experiments based on (13)C direct detection, we would like here to address their relevance when studying IDPs.

The intracellular environment contains high concentrations of macromolecules occupying up to 30% of the total cellular volume. Presence of these macromolecules decreases the effective volume available for the proteins in the cell and thus increases the effective protein concentrations and stabilizes the compact protein conformations. Macromolecular crowding created by various macromolecules such as proteins, nucleic acids, and carbohydrates has been shown to have a significant effect on a variety of cellular processes including protein aggregation. Most studies of macromolecular crowding have used neutral, flexible polysaccharides that function primarily via excluded volume effect as model crowding agents. Here we have examined the effects of more rigid polysaccharides on protein structure and aggregation. Our results indicate that rigid and flexible polysaccharides influence protein aggregation via different mechanisms and suggest that, in addition to excluded volume effect, changes in solution viscosity and non-specific protein–polymer interactions influence the structure and dynamics of proteins in crowded environments.

We present three novel exclusively heteronuclear 5D (13)C direct-detected NMR experiments, namely (H(N-flip)N)CONCACON, (HCA)CONCACON and (H)CACON(CA)CON, designed for easy sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The experiments proposed have been optimized to overcome the drawbacks which may dramatically complicate the characterization of IDPs by NMR, namely the small dispersion of chemical shifts and the fast exchange of the amide protons with the solvent. A fast and reliable automatic assignment of α-synuclein chemical shifts was obtained with the Tool for SMFT-based Assignment of Resonances (TSAR) program based on the information provided by these experiments.

The E7 protein from human papillomavirus (HPV) plays a key role in oncogenesis; for this reason, it is a target of great biomedical interest. To date, no high resolution information is available for the full protein. We present here the NMR characterization of the entire E7 from HPV16, one of the most oncogenic variants of the virus. The protein is very heterogeneous in terms of structural and dynamic properties with a highly flexible N-terminal module and a more structured C terminus. This opens possibilities for studies of molecular-level interactions and post-translational modifications of the protein to unravel functional details that might be linked to its highly oncogenic potential.

International audience; Metal ions are ubiquitous in biochemical and cellular processes. Since many metal ions are paramagnetic due to the presence of unpaired electrons, paramagnetic molecules are an important class of targets for research in structural biology and related fields. Today, NMR spectroscopy plays a central role in the investigation of the structure and chemical properties of paramagnetic metalloproteins, linking the observed paramagnetic phenomena directly to electronic and molecular structure. A major step forward in the study of proteins by solid-state NMR came with the advent of ultrafast magic angle spinning (MAS) and the ability to use (1)H detection. Combined, these techniques have allowed investigators to observe nuclei that previously were invisible in highly paramagnetic metalloproteins. In addition, these techniques have enabled quantitative site-specific measurement of a variety of long-range paramagnetic effects. Instead of limiting solid-state NMR studies of biological systems, paramagnetism provides an information-rich phenomenon that can be exploited in these studies. This Account emphasizes state-of-the-art methods and applications of solid-state NMR in paramagnetic systems in biological chemistry. In particular, we discuss the use of ultrafast MAS and (1)H-detection in perdeuterated paramagnetic metalloproteins. Current methodology allows us to determine the structure and dynamics of metalloenzymes, and, as an example, we describe solid-state NMR studies of microcrystalline superoxide dismutase, a 32 kDa dimer. Data were acquired with remarkably short times, and these experiments required only a few milligrams of sample.

The multi-domain transcriptional coactivators CBP/p300 integrate a multitude of signaling inputs, interacting with more than 400 proteins via one or more of their globular domains. While CBP/p300 function is typically considered in terms of these structured domains, about half of the protein consists of intrinsically disordered regions (IDRs) of varying length. However, these IDRs have only been thought of as linkers that allow flexible spatial arrangement of the structured domains, but recent studies have shown that similar IDRs mediate specific and critical interactions in other proteins. To examine the roles of IDRs in CBP, we performed yeast-two-hybrid screenings of placenta and lung cancer cDNA libraries, which demonstrated that the long IDR linking the KIX domain and bromodomain of CBP (termed ID3) can potentially bind to several proteins. The RNA-binding Zinc-finger protein 106 (ZFP106) detected in both libraries was identified as a novel substrate for CBP-mediated acetylation. Nuclear magnetic resonance (NMR) spectroscopy combined with cross-linking experiments and competition-binding assays showed that the fully disordered isolated ID3 transiently interacts with an IDR of ZFP106 in a fashion that disorder of both regions is maintained. These findings demonstrate that beside the linking function, ID3 can also interact with acetylation substrates of CBP.

HPV-16 E7 is one of the key proteins that, by interfering with the host metabolism through many protein-protein interactions, hijacks cell regulation and contributes to malignancy. Here we report the high resolution investigation of the CR3 region of HPV-16 E7, both as an isolated domain and in the full-length protein. This opens the way to the atomic level study of the many interactions in which HPV-16 E7 is involved. Along these lines we show here the effect of one of the key post-translational modifications of HPV-16 E7, the phosphorylation by casein kinase II.

International audience; Pseudocontact shifts (PCSs) arise in para-magnetic systems in which the susceptibility tensor is anisotropic. PCSs depend upon the distance from the paramagnetic center and the position relative to the susceptibility tensor, and they can be used as structural restraints in protein structure determination. We show that the use of H-1-detected solid-state correlations provides facile and rapid detection and assignment of site-specific PCSs, including resolved H-1 PCSs, in a large metalloprotein, Co2+-substituted superoxide dismutase (Co2+-SOD). With only 3 mg of sample and a small set of experiments, several hundred PCSs were measured and assigned, and these PCSs were subsequently used in combination with H-1-H-1 distance and dihedral angle restraints to determine the protein backbone geometry with a precision paralleling those of state-of-the-art liquid-state determinations of diamagnetic proteins, including a well-defined active site.

Thanks to recent fast progress, NMR is now in a strategic position to provide unique atomic resolution information on a variety of different biological macromolecules in different conditions (solution, solid state, in-cell). We would like here to present recent developments that enable to focus on intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of proteins of increasing size and complexity. They have attracted the attention of the scientific community challenging well accepted ideas and concepts and demanding an expansion of the structure function paradigm.

Metallo-beta-lactamases (M beta Ls) are Zn(II)-based bacterial enzymes that hydrolyze beta-lactam antibiotics, hampering their beneficial effects. In the most relevant subclass (B1), X-ray crystallography studies on the enzyme from point to either two zinc ions in two metal sites (the so-called '3H' and 'DCH' sites) or a single Zn(II) ion in the 3H site, where the ion is coordinated by Asp120, Cys221 and His263 residues. However, spectroscopic studies on the B1 enzyme from . in the mono-zinc form suggested the presence of the Zn(II) ion also in the DCH site, where it is bound to an aspartate, a cysteine, a histidine and a water molecule. A structural model of this enzyme in its DCH mononuclear form, so far lacking, is therefore required for inhibitor design and mechanistic studies. By using force field based and mixed quantum-classical (QM/MM) molecular dynamics (MD) simulations of the protein in aqueous solution we constructed such structural model. The geometry and the H-bond network at the catalytic site of this model, in the free form and in complex with two common beta-lactam drugs, is compared with experimental and theoretical findings of CphA and the recently solved crystal structure of new B2 M beta L from (Sfh-I). These are M beta Ls from the B2 subclass, which features an experimentally well established mono-zinc form, in which the Zn(II) is located in the DCH site. From our simulations the epsilon epsilon I ' and delta epsilon I ' protomers emerge as possible DCH mono-zinc reactive species, giving a novel contribution to the discussion on the M beta L reactivity and to the drug design process.

Order in disorder: The characterization of intrinsically disordered proteins by NMR spectroscopy is a necessity on the one hand and a continuous challenge on the other. We propose two experiments that provide diagnostic parameters to monitor the degree of unfolding of a polypeptide. The test was performed on the yeast Cox17 protein, known to gain its function through maturation from an intrinsically disordered state (see figure).

Provided that (13)C-detected NMR experiments are either preferable or complementary to (1)H detection, we report here tools to determine C(alpha)-C', C'-N, and C(alpha)-H(alpha) residual dipolar couplings on the basis of the CON experiment. The coupling constants determined on ubiquitin are consistent with the subset measured with the (1)H-detected HNCO sequences. Since the utilization of residual dipolar couplings may depend on the mobility of the involved nuclei, we also provide tools to measure longitudinal and transverse relaxation rates of N and C'. This new set of experiments is a further development of a whole strategy based on (13)C direct-detection NMR spectroscopy for the study of biological macromolecules.

Isotropic mixing sequences are one of the key methods to achieve efficient coherence transfer. Among them, the MOCCA-XY16, which keeps the magnetization longitudinal for a significant amount of time, is characterised by favourable relaxation properties. We show here that its adapted version is particularly suited for carbonyl-carbonyl correlations in (13)C direct detection NMR experiments.

The electronic properties of Thermus thermophilus Cu(A) in the oxidized form were studied by (1)H and (13)C NMR spectroscopy. All of the (1)H and (13)C resonances from cysteine and imidazole ligands were observed and assigned in a sequence-specific fashion. The detection of net electron spin density on a peptide moiety is attributed to the presence of a H-bond to a coordinating sulfur atom. This hydrogen bond is conserved in all natural Cu(A) variants and plays an important role for maintaining the electronic structure of the metal site, rendering the two Cys ligands nonequivalent. The anomalous temperature dependence of the chemical shifts is explained by the presence of a low-lying excited state located about 600 cm(-1) above the ground state. The room-temperature shifts can be described as the thermal average of a sigma(u)* ground state and a pi(u) excited state. These results provide a detailed description of the electronic structure of the Cu(A) site at atomic resolution in solution at physiologically relevant temperature.

Carbon-13 direct-detection NMR is becoming increasingly used to complement 1H-detected experiments in biomolecular applications. Here we describe the novel aspects that were addressed to convert 13C direct-detection into a useful routinely applicable tool, a selection of the most useful 13C direct-detection protonless NMR experiments and how they can be exploited for the study of proteins. © 2008 Wiley Periodicals, Inc. Concepts Magn Reson Part A 32A: 183–200, 2008.

Expansions of polyglutamine (polyQ) tracts in nine different proteins cause a family of neurodegenerative disorders called polyQ diseases. Because polyQ tracts are potential therapeutic targets for these pathologies there is great interest in characterizing the conformations that they adopt and in understanding how their aggregation behavior is influenced by the sequences flanking them. We used solution NMR to study at single-residue resolution a 156-residue proteolytic fragment of the androgen receptor that contains a polyQ tract associated with the disease spinobulbar muscular atrophy, also known as Kennedy disease. Our findings indicate that a Leu-rich region preceding the polyQ tract causes it to become α-helical and appears to protect the protein against aggregation, which represents a new, to our knowledge, mechanism by which sequence context can minimize the deleterious properties of these repetitive regions. Our results have implications for drug discovery for polyQ diseases because they suggest that the residues flanking these repetitive sequences may represent viable therapeutic targets.

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.

The major limitation of nuclear magnetic resonance spectroscopy arises from the increase of nuclear transverse relaxation rates with increasing molecular mass. This causes reduction in spectral resolution and coherence transfer efficiency. The use of 2H-labeling to eliminate 1H-mediated relaxation pathways and the constructive use of cross correlation effects (TROSY, CRINEPT) alleviate the phenomenon. An alternative approach is to use direct detection of heteronuclei. Specifically designed 13C direct detection experiments can complement the set of 1H-based NMR experiments commonly used for structure determination providing an additional source of information less affected by the detrimental transverse relaxation effect. We applied this novel methodology to the study of the CutA1 protein (12.3 kDa) from E. coli that forms a homotrimer in solution with a total molecular mass of 37 kDa. In this work we demonstrate that the information available from 13C direct detection experiments makes it possible to completely assign the NMR resonances of the backbone of this 37 kDa trimeric protein without the need of deuteration. The structural and dynamical knowledge obtained for this system may contribute to understand its biological role. Proteins 2008. © 2007 Wiley-Liss, Inc.

International audience; Intrinsically disordered proteins (IDPs) are functional proteins containing large fragments characterized by high local mobility. Bioinformatic studies have suggested that a significant fraction (more than 30%) of eukaryotic proteins has disordered regions of more than 50 amino acids in length. Hence, NMR methods for the characterization of local compactness and solvent accessibility in such highly disordered proteins are of high importance. Among the available approaches, the HET-SOFAST/BEST experiments (Schanda et al., 2006, Rennella et al., 2014) provide semi-quantitative information by monitoring longitudinal (1)H relaxation of amide protons under different initial conditions. However, when approaching physiological sample conditions, the potential of these amide (1)H detected experiments is reduced due to rapid amide proton solvent exchange. (13)C direct detection methods therefore provide a valuable alternative thanks to a higher chemical shift dispersion and their intrinsic insensitivity toward solvent exchange. Here we present two sets of (13)C-detected experiments, which indirectly measure (1)H(N) and (1)H(α) inversion recovery profiles. The experiments consist of an initial spin inversion-recovery block optimized for selective manipulation of different types of proton spins followed by a CON read-out scheme. The proposed experiments were tested on human α-synuclein and ubiquitin, two representative examples of unfolded and folded proteins.

Metal binding to the amyloid β-peptide is suggested to be involved in the pathogenesis of Alzheimer's disease. We used high-resolution NMR to study zinc binding to amyloid β-peptide 1–40 at physiologic pH. Metal binding induces a structural change in the peptide, which is in chemical exchange on an intermediate rate, between the apo-form and the holo-form, with respect to the NMR timescale. This causes loss of NMR signals in the resonances affected by the binding. Heteronuclear correlation experiments, 15N-relaxation and amide proton exchange experiments on amyloid β-peptide 1–40 revealed that zinc binding involves the three histidines (residues 6, 13 and 14) and the N-terminus, similar to a previously proposed copper-binding site [Syme CD, Nadal RC, Rigby SE, Viles JH (2004) J Biol Chem279, 18169–18177]. Fluorescence experiments show that zinc shares a common binding site with copper and that the metals have similar affinities for amyloid β-peptide. The dissociation constant Kd of zinc for the fragment amyloid β-peptide 1–28 was measured by fluorescence, using competitive binding studies, and that for amyloid β-peptide 1–40 was measured by NMR. Both methods gave Kd values in the micromolar range at pH 7.2 and 286 K. Zinc also has a second, weaker binding site involving residues between 23 and 28. At high metal ion concentrations, the metal-induced aggregation should mainly have an electrostatic origin from decreased repulsion between peptides. At low metal ion concentrations, on the other hand, the metal-induced structure of the peptide counteracts aggregation.

Enzyme-inhibitor recognition is considered one of the most fundamental aspects in the area of drug discovery. However, the molecular mechanism of this recognition process (induced fit or prebinding and adaptive selection among multiple conformers) in several cases remains unexplored. In order to shed light toward this step of the recognition process in the case of human angiotensin I converting enzyme (hACE) and its inhibitor captopril, we have established a novel combinatorial approach exploiting solution NMR, flexible docking calculations, mutagenesis, and enzymatic studies. We provide evidence that an equimolar ratio of the cis and trans states of captopril exists in solution and that the enzyme selects only the trans state of the inhibitor that presents architectural and stereoelectronic complementarity with its substrate binding groove. (c) 2006 Elsevier Ltd. All rights reserved. Bioorganic and Medicinal Chemistry Letters

The copper-mediated protein–protein interaction between yeast Atx1 and Ccc2 has been examined by protonless heteronuclear NMR and compared with the already available 1H–15N HSQC information. The observed chemical shift variations are analyzed with respect to the actual solution structure, available through intermolecular NOEs. The advantage of using the CON-IPAP spectrum with respect to the 1H–15N HSQC resides in the increased number of signals observed, including those of prolines. CBCACO-IPAP experiments allow us to focus on the interaction region and on side-chain carbonyls, while a newly designed CEN-IPAP experiment on side-chains of lysines. An attempt is made to rationalize the chemical shift variations on the basis of the structural data involving the interface between the proteins and the nearby regions. It is here proposed that protonless 13C direct-detection NMR is a useful complement to 1H based NMR spectroscopy for monitoring protein–protein and protein–ligand interactions.

Carbon-13 direct detection NMR methods are feasible thanks to the improvements in probehead technology and to the development of new NMR experiments. We present here a complete set of experiments, based on C′ direct detection, developed to perform protein complete assignment of backbone and side-chains (except for aromatic rings). This strategy offers alternative solutions for demanding situations (paramagnetic and/or large molecules) and can be useful in general in conjunction with conventional experiments.

The thermodynamic parameters for reduction of the type-1 (T1) copper site in Rhus vernicifera and Trametes versicolor laccases and for the derivative of the former protein from which the type-2 copper has been selectively removed (T2D) have been determined with UV–vis spectroelectrochemistry. In all cases, the enthalpic term turns out to be the main determinant of the E o′ of the T1 site. Also the difference between the reduction potentials of the two laccases is enthalpy-based and reflects differences in the coordination features of the T1 sites and their protein environment. The T1 sites in native R. vernicifera laccase and its T2D derivative show the same E o′, as a result of compensatory differences in the reduction thermodynamics. This suggests that removal of the type-2 (T2) copper results in modification of the reduction-induced solvent reorganization effects, with no influence in the structure of the multicopper protein site. This conclusion is supported by NMR data recorded on the native, the T2D, and Hg-substituted T1 derivatives of R. vernicifera laccase, which show that the T1 and T2/T3 sites are largely noninteracting.

This article deals with the solution structure determination of paramagnetic metalloproteins by NMR spectroscopy. These proteins were believed not to be suitable for NMR investigations for structure determination until a decade ago, but eventually novel experiments and software protocols were developed, with the aim of making the approach suitable for the goal and as user-friendly and safe as possible. In the article, we also give hints for the optimization of experiments with respect to each particular metal ion, with the aim of also providing a handy tool for nonspecialists. Finally, a section is dedicated to the significant progress made on 13C direct detection, which reduces the negative effects of paramagnetism and may constitute a new chapter in the whole field of NMR spectroscopy.

Two modifications of the triple-resonance CANCO sequence, designed for backbone assignment in proteins [Angew. Chem. Int. Ed. 43 (2004) 2257], are presented here. These two new sequences display the intra-residue Ca–CO correlation selectively, while in the original sequence both the inter- and the intra-residue correlations were present. In addition, one of the two variants benefits from an improved sensitivity. Both sequences are a useful complement to the CANCO sequence for facile sequence-specific protein assignment by protonless NMR.

(13)C-(13)C NOESY experiments were performed under long mixing time conditions on reduced human superoxide dismutase (32 kDa, (15)N, (13C) and 70% (2)H labeled). (13)C-(13)C couplings were successfully eliminated through post-processing of in-phase-anti-phase (IPAP) data. It appears that at mixing time tau(m) of 3.0 s the spin diffusion mechanism allows the detection of 96% of the two-bond correlations involving C' and C(beta). The interpretation was confirmed by simulations. This approach broadens the range of applicability of (13)C-(13)C NOESY spectroscopy.

The possibility of investigating copper proteins by nuclear magnetic resonance is here treated. It is shown that the solution structure and dynamic information can be obtained on Type I Cu(II) proteins, which have a relatively short electron relaxation time (τ S = 10-10 s). The experimental approach, in this case, is routine, although tailored for fast-relaxing nuclei. In the case of Type II Cu(II) proteins, when the electron relaxation times are larger (τ S = 10-8 - 10-9 s) and proton linewidths are broadened beyond detectable limits, heteronuclear 13C spectra with direct detection can be used and the solution structure can again be obtained. In this review, it is shown that Cu(II) proteins are now amenable for NMR investigation, the size being the only limit as in diamagnetic proteins.

In this report, the use of 13C direct detection has been pursued in 2D experiments (13C-13C COSY, 13C-13C COCAMQ, 13C-13C NOESY) to detect broad lines in nuclear magnetic resonance spectra of paramagnetic metalloproteins. The sample is a monomeric oxidized copper, zinc superoxide dismutase. Thanks to direct detection probeheads, cryogenic technology, and implementation of 13C band-selective homodecoupling, many broadened signals were detected. Proton signals for the same residues escaped detection in 1H and 1H-15N HSQC experiments because of the broadening. Only the 13C signals which experience large contact coupling escaped detection, i.e., the 13C nuclei of the metal coordinated histidines. Otherwise, nuclei as close to copper(II) as 4 A can be detected. Paramagnetic-based restraints can in principle be used for solution structure determination of paramagnetic metalloproteins and in copper(II) proteins in particular. The present study is significant also for the study of large diamagnetic proteins for which proton relaxation makes proton-based spectroscopy not adequate.

Thanks to recent improvements in NMR instrumentation, pulse sequence design, and sample preparation, a panoply of new NMR tools has become available for atomic resolution characterization of intrinsically disordered proteins (IDPs) that are optimized for the particular chemical and spectroscopic properties of these molecules. A wide range of NMR observables can now be measured on increasingly complex IDPs that report on their structural and dynamic properties in isolation, as part of a larger complex, or even inside an entire living cell. Herein we present basic NMR concepts, as well as optimised tools available for the study of IDPs in solution. In particular, the following sections are discussed hereafter: a short introduction to NMR spectroscopy and instrumentation (Sect. 3.1), the effect of order and disorder on NMR observables (Sect. 3.2), particular challenges and bottlenecks for NMR studies of IDPs (Sect. 3.3), 2D HN and CON NMR experiments: the fingerprint of an IDP (Sect. 3.4), tools for overcoming major bottlenecks of IDP NMR studies (Sect. 3.5), 13C detected experiments (Sect. 3.6), from 2D to 3D: from simple snapshots to site-resolved characterization of IDPs (Sect. 3.7), sequential NMR assignment: 3D experiments (Sect. 3.8), high-dimensional NMR experiments (nD, with n>3) (Sect. 3.9) and conclusions and perspectives (Sect. 3.10).

We provide an atomic-resolution description based on NMR spectroscopy, of the intrinsically disordered C-terminal domain of the Nipah virus nucleoprotein (NTAIL ), both in its isolated state and within the nucleocapsid (NC). Within the NC the second half of NTAIL retains conformational behavior similar to that of isolated NTAIL , whereas the first half of NTAIL becomes much more rigid. In spite of the mostly disordered nature of NTAIL , chemical shifts and relaxation measurements show a significant degree of α-helical sampling in the molecular recognition element (MoRE) involved in binding to the X domain (XD) of the phosphoprotein, with this preconfiguration being more pronounced than in the NTAIL domain from the cognate Hendra virus. Outside the MoRE, an additional region exhibiting reduced flexibility was identified within NTAIL and found to be involved in binding to the XD. (1) H- and (13) C-detected titration NMR experiments support a highly dynamic binding of NTAIL at the surface of the XD.

The kinetics of lanthanide (III) exchange for calcium(II) in the C-terminal EF-hand of the protein calbindin D9khave been studied by one-dimensional (1D) stopped-flow NMR. By choosing a paramagnetic lanthanide (Ce3+), kinetics in the sub-second range can be easily measured. This is made possible by the fact that (i) the kinetic behaviour of hyperfine shifted signals can be monitored in 1D NMR and (ii) fast repetition rates can be employed because these hyperfine shifted signals relax fast. It is found that the Ce3+-Ca2+exchange process indeed takes place on a sub-second timescale and can be easily monitored with this technique. As the rate of calcium-cerium substitution was found not to depend on the presence of excess calcium in solution, the kinetics of the process were interpreted in terms of a bimolecular associative mechanism, and the rate constants extracted. Interestingly, the dissociative mechanism involving the apoform of the protein, which is generally assumed for metal ion exchange at protein binding sites, was not in agreement with our data.

A large number of proteins carry out their function in highly flexible and disordered states, lacking a well-defined 3D structure. These proteins, referred to as intrinsically disordered proteins (IDPs), are now in the spotlight of modern structural biology. Nuclear magnetic resonance (NMR) spectroscopy represents a unique tool for accessing atomic resolution information on IDPs in complex environments as whole cells, provided that the methods are optimized to their peculiar properties and to the characteristics of in-cell experiments. We describe procedures for the preparation of in-cell NMR samples, as well as for the setup of NMR experiments and their application to in-cell studies, using human α-synuclein overexpressed in Escherichia coli as an example. The expressed protein is labeled with (13)C and (15)N stable isotopes to enable the direct recording of (13)C-detected NMR experiments optimized for the properties of IDPs. The entire procedure covers 24 h, including cell transformation, cell growth overnight, setup of the spectrometer and NMR experiment recording.

A prototype 2.5-mm (1)H high-resolution probe for an 18.8-T (800 MHz) nuclear magnetic resonance spectrometer has been designed, together with a dedicated amplifier capable of delivering up to 1 kW of power. This probe permits a 90 degrees pulse length of 2 mus to be achieved at 300 W, corresponding to an excitation bandwidth of +/-125 kHz. Probe performances were tested on samples commonly used for this purpose as well as on protein and paramagnetic model compound samples. It is shown that this probe is useful for a wide range of applications at high magnetic field, especially in the study of systems characterized by very broad and far-shifted resonances and in experiments that require high-power radiofrequency irradiation.

Formation of a single carbon-sulfur bond is described. The reaction of incomplete cubane-type sulfur and oxygen-bridged isothiocyanato tungsten cluster [W3(mu3-S)(mu-O)(mu-S)2(NCS)9]5- (7) with acetylene affords [W3(mu3-S)(mu-O)(mu-S)(mu-SCH=CH2)(NCS)9]4- (8). The cluster 8 has been isolated as K0.5(Hpy)3.5[W3(mu3-S)(mu-O)(mu-S)(mu-SCH=CH2)(NCS)9] (8'), whose structure has been characterized by X-ray crystallography, electronic spectra, and 1H and 13C NMR spectroscopy. Crystal data of 8': triclinic system, space group P1, a = 14.465(5) A, b = 17.353(3) A, c = 10.202(2) A, alpha = 90.98(1) degrees, beta = 108.59(2) degrees, gamma = 98.13(2) degrees, V = 2397.6(10) A(3), Z = 2, D(c) = 2.096 g cm(-3), Dm = 2.08 g cm(-3), R (Rw) = 3.6 (5.5)% for 8786 reflections (I > 1.50 sigma(I)). The carbon-carbon distance is 1.27(1) A and is almost equidistant between ethylene (1.339 A) and acetylene (1.203 A). The electronic spectrum of 8' in 1.0 M HCl containing 1.5 M KSCN has a characteristic broad peak in the near-infrared region [lambda(max), nm (epsilon, M(-1) cm(-1)): 840 (650), 575 (1450)]. (1)H NMR and HH correlation spectroscopy (COSY) of 8' in CD3CN support the results of the X-ray structural analysis. The (1)H NMR spectrum shows three signals at 2.42 (1H, dd), 4.84 (1H, d, J = 8.8 Hz), and 4.89 (1H, d, J = 16.2 Hz) ppm due to the mu-SCH=CH2 moiety of 8'. The correlation spectrum shows spin couplings of the signal at 2.42 ppm with the signals at 4.84 and 4.89 ppm. The mechanism of the formation of 8 is suggested to proceed through an intermediate with acetylene bridging two of the sulfur atoms.

The oxidized blue copper proteins azurin and stellacyanin have been investigated through 1H NMR at 800 MHz and the results compared with those for plastocyanin (Bertini, I.; Ciurli, S.; Dikiy, A.; Gasanov, R.; Luchinat, C.; Martini, G.; Safarov, N. J. Am. Chem. Soc. 1999, 121, 2037). By exploiting saturation transfer between the oxidized and the reduced forms, all the hyperfine shifted signals can be assigned, including the β-CH2 protons of the coordinated cysteines, which are so broad not to be detected under direct observation. Both hyperfine shifts and line widths of the latter signals differ dramatically from one protein to another: average hyperfine shifts of about 850, 600, and 400 ppm and average line widths of 1.2, 0.45, and 0.25 MHz are observed for azurin, plastocyanin, and stellacyanin, in that order. The observation of a nuclear line width of 1.2 MHz is unprecedented in high-resolution NMR in solution. These data are interpreted as a measure of the out-of-plane displacement of the copper ion,...

13C shieldings, δ(13C), 17O shieldings, δ(17O), and 18O isotope effects on 13C shieldings, 1Δ13C(18O/16O), of carbon monoxide (99.7% 13C, 0.9% 17O, and 11.8% 18O enriched) in a variety of solvents and of the Fe−C−O unit of several carbonmonoxy hemoprotein models with varying polar and steric effects of the distal organic superstructure and constraints of the proximal side are reported. This enables, first, comparisons with hemoproteins, C−O vibrational frequencies, ν(C−O), and X-ray structural data to be made; second, to investigate whether polarizable CO is an adequate model for distal ligand effects in carbonmonoxy heme proteins and synthetic model compounds; third, to investigate the effect of electronic perturbation within the heme pocket and pocket deformation on δ(13C), δ(17O), 1Δ13C(18O/16O), and ν(C−O). A variety of solvents with varying dielectric constants and solvation abilities appears to have negligible effect on δ(17O), δ(13C), and 1Δ13C(18O/16O) and little direct effect on ν(C−O) of dissolv...

57Fe NMR spectra of several carbonmonoxy hemoprotein models with varying polar and steric effects of the distal organic superstructure, constraints of the proximal side, and porphyrin ruffling are reported. 57Fe shieldings, δ(57Fe), vary by nearly 900 ppm among various hemes, and an excellent correlation was found between δ(57Fe) and the absolute crystallographic average displacement of the meso carbon atoms, |Cm|, relative to the porphyrin core mean plane. The great variation of δ(57Fe) as a function of |Cm| (∼140 ppm/0.1 A) demonstrates that iron-57 shieldings can be used in structure refinement protocols for the extraction of more accurate structures for heme rings in heme model compounds. The excellent correlation between iron-57 shieldings and the average shieldings of the meso carbons of the porphyrin skeleton of TPP derivatives suggests that the two probes reflect similar types of electronic and structural perturbations, which are primarily due to porphyrin ruffling. The present findings also empha...

The 1H and 13C hyperfine shifts of the heme methyls of horse heart ferricytochrome c have been measured over the temperature range 278−328 K in order to interpret the “anomalous” temperature-dependence of the hyperfine shifts in terms of their pseudocontact and contact shifts. By taking advantage of the available pseudocontact shifts for protein nuclei measured at 303 and 323 K (Santos, H.; Turner, D. L. Eur. J. Biochem. 1992, 206, 721−728), the metal-centered pseudocontact shifts have been analyzed in terms of a thermally accessible excited state lying 355−590 cm-1 to higher energy which has a magnetic susceptibility tensor with the rhombic anisotropy, Δχrh, which is rotated by 90° to that of the ground state. The metal-centered pseudocontact shifts have been evaluated at all temperatures at which the chemical shifts were measured, and these calculated values were used to evaluate the contact shifts of each heme methyl for the two nuclei. The temperature dependence of the heme methyl contact shifts for b...

International audience; The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states.

Summary The interaction of Zn(II)- and Co(II)-carbonic anhydrase (CA) with a series of compounds possessing moieties resembling the aromatic sulfonamides, such as sulfamide, sulfamic acid, N -substituted aromatic sulfonamides, sulfenamides, sulfinic and seleninic acids, was investigated using kinetic and spectroscopic techniques. All these compounds inhibit the hydrasic and esterasic activity of the enzyme. Their binding within the active site of isozymes I and II is discussed on the basis of modifications of electronic and 1 H-NMR spectra of their adducts with the Co(II) enzyme. Some of these compounds represent novel classes of CA inhibitors, possessing equal or stronger potencies than the prototypical inhibitors, the unsubstituted sulfonamides. Qualitative structure-activity correlations are discussed.

Carbon-13 direct detection NMR provides a complementary tool for biomolecular applications, thanks to the development of a large variety of experimental variants and to recent improvements in instrumental sensitivity. It can be used as a general tool for any protein study and it can provide unique information very relevant for the characterization of a variety of different systems such as paramagnetic proteins and large multimeric protein assemblies, as well as intrinsically disordered proteins. The different properties of 13 C respect to 1 H, which provide the rational for the experiments developed, are discussed. The technical aspects that needed to be solved, as well as the many experimental variants developed to address different cases, are presented. Application areas where these experiment result particularly useful are also described.