Efficient analysis of protein 2D NMR spectra using the software package EASY.

abstract：:Protein structure determination of low affinity complexes of interacting macromolecules is often hampered by a lack of observable NOEs between the binding partners. Covalent linkage offers a way to shift the equilibrium of the interaction partners to the bound state. Here we show that a single-chain protein containing...

journal_title：Journal of biomolecular NMR

authors： Freund C,Kühne R,Park S,Thiemke K,Reinherz EL,Wagner G

更新日期：2003-10-01 00:00:00

abstract：:For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simul...

journal_title：Journal of biomolecular NMR

authors： Schmid N,Allison JR,Dolenc J,Eichenberger AP,Kunz AP,van Gunsteren WF

更新日期：2011-11-01 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：:Spectral densities of the 15N amide in Escherichia coli ribonuclease HI, obtained from NMR relaxation experiments, were compared with those calculated using a molecular dynamics (MD) simulation. All calculations and comparisons assumed that the auto-correlation function describing the internal motions of the molecule ...

journal_title：Journal of biomolecular NMR

authors： Ishima R,Yamasaki K,Saito M,Nagayama K

更新日期：1995-09-01 00:00:00

abstract：:Simple pulse schemes are presented for the measurement of methyl (13)C and (1)H CSA values from (1)H-(13)C dipole/(13)C CSA and (1)H-(13)C dipole/(1)H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average (13)C CSA values are considerably smaller for Ile than Leu/Val (...

journal_title：Journal of biomolecular NMR

authors： Tugarinov V,Scheurer C,Brüschweiler R,Kay LE

更新日期：2004-12-01 00:00:00

abstract：:An improved version of the three-dimensional HCCH-COSY NMR experiment is described that correlates the resonances of geminal and vicinal proton pairs with the chemical shift of the 13C nucleus attached to one of the protons. The experiment uses constant-time evolution of transverse 13C magnetization which optimizes tr...

journal_title：Journal of biomolecular NMR

authors： Ikura M,Kay LE,Bax A

更新日期：1991-09-01 00:00:00

abstract：:Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The importance of the a...

journal_title：Journal of biomolecular NMR

authors： Feenstra KA,Peter C,Scheek RM,van Gunsteren WF,Mark AE

更新日期：2002-07-01 00:00:00

abstract：:Considerable excitement has been aroused by recent new methods for speeding up multidimensional NMR experiments by radically modifying the normal time-domain sampling protocols. These new schemes include the filter diagonalization method, GFT-NMR, the single-scan two-dimensional technique, Hadamard spectroscopy, and a...

journal_title：Journal of biomolecular NMR

authors： Freeman R,Kupce E

更新日期：2003-10-01 00:00:00

abstract：:In this work, we show how the water flip-back approach that is widely employed in solution-state NMR can be adapted to proton-detected MAS solid-state NMR of highly deuterated proteins. The scheme allows to enhance the sensitivity of the experiment by decreasing the recovery time of the proton longitudinal magnetizati...

journal_title：Journal of biomolecular NMR

authors： Chevelkov V,Xiang S,Giller K,Becker S,Lange A,Reif B

更新日期：2015-02-01 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：:We have developed an improved isotope-filtered pulse scheme in combination with a double-tuned filter, a hyperbolic secant inversion pulse, and a z-filter with a pulsed field gradient. These filtering pulse schemes have been incorporated into several one-, two-, and three-dimensional experiments, which were applied to...

journal_title：Journal of biomolecular NMR

authors： Ogura K,Terasawa H,Inagaki F

更新日期：1996-12-01 00:00:00

abstract：:Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attent...

journal_title：Journal of biomolecular NMR

authors： Gledhill JM Jr,Wand AJ

更新日期：2012-01-01 00:00:00

abstract：:No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophy...

journal_title：Journal of biomolecular NMR

authors： Keiffer S,Carneiro MG,Hollander J,Kobayashi M,Pogoryelev D,Ab E,Theisgen S,Müller G,Siegal G

更新日期：2020-11-01 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：:We have developed a tool for computer-assisted assignments of protein NMR spectra from triple resonance data. The program is designed to resemble established manual assignment procedures as closely as possible. IBIS exports its results in XEASY format. Thus, using IBIS the operator has continuous visual and accounting...

journal_title：Journal of biomolecular NMR

authors： Hyberts SG,Wagner G

更新日期：2003-08-01 00:00:00

abstract：:HET(ex)-SOFAST NMR (Schanda et al. in J Biomol NMR 33:199-211, 2006) has been proposed some years ago as a fast and sensitive method for semi-quantitative measurement of site-specific amide-water hydrogen exchange effects along the backbone of proteins. Here we extend this concept to BEST readout sequences that provid...

journal_title：Journal of biomolecular NMR

authors： Rennella E,Solyom Z,Brutscher B

更新日期：2014-11-01 00:00:00

abstract：:Three different conformations of proline rings in a protein in solution, Up, Down and Twist, have been distinguished, and stereospecific assignments of the pyrrolidine beta-, gamma- and delta-hydrogens have been made on the basis of 1H-1H vicinal coupling constant patterns and intraresidue NOEs. For all three conforma...

journal_title：Journal of biomolecular NMR

authors： Cai M,Huang Y,Liu J,Krishnamoorthi R

更新日期：1995-09-01 00:00:00

abstract：:In 2HJ(NN)-COSY experiments, which correlate protons with donor/acceptor nitrogens across Nd...HNa bonds, the receptor nitrogen needs to be assigned in order to unambiguously identify the hydrogen bond. For many situations this is a non-trivial task which is further complicated by poor dispersion of (Na,Nd) resonances...

journal_title：Journal of biomolecular NMR

authors： Majumdar A,Gosser Y,Patel DJ

更新日期：2001-12-01 00:00:00

abstract：:Recent progress in magic-angle spinning (MAS) solid-state NMR (SSNMR) has enabled multidimensional studies of large, macroscopically unoriented membrane proteins with associated lipids, without the requirement of solubility that limits other structural techniques. Here we present initial sample preparation and SSNMR s...

journal_title：Journal of biomolecular NMR

authors： Frericks HL,Zhou DH,Yap LL,Gennis RB,Rienstra CM

更新日期：2006-09-01 00:00:00

abstract：:Methyl groups have emerged as powerful probes of protein dynamics with timescales from picoseconds to seconds. Typically, studies involving high molecular weight complexes exploit (13)CH3- or (13)CHD2-labeling in otherwise highly deuterated proteins. The (13)CHD2 label offers the unique advantage of providing (13)C, (...

journal_title：Journal of biomolecular NMR

authors： Rennella E,Schuetz AK,Kay LE

更新日期：2016-06-01 00:00:00

abstract：:The solvent-exposed regions of (U-13C)ascomycin when bound to its putative target protein, FKBP, have been identified based on the different proton longitudinal relaxation rates (R1 = 1/T1) measured in the absence and presence of the paramagnetic relaxation reagent, 4-hydroxy-2,2,6,6-tetramethyl-piperidinyl-1-oxy (HyT...

journal_title：Journal of biomolecular NMR

authors： Petros AM,Neri P,Fesik SW

更新日期：1992-01-01 00:00:00

abstract：:The biological environment in which a protein performs its function is a crowded milieu containing millions of molecules that can potentially lead to a great many transient, non-specific interactions. NMR spectroscopy is especially well suited to study these weak molecular contacts. Here, non-specific interactions bet...

journal_title：Journal of biomolecular NMR

authors： Latham MP,Kay LE

更新日期：2013-03-01 00:00:00

abstract：:The arrival of very high field magnets and cryogenic circuitries, and the development of relaxation-optimized pulse sequences have added powerful tools for increasing sensitivity and resolution in NMR studies of biomacromolecules. The potential of these advances is not fully realized in practice, however, since curren...

journal_title：Journal of biomolecular NMR

authors： Rovnyak D,Hoch JC,Stern AS,Wagner G

更新日期：2004-09-01 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：:NifU-like proteins are a highly conserved protein that serves as the scaffold for assembly of Fe-S clusters. Chloroplastic NifU-like proteins have tandem NifU like domains, named domain I and domain II. Although the amino acid sequences of these domains are very similar to each other, the predicted functional region f...

journal_title：Journal of biomolecular NMR

authors： Kumeta H,Ogura K,Asayama M,Katoh S,Katoh E,Teshima K,Inagaki F

更新日期：2007-06-01 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：:The kinetics of lanthanide (III) exchange for calcium(II) in the C-terminal EF-hand of the protein calbindin D9k have 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) ...

journal_title：Journal of biomolecular NMR

authors： Barbieri R,Hore PJ,Luchina C,Pierattelli R

更新日期：2002-08-01 00:00:00

abstract：:This paper describes the use of single transition-to-single transition polarization transfer (ST2-PT) in transverse relaxation-optimized spectroscopy (TROSY), where it affords a [Formula: see text] sensitivity enhancement for kinetically stable amide 15N-1H groups in proteins. Additional, conventional improvements of ...

journal_title：Journal of biomolecular NMR

authors： Pervushin KV,Wider G,Wüthrich K

更新日期：1998-08-01 00:00:00

abstract：:A pulse sequence is described for recording single-quantum (13)C-methyl relaxation dispersion profiles of (13)C-selectively labeled methyl groups in proteins that offers significant improvements in sensitivity relative to existing approaches where initial magnetization derives from (13)C polarization. Sensitivity gain...

journal_title：Journal of biomolecular NMR

authors： Lundström P,Vallurupalli P,Religa TL,Dahlquist FW,Kay LE

更新日期：2007-05-01 00:00:00

abstract：:The key to obtaining the model-free description of the dynamics of a macromolecule is the optimisation of the model-free and Brownian rotational diffusion parameters using the collected R (1), R (2) and steady-state NOE relaxation data. The problem of optimising the chi-squared value is often assumed to be trivial, ho...

journal_title：Journal of biomolecular NMR

authors： d'Auvergne EJ,Gooley PR

更新日期：2008-02-01 00:00:00