Structure and conformation in solution of the parallel-stranded hybrid alpha-d(CGCAATTCGC).beta-d(GCGTTAAGCG) by high-resolution 2D NMR.

abstract：:The process of resonance assignment represents a time-consuming and potentially error-prone bottleneck in structural studies of proteins by solid-state NMR (ssNMR). Software for the automation of this process is therefore of high interest. Procedures developed through the last decades for solution-state NMR are not di...

journal_title：Journal of biomolecular NMR

authors： Nielsen JT,Kulminskaya N,Bjerring M,Nielsen NC

更新日期：2014-06-01 00:00:00

abstract：:The solution molecular structure of the four-iron ferredoxin (Fd) from the hyperthermophilic archaeon Thermococcus litoralis (Tl) has been investigated by 1H NMR spectroscopy. TOCSY and NOESY experiments in H2O, tailored to detect both weakly and strongly relaxed resonances, together with steady-state NOEs in both H2O...

journal_title：Journal of biomolecular NMR

authors： Donaire A,Zhou ZH,Adams MM,La Mar GN

更新日期：1996-01-01 00:00:00

abstract：:The chemical shifts of (13)C2 of adenosine residues of DNA were observed to experience a through-space or trans-hydrogen bond isotope effect as a result of deuterium substitution at the imino hydrogen site of base-paired thymidine residues. NMR measurements of several self-complementary DNA duplexes at natural abundan...

journal_title：Journal of biomolecular NMR

authors： Vakonakis I,LiWang AC

更新日期：2004-05-01 00:00:00

abstract：:Four novel amino acid type-selective triple resonance experiments to identify the backbone amino proton and nitrogen resonances of Arg and Lys and of their sequential neighbors in (13C,15N)-labeled proteins are presented: the R(i+1)-HSQC and R(i,i+1)-HSQC select signals originating from Arg side chains, the K(i+1)-HSQ...

journal_title：Journal of biomolecular NMR

authors： Schubert M,Oschkinat H,Schmieder P

更新日期：2001-08-01 00:00:00

abstract：:We perform a detailed comparison of fast backbone dynamics probed at amide nitrogen versus carbonyl carbon sites for dematin headpiece C-terminal domain (DHP) and its S74E mutant (DHPS74E). Carbonyl dynamics is probed via auto-correlated longitudinal rates and transverse C'/C'-C(alpha) CSA/dipolar and C'/C'-N CSA/dipo...

journal_title：Journal of biomolecular NMR

authors： Vugmeyster L,Ostrovsky D,Li Y

更新日期：2010-06-01 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

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：:Ubiquitination plays an important role in many biological processes, including DNA repair, cell cycle regulation, and protein degradation. In the latter pathway the ubiquitin-conjugating enzymes or E2 enzymes are important proteins forming a key E2-ubiquitin thiolester prior to substrate labelling. While the structure...

journal_title：Journal of biomolecular NMR

authors： Merkley N,Shaw GS

更新日期：2003-06-01 00:00:00

abstract：:This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shif...

journal_title：Journal of biomolecular NMR

authors： Peng C,Unger SW,Filipp FV,Sattler M,Szalma S

更新日期：2004-08-01 00:00:00

abstract：:One-dimensional transient NOE build-up curves were measured for the synthetic disaccharide alpha-D-Fuc-(1-->4)-beta-D-GlcNAc 1 utilizing Gaussian shaped pulses. Simulated build-up curves from Metropolis Monte Carlo simulations were compared to the experimental data. Disaccharide 1 is structurally related to methyl bet...

journal_title：Journal of biomolecular NMR

authors： Weimar T,Meyer B,Peters T

更新日期：1993-07-01 00:00:00

abstract：:Protein expression in E. coli grown in shaker flasks is a routine and pivotal tool in many research laboratories. To maximize protein yields, cells are normally induced in the middle of the linear growth phase, typically at an OD600 of ≤ 1 for cells grown in Luria-Bertani (LB) medium at 37 °C. We recently showed that ...

journal_title：Journal of biomolecular NMR

authors： Cai M,Huang Y,Craigie R,Clore GM

更新日期：2019-12-01 00:00:00

abstract：:NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak...

journal_title：Journal of biomolecular NMR

authors： Johnson BA,Blevins RA

更新日期：1994-09-01 00:00:00

abstract：:Carr-Purcell-Meiboom-Gill relaxation dispersion (CPMG RD) NMR spectroscopy has emerged as a powerful tool for quantifying the kinetics and thermodynamics of millisecond time-scale exchange processes involving the interconversion between a visible ground state and one or more minor, sparsely populated invisible 'excite...

journal_title：Journal of biomolecular NMR

authors： Baldwin AJ,Kay LE

更新日期：2012-05-01 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：: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：: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：: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：:RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a sialic-acid-binding lectin purified from Rana catesbeiana (bullfrog) oocytes. This 111-amino acid protein exhibits cytotoxicity toward several tumor cell lines. In this paper we report the assignments of proton NMR resonances and the identification ...

journal_title：Journal of biomolecular NMR

authors： Chen C,Hom K,Huang RF,Chou PJ,Liao YD,Huang T

更新日期：1996-10-01 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：:Complex mixtures are at the heart of biology, and biomacromolecules almost always exhibit their function in a mixture, e.g., the mode of action for a spider venom is typically dependent on a cocktail of compounds, not just the protein. Information about diseases is encoded in body fluids such as urine and plasma in th...

journal_title：Journal of biomolecular NMR

authors： Björnerås J,Botana A,Morris GA,Nilsson M

更新日期：2014-04-01 00:00:00

abstract：:The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initial...

journal_title：Journal of biomolecular NMR

authors： Vila JA,Villegas ME,Baldoni HA,Scheraga HA

更新日期：2007-07-01 00:00:00

abstract：:In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignmen...

journal_title：Journal of biomolecular NMR

authors： Yamaguchi Y,Takizawa T,Kato K,Arata Y,Shimada I

更新日期：2000-12-01 00:00:00

abstract：:The interference between conformational exchange-induced time-dependent variations of chemical shifts in a pair of scalar coupled 1H and 15N spins is used to construct novel TROSY-type NMR experiments to suppress NMR signal loss in [15N,1H]-correlation spectra of a 14-mer DNA duplex free in solution and complexed with...

journal_title：Journal of biomolecular NMR

authors： Pervushin K

更新日期：2001-07-01 00:00:00

abstract：:Residual dipolar couplings (RDC) between nuclear spins in partially aligned samples offer unique insights into biomacromolecular structure and dynamics. To fully benefit from the RDC data, accurate knowledge of the magnitude ( D (a)) and rhombicity ( R ) of the molecular alignment tensor, A, is important. An extended ...

journal_title：Journal of biomolecular NMR

authors： Bryce DL,Bax A

更新日期：2004-03-01 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：:The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure c...

journal_title：Journal of biomolecular NMR

authors： Tang W,Bhatt A,Smith AN,Crowley PJ,Brady LJ,Long JR

更新日期：2016-02-01 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：:Melittin is a naturally occurring hexacosa peptide which forms an amphiphilic helix in methanol, a random coil in water, and a tetramer of helices at basic pH or in the presence of a high salt concentration. The monomeric structure in methanol has been well characterized by proton NMR (Pastore et al. (1989) Eur. Bioph...

journal_title：Journal of biomolecular NMR

authors： Buckley P,Edison AS,Kemple MD,Prendergast FG

更新日期：1993-11-01 00:00:00

abstract：:One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assig...

journal_title：Journal of biomolecular NMR

authors： Croft D,Kemmink J,Neidig KP,Oschkinat H

更新日期：1997-10-01 00:00:00

abstract：:NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often co...

journal_title：Journal of biomolecular NMR

authors： Niklasson M,Otten R,Ahlner A,Andresen C,Schlagnitweit J,Petzold K,Lundström P

更新日期：2017-10-01 00:00:00