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Journal Cover Journal of Biomolecular NMR
  [SJR: 2.043]   [H-I: 89]   [7 followers]  Follow
    
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1573-5001 - ISSN (Online) 0925-2738
   Published by Springer-Verlag Homepage  [2355 journals]
  • POTENCI: prediction of temperature, neighbor and pH-corrected chemical
           shifts for intrinsically disordered proteins
    • Authors: Jakob Toudahl Nielsen; Frans A. A. Mulder
      Abstract: Chemical shifts contain important site-specific information on the structure and dynamics of proteins. Deviations from statistical average values, known as random coil chemical shifts (RCCSs), are extensively used to infer these relationships. Unfortunately, the use of imprecise reference RCCSs leads to biased inference and obstructs the detection of subtle structural features. Here we present a new method, POTENCI, for the prediction of RCCSs that outperforms the currently most authoritative methods. POTENCI is parametrized using a large curated database of chemical shifts for protein segments with validated disorder; It takes pH and temperature explicitly into account, and includes sequence-dependent nearest and next-nearest neighbor corrections as well as second-order corrections. RCCS predictions with POTENCI show root-mean-square values that are lower by 25–78%, with the largest improvements observed for 1Hα and 13C′. It is demonstrated how POTENCI can be applied to analyze subtle deviations from RCCSs to detect small populations of residual structure in intrinsically disorder proteins that were not discernible before. POTENCI source code is available for download, or can be deployed from the URL http://www.protein-nmr.org.
      PubDate: 2018-02-05
      DOI: 10.1007/s10858-018-0166-5
       
  • Simultaneous detection of intra- and inter-molecular paramagnetic
           relaxation enhancements in protein complexes
    • Authors: Cristina Olivieri; Manu Veliparambil Subrahmanian; Youlin Xia; Jonggul Kim; Fernando Porcelli; Gianluigi Veglia
      Abstract: Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein–protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner is labeled with stable isotopes (15N or 13C). Multiple paramagnetic labeled centers or reversed labeling schemes are often necessary to obtain sufficient distance restraints to model protein–protein complexes, making this approach time consuming and expensive. Here, we show a new strategy that combines a modified pulse sequence (1HN-Γ2-CCLS) with an asymmetric labeling scheme to enable the detection of both intra- and inter-molecular PREs simultaneously using only one sample preparation. We applied this strategy to the non-covalent dimer of ubiquitin. Our method confirmed the previously identified binding interface for the transient di-ubiquitin complex, and at the same time, unveiled the internal structural dynamics rearrangements of ubiquitin upon interaction. In addition to reducing the cost of sample preparation and speed up PRE measurements, by detecting the intra-molecular PRE this new strategy will make it possible to measure and calibrate inter-molecular distances more accurately for both symmetric and asymmetric protein–protein complexes.
      PubDate: 2018-02-02
      DOI: 10.1007/s10858-018-0165-6
       
  • A new class of CEST experiment based on selecting different magnetization
           components at the start and end of the CEST relaxation element: an
           application to 1 H CEST
    • Authors: Tairan Yuwen; Lewis E. Kay
      Abstract: Chemical exchange saturation transfer (CEST) experiments are becoming increasingly popular for investigating biomolecular exchange dynamics with rates on the order of approximately 50–500 s−1 and a rich toolkit of different methods has emerged over the past few years. Typically, experiments are based on the evolution of longitudinal magnetization, or in some cases two-spin order, during a fixed CEST relaxation delay, with the same class of magnetization prepared at the start and selected at end of the CEST period. Here we present a pair of TROSY-based pulse schemes for recording amide and methyl 1H CEST profiles where longitudinal magnetization at the start evolves to produce two-spin order that is then selected at the completion of the CEST element. This selection process subtracts out contributions from 1H–1H cross-relaxation on the fly that would otherwise complicate analysis of the data. It also obviates the need to record spin-state selective CEST profiles as an alternative to eliminating NOE effects, leading to significant improvements in sensitivity. The utility of the approach is demonstrated on a sample of a cavity mutant of T4 lysozyme that undergoes chemical exchange between conformations where the cavity is free and occupied.
      PubDate: 2018-01-19
      DOI: 10.1007/s10858-017-0161-2
       
  • (3, 2)D 1 H, 13 C BIRD r,X -HSQC-TOCSY for NMR structure elucidation of
           mixtures: application to complex carbohydrates
    • Authors: Natalia Brodaczewska; Zuzana Košťálová; Dušan Uhrín
      Abstract: Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1H chemical shifts; larger dispersion of 13C chemical shifts is often used to reduce this overlap, while still providing the proton–proton correlation information e.g. in the form of a 2D 1H, 13C HSQC-TOCSY experiment. For this methodology to work, 13C chemical shift must be resolved. In case of 13C chemical shifts overlap, 1H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F1 dimension. The required high-resolution in the 13C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.
      PubDate: 2018-01-11
      DOI: 10.1007/s10858-018-0163-8
       
  • Whole cell solid-state NMR study of Chlamydomonas reinhardtii microalgae
    • Authors: Alexandre A. Arnold; Jean-Philippe Bourgouin; Bertrand Genard; Dror E. Warschawski; Réjean Tremblay; Isabelle Marcotte
      Abstract: In vivo or whole-cell solid-state NMR is an emerging field which faces tremendous challenges. In most cases, cell biochemistry does not allow the labelling of specific molecules and an in vivo study is thus hindered by the inherent difficulty of identifying, among a formidable number of resonances, those arising from a given molecule. In this work we examined the possibility of studying, by solid-state NMR, the model organism Chlamydomonas reinhardtii fully and non-specifically 13C labelled. The extension of NMR-based dynamic filtering from one-dimensional to two-dimensional experiments enabled an enhanced selectivity which facilitated the assignment of cell constituents. The number of resonances detected with these robust and broadly applicable experiments appears to be surprisingly sparse. Various constituents, notably galactolipids abundant in organelle membranes, carbohydrates from the cell wall, and starch from storage grains could be unambiguously assigned. Moreover, the dominant crystal form of starch could be determined in situ. This work illustrates the feasibility and caveats of using solid-state NMR to study intact non-specifically 13C labelled micro-organisms.
      PubDate: 2018-01-11
      DOI: 10.1007/s10858-018-0164-7
       
  • Methyl group assignment using pseudocontact shifts with PARAssign
    • Authors: Mathilde Lescanne; Simon P. Skinner; Anneloes Blok; Monika Timmer; Linda Cerofolini; Marco Fragai; Claudio Luchinat; Marcellus Ubbink
      Pages: 183 - 195
      Abstract: A new version of the program PARAssign has been evaluated for assignment of NMR resonances of the 76 methyl groups in leucines, isoleucines and valines in a 25 kDa protein, using only the structure of the protein and pseudocontact shifts (PCS) generated with a lanthanoid tag at up to three attachment sites. The number of reliable assignments depends strongly on two factors. The principle axes of the magnetic susceptibility tensors of the paramagnetic centers should not be parallel so as to avoid correlated PCS. Second, the fraction of resonances in the spectrum of a paramagnetic sample that can be paired with the diamagnetic counterparts is critical for the assignment. With the data from two tag positions a reliable assignment could be obtained for 60% of the methyl groups and for many of the remaining resonances the number of possible assignments is limited to two or three. With a single tag, reliable assignments can be obtained for methyl groups with large PCS near the tag. It is concluded that assignment of methyl group resonances by paramagnetic tagging can be particularly useful in combination with some additional data, such as from mutagenesis or NOE-based experiments. Approaches to yield the best assignment results with PCS generating tags are discussed.
      PubDate: 2017-12-01
      DOI: 10.1007/s10858-017-0136-3
      Issue No: Vol. 69, No. 4 (2017)
       
  • Erratum to: Nitrogen detected TROSY at high field yields high resolution
           and sensitivity for protein NMR
    • Authors: Koh Takeuchi; Haribabu Arthanari; Ichio Shimada; Gerhard Wagner
      Pages: 245 - 245
      Abstract: The authors regret a mistake appeared in the supplement of this paper.
      PubDate: 2017-12-01
      DOI: 10.1007/s10858-017-0131-8
      Issue No: Vol. 69, No. 4 (2017)
       
  • Correction to: NMR structure of the HIV-1 reverse transcriptase thumb
           subdomain
    • Authors: Naima G. Sharaf; Andrew E. Brereton; In-Ja L. Byeon; P. Andrew Karplus; Angela M. Gronenborn
      Pages: 247 - 247
      Abstract: In the original publication of the article, the given name and family name of the author P. Andrew Karplus was published incorrectly. The name should read as "P. Andrew" – Given name and "Karplus" – Family name.
      PubDate: 2017-12-01
      DOI: 10.1007/s10858-017-0139-0
      Issue No: Vol. 69, No. 4 (2017)
       
  • Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in
           situ protein NMR analysis
    • Authors: Jia-Liang Chen; Yu Zhao; Yan-Jun Gong; Bin-Bin Pan; Xiao Wang; Xun-Cheng Su
      Abstract: Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein–ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.
      PubDate: 2017-12-09
      DOI: 10.1007/s10858-017-0160-3
       
  • Interaction study between HCV NS5A-D2 and NS5B using 19 F NMR
    • Authors: Marie Dujardin; François-Xavier Cantrelle; Guy Lippens; Xavier Hanoulle
      Abstract: The non structural protein 5A (NS5A) regulates the replication of the hepatitis C viral RNA through a direct molecular interaction of its domain 2 (NS5A-D2) with the RNA dependent RNA polymerase NS5B. Because of conflicting data in the literature, we study here this molecular interaction using fluorinated versions of the NS5A-D2 protein derived from the JFH1 Hepatitis C Virus strain. Two methods to prepare fluorine-labelled NS5A-D2 involving the biosynthetic incorporation of a 19F-tryptophan using 5-fluoroindole and the posttranslational introduction of fluorine by chemical conjugation of 2-iodo-N-(trifluoromethyl)acetamide with the NS5A-D2 cysteine side chains are presented. The dissociation constants (KD) between NS5A-D2 and NS5B obtained with these two methods are in good agreement, and yield values comparable to those derived previously from a surface plasmon resonance study. We compare benefits and limitations of both labeling methods to study the interaction between an intrinsically disordered protein and a large molecular target by 19F NMR.
      PubDate: 2017-12-07
      DOI: 10.1007/s10858-017-0159-9
       
  • Genetically encoded amino acids with tert -butyl and trimethylsilyl groups
           for site-selective studies of proteins by NMR spectroscopy
    • Authors: Choy Theng Loh; Luke A. Adams; Bim Graham; Gottfried Otting
      Abstract: The amino acids 4-(tert-butyl)phenylalanine (Tbf) and 4-(trimethylsilyl)phenylalanine (TMSf), as well as a partially deuterated version of Tbf (dTbf), were chemically synthesized and site-specifically incorporated into different proteins, using an amber stop codon, suppressor tRNA and the broadband aminoacyl-tRNA synthetase originally evolved for the incorporation of p-cyano-phenylalanine. The 1H-NMR signals of the tert-butyl and TMS groups were compared to the 1H-NMR signal of tert-butyltyrosine (Tby) in protein systems with molecular weights ranging from 8 to 54 kDa. The 1H-NMR resonance of the TMS group appeared near 0 ppm in a spectral region with few protein resonances, facilitating the observation of signal changes in response to ligand binding. In all proteins, the R 2 relaxation rate of the tert-butyl group of Tbf was only little greater than that of Tby (less than two-fold). Deuteration of the phenyl ring of Tbf made only a relatively small difference. The effective T 2 relaxation time of the TMS signal was longer than 140 ms even in the 54 kDa system.
      PubDate: 2017-12-02
      DOI: 10.1007/s10858-017-0157-y
       
  • Selective labeling and unlabeling strategies in protein solid-state NMR
           spectroscopy
    • Authors: Denis Lacabanne; Beat H. Meier; Anja Böckmann
      Abstract: Selective isotope labeling is central in NMR experiments and often allows to push the limits on the systems investigated. It has the advantage to supply additional resolution by diminishing the number of signals in the spectra. This is particularly interesting when dealing with the large protein systems which are currently becoming accessible to solid-state NMR studies. Isotope labeled proteins for NMR experiments are most often expressed in E. coli systems, where bacteria are grown in minimal media supplemented with 15NH4Cl and 13C-glucose as sole source of nitrogen and carbon. For amino acids selective labeling or unlabeling, specific amino acids are supplemented in the minimal medium. The aim is that they will be incorporated in the protein by the bacteria. However, E. coli amino-acid anabolism and catabolism tend to interconnect different pathways, remnant of a subway system. These connections lead to inter conversion between amino acids, called scrambling. A thorough understanding of the involved pathways is thus important to obtain the desired labeling schemes, as not all combinations of amino acids are adapted. We present here a detailed overview of amino-acid metabolism in this context. Each amino-acid pathway is described in order to define accessible combinations for 13C or 15N specific labeling or unlabeling. Using as example the ABC transporter BmrA, a membrane protein of 600 residues, we demonstrate how these strategies can be applied. Indeed, even though there is no size limit in solid-state NMR, large (membrane) proteins are still a challenge due to heavy signal overlap. To initiate resonance assignment in these large systems, we describe how selectively labeled samples can be obtained with the addition of labeled or unlabeled amino acids in the medium. The reduced spectral overlap enabled us to identify typical spectral fingerprints and to initiate sequential assignment using the more sensitive 2D DARR experiments with long mixing time showing inter-residue correlations. Graphical
      PubDate: 2017-12-02
      DOI: 10.1007/s10858-017-0156-z
       
  • Direct assignment of 13 C solid-state NMR signals of TF o F 1 ATP synthase
           subunit c -ring in lipid membranes and its implication for the ring
           structure
    • Authors: Su-Jin Kang; Yasuto Todokoro; Suyeon Bak; Toshiharu Suzuki; Masasuke Yoshida; Toshimichi Fujiwara; Hideo Akutsu
      Abstract: FoF1-ATP synthase catalyzes ATP hydrolysis/synthesis coupled with a transmembrane H+ translocation in membranes. The Fo c-subunit ring plays a major role in this reaction. We have developed an assignment strategy for solid-state 13C NMR (ssNMR) signals of the Fo c-subunit ring of thermophilic Bacillus PS3 (TFo c-ring, 72 residues), carrying one of the basic folds of membrane proteins. In a ssNMR spectrum of uniformly 13C-labeled sample, the signal overlap has been a major bottleneck because most amino acid residues are hydrophobic. To overcome signal overlapping, we developed a method designated as COmplementary Sequential assignment with MInimum Labeling Ensemble (COSMILE). According to this method, we generated three kinds of reverse-labeled samples to suppress signal overlapping. To assign the carbon signals sequentially, two-dimensional Cα(i+1)–C′Cα(i) correlation and dipolar assisted rotational resonance (DARR) experiments were performed under magic-angle sample spinning. On the basis of inter- and intra-residue 13C–13C chemical shift correlations, 97% of Cα, 97% of Cβ and 92% of C′ signals were assigned directly from the spectra. Secondary structure analysis predicted a hairpin fold of two helices with a central loop. The effects of saturated and unsaturated phosphatidylcholines on TFo c-ring structure were examined. The DARR spectra at 15 ms mixing time are essentially similar to each other in saturated and unsaturated lipid membranes, suggesting that TFo c-rings have similar structures under the different environments. The spectrum of the sample in saturated lipid membranes showed better resolution and structural stability in the gel state. The C-terminal helix was suggested to locate in the outer layer of the c-ring.
      PubDate: 2017-12-02
      DOI: 10.1007/s10858-017-0158-x
       
  • Rapid and reliable protein structure determination via chemical shift
           threading
    • Authors: Noor E. Hafsa; Mark V. Berjanskii; David Arndt; David S. Wishart
      Abstract: Protein structure determination using nuclear magnetic resonance (NMR) spectroscopy can be both time-consuming and labor intensive. Here we demonstrate how chemical shift threading can permit rapid, robust, and accurate protein structure determination using only chemical shift data. Threading is a relatively old bioinformatics technique that uses a combination of sequence information and predicted (or experimentally acquired) low-resolution structural data to generate high-resolution 3D protein structures. The key motivations behind using NMR chemical shifts for protein threading lie in the fact that they are easy to measure, they are available prior to 3D structure determination, and they contain vital structural information. The method we have developed uses not only sequence and chemical shift similarity but also chemical shift-derived secondary structure, shift-derived super-secondary structure, and shift-derived accessible surface area to generate a high quality protein structure regardless of the sequence similarity (or lack thereof) to a known structure already in the PDB. The method (called E-Thrifty) was found to be very fast (often < 10 min/structure) and to significantly outperform other shift-based or threading-based structure determination methods (in terms of top template model accuracy)—with an average TM-score performance of 0.68 (vs. 0.50–0.62 for other methods). Coupled with recent developments in chemical shift refinement, these results suggest that protein structure determination, using only NMR chemical shifts, is becoming increasingly practical and reliable. E-Thrifty is available as a web server at http://ethrifty.ca.
      PubDate: 2017-12-01
      DOI: 10.1007/s10858-017-0154-1
       
  • Solvent saturation transfer to proteins (SSTP) for structural and
           functional characterization of proteins
    • Authors: Pushpa Mishra; C. Ashley Barnes; Madeleine Strickland; Nico Tjandra
      Abstract: Protein structure determination using NMR is dependent on experimentally acquired distance restraints. Often, however, an insufficient number of these restraints are available for determining a protein’s correct fold, much less its detailed three-dimensional structure. In consideration of this problem, we propose a simple means to acquire supplemental structural restraints from protein surface accessibilities using solvent saturation transfer to proteins (SSTP), based on the principles of paramagnetic chemical-exchange saturation transfer. Here, we demonstrate the utility of SSTP in structure calculations of two proteins, TSG101 and ubiquitin. The observed SSTP was found to be directly proportional to solvent accessibility. Since SSTP does not involve the direct excitation of water, which compromises the analysis of protein protons entangled in the breadth of the water resonance, it has an advantage over conventional water-based magnetization transfers. Inclusion of structural restraints derived from SSTP improved both the precision and accuracy of the final protein structures in comparison to those determined by traditional approaches, when using minimal amounts of additional structural data. Furthermore, we show that SSTP can detect weak protein–protein interactions which are unobservable by chemical shift perturbations.
      PubDate: 2017-11-30
      DOI: 10.1007/s10858-017-0151-4
       
  • Enhancing the sensitivity of multidimensional NMR experiments by using
           triply-compensated π pulses
    • Authors: Youlin Xia; Paolo Rossi; Manu V. Subrahmanian; Chengdong Huang; Tamjeed Saleh; Cristina Olivieri; Charalampos G. Kalodimos; Gianluigi Veglia
      Abstract: In multidimensional solution NMR experiments, π pulses are used extensively for inversion and refocusing operations on 1H, 13C and 15N nuclei. Pulse miscalibration, off-resonance effects, and J-coupling evolution during π pulse execution result in severe signal losses that are exacerbated at high magnetic fields. Here, we report the implementation of a triply-compensated π pulse (G5) optimized for both inversion and refocusing in widely used 2- and 3-dimensional experiments. By replacing most of the hard π pulses, adiabatic or composite pulses on the 1H, 13C and 15N channels with G5 pulses, we obtained signal enhancements ranging from 80 to 240%. We anticipate that triply-compensated pulses will be crucial for improving the performance of multidimensional and multinuclear pulse sequences at ultra-high fields.
      PubDate: 2017-11-21
      DOI: 10.1007/s10858-017-0153-2
       
  • Label-free NMR-based dissociation kinetics determination
    • Authors: Pablo Trigo-Mouriño; Christian Griesinger; Donghan Lee
      Abstract: Understanding the dissociation of molecules is the basis to modulate interactions of biomedical interest. Optimizing drugs for dissociation rates is found to be important for their efficacy, selectivity, and safety. Here, we show an application of the high-power relaxation dispersion (RD) method to the determination of the dissociation rates of weak binding ligands from receptors. The experiment probes proton RD on the ligand and, therefore, avoids the need for any isotopic labeling. The large ligand excess eases the detection significantly. Importantly, the use of large spin-lock fields allows the detection of faster dissociation rates than other relaxation approaches. Moreover, this experimental approach allows to access directly the off-rate of the binding process without the need for analyzing a series of samples with increasing ligand saturation. The validity of the method is shown with small molecule interactions using two macromolecules, bovine serum albumin and tubulin heterodimers.
      PubDate: 2017-11-16
      DOI: 10.1007/s10858-017-0150-5
       
  • Bidirectional band-selective magnetization transfer along the protein
           backbone doubles the information content of solid-state NMR correlation
           experiments
    • Authors: M. M. Jolly; J. A. Jarvis; M. Carravetta; M. H. Levitt; P. T. F. Williamson
      Abstract: Resonance assignment is the first stage towards solving the structure of a protein. This is normally achieved by the employment of separate inter and intra residue experiments. By utilising the mixed rotation and rotary recoupling (MIRROR) condition it is possible to double the information content through the efficient bidirectional transfer of magnetization from the CO to its adjacent Cα and the Cα of the subsequent amino acid. We have incorporated this into a 3D experiment, a 3D-MIRROR-NCOCA, where correlations present in the 3D spectrum permit the sequential assignment of the protein backbone from a single experiment as we have demonstrated on a microcrystalline preparation of GB3. Furthermore, the low-power requirements of the MIRROR recoupling sequence facilitate the development of a low-power 3D-NCOCA experiment. This has enabled us to realise significant reductions in acquisition times, allowing the acquisition of a single 3D-NCOCA spectrum suitable for a full backbone resonance assignment of GB3 in less than 24 h.
      PubDate: 2017-11-08
      DOI: 10.1007/s10858-017-0147-0
       
  • Automatic methyl assignment in large proteins by the MAGIC algorithm
    • Authors: Yoan R. Monneau; Paolo Rossi; Anusarka Bhaumik; Chengdong Huang; Yajun Jiang; Tamjeed Saleh; Tao Xie; Qiong Xing; Charalampos G. Kalodimos
      Abstract: Selective methyl labeling is an extremely powerful approach to study the structure, dynamics and function of biomolecules by NMR. Despite spectacular progress in the field, such studies remain rather limited in number. One of the main obstacles remains the assignment of the methyl resonances, which is labor intensive and error prone. Typically, NOESY crosspeak patterns are manually correlated to the available crystal structure or an in silico template model of the protein. Here, we propose methyl assignment by graphing inference construct, an exhaustive search algorithm with no peak network definition requirement. In order to overcome the combinatorial problem, the exhaustive search is performed locally, i.e. for a small number of methyls connected through-space according to experimental 3D methyl NOESY data. The local network approach drastically reduces the search space. Only the best local assignments are combined together to provide the final output. Assignments that match the data with comparable scores are made available to the user for cross-validation by additional experiments such as methyl-amide NOEs. Several NMR datasets for proteins in the 25–50 kDa range were used during development and for performance evaluation against the manually assigned data. We show that the algorithm is robust, reliable and greatly speeds up the methyl assignment task.
      PubDate: 2017-11-02
      DOI: 10.1007/s10858-017-0149-y
       
  • The conformation of the Congo-red ligand bound to amyloid fibrils
           HET-s(218–289): a solid-state NMR study
    • Authors: Chandrakala Gowda; Giorgia Zandomeneghi; Herbert Zimmermann; Anne K. Schütz; Anja Böckmann; Matthias Ernst; Beat H. Meier
      Abstract: We have previously shown that Congo red (CR) binds site specifically to amyloid fibrils formed by HET-s(218–289) with the long axis of the CR molecule almost parallel to the fibril axis. HADDOCK docking studies indicated that CR adopts a roughly planar conformation with the torsion angle ϕ characterizing the relative orientation of the two phenyl rings being a few degrees. In this study, we experimentally determine the torsion angle ϕ at the center of the CR molecule when bound to HET-s(218–289) amyloid fibrils using solid-state NMR tensor-correlation experiments. The method described here relies on the site-specific 13C labeling of CR and on the analysis of the two-dimensional magic-angle spinning tensor-correlation spectrum of 13C2-CR. We determined the torsion angle ϕ to be 19°.
      PubDate: 2017-11-01
      DOI: 10.1007/s10858-017-0148-z
       
 
 
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