Methyl groups as probes of supra-molecular structure, dynamics and function.

abstract：:Although the order of the time steps in which the non-uniform sampling (NUS) schedule is implemented when acquiring multi-dimensional NMR spectra is of limited importance when sample conditions remain unchanged over the course of the experiment, it is shown to have major impact when samples are unstable. In the latter...

journal_title：Journal of biomolecular NMR

authors： Ying J,Barnes CA,Louis JM,Bax A

更新日期：2019-09-01 00:00:00

abstract：:The question is addressed of how maximal structural NOE data on double labelled proteins can be acquired with a minimal set of NOESY experiments. Two 3D-NOESY spectra are reported which, in concert with other commonly used spectra, provide a convenient strategy for NOE assignment. The 3D CNH-NOESY and 3D NCH-NOESY pro...

journal_title：Journal of biomolecular NMR

authors： Diercks T,Coles M,Kessler H

更新日期：1999-10-01 00:00:00

abstract：:Simulated neural networks are described which aid the assignment of protein NMR spectra. A network trained to recognize amino acid type from TOCSY data was trained on 148 assigned spin systems from E. coli acyl carrier proteins (ACPs) and tested on spin systems from spinach ACP, which has a 37% sequence homology with ...

journal_title：Journal of biomolecular NMR

authors： Hare BJ,Prestegard JH

更新日期：1994-01-01 00:00:00

abstract：:The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame whic...

journal_title：Journal of biomolecular NMR

authors： Xia Z,Nguyen BD,La Mar GN

更新日期：2000-06-01 00:00:00

abstract：:This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that meth...

journal_title：Journal of biomolecular NMR

authors： Farès C,Lakomek NA,Walter KF,Frank BT,Meiler J,Becker S,Griesinger C

更新日期：2009-09-01 00:00:00

abstract：:Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality s...

journal_title：Journal of biomolecular NMR

authors： Takeuchi K,Arthanari H,Shimada I,Wagner G

更新日期：2015-12-01 00:00:00

abstract：:Due to practical limitations in available 15N rf field strength, imperfections in 15N 180 degrees pulses arising from off-resonance effects can result in significant sensitivity loss, even if the chemical shift offset is relatively small. Indeed, in multi-dimensional NMR experiments optimized for protein backbone amid...

journal_title：Journal of biomolecular NMR

authors： Iwahara J,Clore GM

更新日期：2006-12-01 00:00:00

abstract：:Protein-fusion constructs have been used with great success for enhancing expression of soluble recombinant protein and as tags for affinity purification. Unfortunately the most popular tags, such as GST and MBP, are large, which hinders direct NMR studies of the fusion proteins. Cleavage of the fusion proteins often ...

journal_title：Journal of biomolecular NMR

authors： Zhou P,Lugovskoy AA,Wagner G

更新日期：2001-05-01 00:00:00

abstract：:Mollib is a software framework for the analysis of molecular structures, properties and data with an emphasis on data collected by NMR. It uses an open source model and a plugin framework to promote community-driven development of new and enhanced features. Mollib includes tools for the automatic retrieval and caching...

journal_title：Journal of biomolecular NMR

authors： Lorieau JL

更新日期：2017-10-01 00:00:00

abstract：:A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly (13)C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold v...

journal_title：Journal of biomolecular NMR

authors： Hansen AL,Kay LE

更新日期：2011-08-01 00:00:00

abstract：:We present a time-shared 3D HSQC-NOESY experiment that enables one to simultaneously record (13)C- and (15)N-dispersed spectra in Ile, Leu and Val (ILV) methyl-labeled samples. This experiment is designed to delineate the two spectra which would otherwise overlap with one another when acquired together. These spectra ...

journal_title：Journal of biomolecular NMR

authors： Frueh DP,Leed A,Arthanari H,Koglin A,Walsh CT,Wagner G

更新日期：2009-11-01 00:00:00

abstract：:Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. 15N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These ex...

journal_title：Journal of biomolecular NMR

authors： Tiwari VP,Pandit S,Vallurupalli P

更新日期：2019-02-01 00:00:00

abstract：:Dynamics of large-amplitude conformational motions in proteins are complex and less understood, although these processes are intimately associated with structure, folding, stability, and function of proteins. Here, we use a large set of spectra obtained by cross-relaxation suppressed exchange NMR spectroscopy (EXSY) t...

journal_title：Journal of biomolecular NMR

authors： Rao DK,Bhuyan AK

更新日期：2007-11-01 00:00:00

abstract：:Recently we have shown that HMQC spectra of protonated methyl groups in high molecular weight, highly deuterated proteins have large enhancements in sensitivity and resolution relative to HSQC-generated data sets. These enhancements derive from a TROSY effect in which complete cancellation of intra-methyl (1)H-(1)H an...

journal_title：Journal of biomolecular NMR

authors： Tugarinov V,Kay LE

更新日期：2004-02-01 00:00:00

abstract：:The kinetic process of folding of bovine pancreatic ribonuclease A in a 2H2O environment at pH 1.2 was examined by a recently developed temperature-jump NMR method (Akasaka et al., (1990) Rev. Sci. Instrum. 61, 66-68). Upon temperature-jump down from 45 degrees C to 29 degrees C, which was attained within 6 s, the pro...

journal_title：Journal of biomolecular NMR

authors： Akasaka K,Naito A,Nakatani H

更新日期：1991-05-01 00:00:00

abstract：:Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins with...

journal_title：Journal of biomolecular NMR

authors： Damman R,Lucini Paioni A,Xenaki KT,Beltrán Hernández I,van Bergen En Henegouwen PMP,Baldus M

更新日期：2020-09-01 00:00:00

abstract：:Solid-state NMR spectroscopy (ssNMR) has made significant progress towards the study of membrane proteins in their native cellular membranes. However, reduced spectroscopic sensitivity and high background signal levels can complicate these experiments. Here, we describe a method for ssNMR to specifically label a singl...

journal_title：Journal of biomolecular NMR

authors： Baker LA,Daniëls M,van der Cruijsen EA,Folkers GE,Baldus M

更新日期：2015-06-01 00:00:00

abstract：:The transmembrane protein YuaF from B. subtilis is a member of the NfeD-like clan with a potential role in maintaining membrane integrity during conditions of cellular stress. nfeD-genes are primarily found in highly conserved operon structures together with the gene of another membrane protein belonging to the SPFH s...

journal_title：Journal of biomolecular NMR

authors： Walker CA,Hinderhofer M,Witte DJ,Boos W,Möller HM

更新日期：2008-09-01 00:00:00

abstract：:1H alpha, 13C alpha, and 15N alpha secondary shifts, defined as the difference between the observed value and the random coil value, have been calculated for interleukin-1 receptor antagonist protein and interleukin-1 beta. Averaging of the secondary chemical shifts with those of adjacent residues was used to smooth o...

journal_title：Journal of biomolecular NMR

authors： Stockman BJ,Scahill TA,Strakalaitis NA,Brunner DP,Yem AW,Deibel MR Jr

更新日期：1992-11-01 00:00:00

abstract：:Two-dimensional (2D) 1H NMR experiments using deuterium labeling have been carried out to investigate the solution of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), which consists of 155 amino acids. To simplify the 1H NMR spectra, two fully deuterated enzymes bearing several protonated amino acids were p...

journal_title：Journal of biomolecular NMR

authors： Oda Y,Nakamura H,Yamazaki T,Nagayama K,Yoshida M,Kanaya S,Ikehara M

更新日期：1992-03-01 00:00:00

abstract：:S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S(3)E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrate...

journal_title：Journal of biomolecular NMR

authors： Novák P,Zídek L,Motácková V,Padrta P,Svenková A,Nuzillard JM,Krásný L,Sklenár V

更新日期：2010-02-01 00:00:00

abstract：:A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploi...

journal_title：Journal of biomolecular NMR

authors： Wiedemann C,Goradia N,Häfner S,Herbst C,Görlach M,Ohlenschläger O,Ramachandran R

更新日期：2015-10-01 00:00:00

abstract：:Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of...

journal_title：Journal of biomolecular NMR

authors： Tozawa K,Ferguson SJ,Redfield C,Smith LJ

更新日期：2015-06-01 00:00:00

abstract：:We report here the backbone 1HN, 15N, 13C alpha, 13CO, and 1H alpha NMR assignments for the catalytic domain of human fibroblast collagenase (HFC). Three independent assignment pathways (matching 1H, 13C alpha, and 13CO resonances) were used to establish sequential connections. The connections using 13C alpha resonanc...

journal_title：Journal of biomolecular NMR

authors： McCoy MA,Dellwo MJ,Schneider DM,Banks TM,Falvo J,Vavra KJ,Mathiowetz AM,Qoronfleh MW,Ciccarelli R,Cook ER,Pulvino TA,Wahl RC,Wang H

更新日期：1997-01-01 00:00:00

abstract：:Two new techniques offering considerable improvements in the quality of 1H photo-CIDNP spectra of proteins are demonstrated. Both focus on the problem of progressive photo-degradation of the flavin dye used to generate polarization in exposed tryptophan, tyrosine and histidine side-chains. One approach uses rapid addi...

journal_title：Journal of biomolecular NMR

authors： Maeda K,Lyon CE,Lopez JJ,Cemazar M,Dobson CM,Hore PJ

更新日期：2000-03-01 00:00:00

abstract：:Under the condition that the longitudinal relaxation time of spin I is shorter than the longitudinal relaxation time of spin S the steady-state magnetization in [S,I]-TROSY-type experiments can be enhanced by intermediate storage of a part of the steady-state magnetization of spin I on spin S with a pulse sequence ele...

journal_title：Journal of biomolecular NMR

authors： Riek R

更新日期：2001-10-01 00:00:00

abstract：:Protein-ligand titrations can readily be monitored with a trimethylsilyl (TMS) tag. Owing to the intensity, narrow line shape and unique chemical shift of a TMS group, dissociation constants can be determined from straightforward 1D 1H-NMR spectra not only in the fast but also in the slow exchange limit. The tag is ea...

journal_title：Journal of biomolecular NMR

authors： Becker W,Adams LA,Graham B,Wagner GE,Zangger K,Otting G,Nitsche C

更新日期：2018-04-01 00:00:00

abstract：:Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established ...

journal_title：Journal of biomolecular NMR

authors： Mikula KM,Krumwiede L,Plückthun A,Iwaï H

更新日期：2018-08-01 00:00:00

abstract：:Accessible surface area (ASA) is the surface area of an atom, amino acid or biomolecule that is exposed to solvent. The calculation of a molecule's ASA requires three-dimensional coordinate data and the use of a "rolling ball" algorithm to both define and calculate the ASA. For polymers such as proteins, the ASA for i...

journal_title：Journal of biomolecular NMR

authors： Hafsa NE,Arndt D,Wishart DS

更新日期：2015-07-01 00:00:00

abstract：:Silkworms serve as promising bioreactors for the production of recombinant proteins, including glycoproteins and membrane proteins, for structural and functional protein analyses. However, lack of methodology for stable isotope labeling has been a major deterrent to using this expression system for nuclear magnetic re...

journal_title：Journal of biomolecular NMR

authors： Yagi H,Nakamura M,Yokoyama J,Zhang Y,Yamaguchi T,Kondo S,Kobayashi J,Kato T,Park EY,Nakazawa S,Hashii N,Kawasaki N,Kato K

更新日期：2015-06-01 00:00:00