Parametrisation of time-averaged distance restraints in MD simulations.

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：: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：:Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding (1)H,(15)N-HSQC NMR spectra for homologous protein...

journal_title：Journal of biomolecular NMR

authors： Robertson IM,Boyko RF,Sykes BD

更新日期：2011-09-01 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：:G protein-coupled receptors (GPCRs) are transmembrane signal transducers which regulate many key physiological process. Since their discovery, their analysis has been limited by difficulties in obtaining sufficient amounts of the receptors in high-quality, functional form from heterologous expression hosts. Albeit hig...

journal_title：Journal of biomolecular NMR

authors： Abiko LA,Rogowski M,Gautier A,Schertler G,Grzesiek S

更新日期：2021-01-27 00:00:00

abstract：:New base-type-edited transverse-relaxation optimized CT-HCN(C) experiments are presented that yield intra-base and sugar-to-base correlations for 13C-15N labeled RNA. High spectral resolution in the 13C and 15N dimensions is achieved by constant time (CT) frequency editing. A spectral editing filter applied during the...

journal_title：Journal of biomolecular NMR

authors： Van Melckebeke H,Pardi A,Boisbouvier J,Simorre JP,Brutscher B

更新日期：2005-08-01 00:00:00

abstract：:NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to ...

journal_title：Journal of biomolecular NMR

authors： Waudby CA,Ouvry M,Davis B,Christodoulou J

更新日期：2020-01-01 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：:Glycoproteins are characterized by the heterogeneous and dynamic nature of their glycan moieties, which hamper crystallographic analysis. NMR spectroscopy provides potential advantages in dealing with such complicated systems, given that the target molecules can be isotopically labeled. Methods of metabolic isotope la...

journal_title：Journal of biomolecular NMR

authors： Yanaka S,Yagi H,Yogo R,Yagi-Utsumi M,Kato K

更新日期：2018-07-01 00:00:00

abstract：:Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomeri...

journal_title：Journal of biomolecular NMR

authors： Shinya S,Ghinet MG,Brzezinski R,Furuita K,Kojima C,Shah S,Kovrigin EL,Fukamizo T

更新日期：2017-04-01 00:00:00

abstract：:Simultaneous recording of different NMR parameters is an efficient way to reduce the overall experimental time and speed up structural studies of biological macromolecules. This can especially be beneficial in the case of fast NMR-based drug screening applications or for collecting NOE restraints, where prohibitively ...

journal_title：Journal of biomolecular NMR

authors： Würtz P,Aitio O,Hellman M,Permi P

更新日期：2007-10-01 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

abstract：:Although beta-lactoglobulin (beta-LG) has been studied extensively for more than 50 years, its physical properties in solution are not yet understood fully in terms of its three-dimensional (3D) structure. For example, despite a recent high-resolution crystal structure, it is still not clear why the two common variant...

journal_title：Journal of biomolecular NMR

authors： Uhrínová S,Uhrín D,Denton H,Smith M,Sawyer L,Barlow PN

更新日期：1998-07-01 00:00:00

abstract：:We have developed an approach for simultaneous structure calculation and automatic Nuclear Overhauser Effect (NOE) assignment to solve nuclear magnetic resonance (NMR) structures from unassigned NOESY data. The approach, autoNOE-Rosetta, integrates Resolution Adapted Structural RECombination (RASREC) Rosetta NMR calcu...

journal_title：Journal of biomolecular NMR

authors： Lange OF

更新日期：2014-07-01 00:00:00

abstract：:The first reconstitution of an Fe2S2 ferredoxin with a diamagnetic prosthetic group was recently described [Kazanis et al. (1995) J. Am. Chem. Soc., 117, 6625-6626]. The replacement of the iron-sulfur cluster of the bacterial ferredoxin putidaredoxin (Pdx) by gallium (Ga3+) renders the protein diamagnetic and permits ...

journal_title：Journal of biomolecular NMR

authors： Kazanis S,Pochapsky TC

更新日期：1997-06-01 00:00:00

abstract：:A MAS solid state NMR approach for achieving efficient scalar coupling mediated through-bond (13)C chemical shift correlations of the aliphatic carbons in uniformly labelled peptides/proteins is described. The method involves the application of a continuous train of adiabatic inversion pulses, as in the adiabatic TOCS...

journal_title：Journal of biomolecular NMR

authors： Leppert J,Ohlenschläger O,Görlach M,Ramachandran R

更新日期：2004-06-01 00:00:00

abstract：:Prerequisite for chemical shift (CS) and CS tensor calculations are highly refined structures defining the molecular surroundings of the nuclei under study. Here, we present geometry optimizations with 13C and 15N CS constraints for large bio-molecules like peptides and proteins. The method discussed here provides bot...

journal_title：Journal of biomolecular NMR

authors： Sternberg U,Witter R

更新日期：2019-12-01 00:00:00

abstract：:Higher sensitivity of NMR spectrometers and novel isotopic labeling schemes have ushered the development of rapid data acquisition methodologies, improving the time resolution with which NMR data can be acquired. For nucleic acids, longitudinal relaxation optimization in conjunction with Ernst angle excitation (SOFAST...

journal_title：Journal of biomolecular NMR

authors： Sathyamoorthy B,Lee J,Kimsey I,Ganser LR,Al-Hashimi H

更新日期：2014-11-01 00:00:00

abstract：:19F solid-state NMR is an excellent approach for measuring long-range distances for structure determination and for studying molecular motion. For multi-fluorinated proteins, assignment of 19F chemical shifts has been traditionally carried out using mutagenesis. Here we show 2D 19F-13C correlation experiments that all...

journal_title：Journal of biomolecular NMR

authors： Shcherbakov AA,Roos M,Kwon B,Hong M

更新日期：2020-03-01 00:00:00

abstract：:The inclusion of explicit solvent water in molecular dynamics refinement of NMR structures ought to provide the most physically meaningful accounting for the effects of solvent on structure, but is computationally expensive. In order to evaluate the validity of commonly used vacuum refinements and of recently develope...

journal_title：Journal of biomolecular NMR

authors： Xia B,Tsui V,Case DA,Dyson HJ,Wright PE

更新日期：2002-04-01 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：:In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assign...

journal_title：Journal of biomolecular NMR

authors： Vammi V,Song G

更新日期：2015-12-01 00:00:00

abstract：:The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs runni...

journal_title：Journal of biomolecular NMR

authors： Delaglio F,Grzesiek S,Vuister GW,Zhu G,Pfeifer J,Bax A

更新日期：1995-11-01 00:00:00

abstract：:In aqueous solution, exchanging peptide NH protons experience two environments, that of the peptide itself with a relatively slow diffusion coefficient and that of the water solvent with a faster diffusion coefficient. Although in slow exchange on the NMR chemical shift timescale, the magnetic field gradient dependenc...

journal_title：Journal of biomolecular NMR

authors： Liu M,Toms HC,Hawkes GE,Nicholson JK,Lindon JC

更新日期：1999-01-01 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：:It has been demonstrated that protein folds can be determined using appropriate computational protocols with NMR chemical shifts as the sole source of experimental restraints. While such approaches are very promising they still suffer from low convergence resulting in long computation times to achieve accurate results...

journal_title：Journal of biomolecular NMR

authors： Rasia RM,Lescop E,Palatnik JF,Boisbouvier J,Brutscher B

更新日期：2011-11-01 00:00:00

abstract：:The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] 13C-filtered NOESY experiment that empl...

journal_title：Journal of biomolecular NMR

authors： Iwahara J,Wojciak JM,Clubb RT

更新日期：2001-03-01 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：:Many regulatory RNAs undergo dynamic exchanges that are crucial for their biological functions and NMR spectroscopy is a versatile tool for monitoring dynamic motions of biomolecules. Meaningful information on biomolecular dynamics requires an accurate measurement of relaxation parameters such as longitudinal (R1) rat...

journal_title：Journal of biomolecular NMR

authors： Nam H,Becette O,LeBlanc RM,Oh D,Case DA,Dayie TK

更新日期：2020-07-01 00:00:00

abstract：:Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the...

journal_title：Journal of biomolecular NMR

authors： Habeck M,Nilges M,Rieping W

更新日期：2008-02-01 00:00:00