Efficient sequential assignments in proteins with reduced dimensionality 3D HN(CA)NH.

abstract：:NMR spectroscopy was used to evaluate growth media and the cellular metabolome in two systems of interest to biomedical research. The first of these was a Chinese hamster ovary cell line engineered to express a recombinant protein. Here, NMR spectroscopy and a quantum mechanical total line shape analysis were utilized...

journal_title：Journal of biomolecular NMR

authors： Aranibar N,Borys M,Mackin NA,Ly V,Abu-Absi N,Abu-Absi S,Niemitz M,Schilling B,Li ZJ,Brock B,Russell RJ 2nd,Tymiak A,Reily MD

更新日期：2011-04-01 00:00:00

abstract：:Solid-state NMR spectra of membrane proteins often show significant line broadening at cryogenic temperatures. Here we investigate the effects of several cryoprotectants to preserve the spectral resolution of lipid membranes and membrane peptides at temperatures down to ~200 K. Trehalose, glycerol, dimethylsulfoxide (...

journal_title：Journal of biomolecular NMR

authors： Lee M,Hong M

更新日期：2014-08-01 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：: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：:The NMR derived translational diffusion coefficients were performed on unlabeled and uniformly labeled 13C,15N human insulin in water, both in neat, with zinc ions only, and in pharmaceutical formulation, containing only m-cresol as phenolic ligand, glycerol and zinc ions. The results show the dominant role of the pH ...

journal_title：Journal of biomolecular NMR

authors： Sitkowski J,Bocian W,Bednarek E,Urbańczyk M,Koźmiński W,Borowicz P,Płucienniczak G,Łukasiewicz N,Sokołowska I,Kozerski L

更新日期：2018-06-01 00:00:00

abstract：:We present and test two methods to use quantum chemical calculations to improve standard protein structure refinement by molecular dynamics simulations restrained to experimental NMR data. In the first, we replace the molecular mechanics force field (employed in standard refinement to supplement experimental data) for...

journal_title：Journal of biomolecular NMR

authors： Hsiao YW,Drakenberg T,Ryde U

更新日期：2005-02-01 00:00:00

abstract：:A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [(13)C, (15)N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3 mM sampl...

journal_title：Journal of biomolecular NMR

authors： Krähenbühl B,Lukavsky P,Wider G

更新日期：2014-08-01 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

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：:The Biological Magnetic Resonance Data Bank contains NMR chemical shift depositions for 132 RNAs and RNA-containing complexes. We have analyzed the (1)H NMR chemical shifts reported for non-exchangeable protons of residues that reside within A-form helical regions of these RNAs. The analysis focused on the central bas...

journal_title：Journal of biomolecular NMR

authors： Barton S,Heng X,Johnson BA,Summers MF

更新日期：2013-01-01 00:00:00

abstract：:A new isotope labeling technique for peptide segments in a protein sample was recently established using the protein splicing element intein [Yamazaki et al. (1998) J. Am. Chem. Soc., 120, 5591-5592]. This method makes it possible to observe signals of a selected amino (N-) or carboxyl (C-) terminal region along a pep...

journal_title：Journal of biomolecular NMR

authors： Otomo T,Teruya K,Uegaki K,Yamazaki T,Kyogoku Y

更新日期：1999-06-01 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 membrane proteins of viruses play critical roles in the virus life cycle and are attractive targets for therapeutic intervention. Virus-like particles (VLP) present the possibility to study the biochemical and biophysical properties of viral membrane proteins in their native environment. Specifically, the VLP cons...

journal_title：Journal of biomolecular NMR

authors： Antanasijevic A,Kingsley C,Basu A,Bowlin TL,Rong L,Caffrey M

更新日期：2016-03-01 00:00:00

abstract：:Analysis of 2D [(13)C,(1)H]-HSQC spectra of biosynthetic fractionally (13)C labeled proteins is a reliable, straightforward means to obtain stereospecific assignments of Val and Leu methyl sites in proteins. Herein we show that the same fractionally labeled protein sample facilitates observation and identification of ...

journal_title：Journal of biomolecular NMR

authors： Jacob J,Louis JM,Nesheiwat I,Torchia DA

更新日期：2002-11-01 00:00:00

abstract：:We present a computer algorithm for the automated assignment of polypeptide backbone and 13C beta resonances of a protein of known primary sequence. Input to the algorithm consists of cross peaks from several 3D NMR experiments: HNCA, HN(CA)CO, HN(CA)HA, HNCACB, COCAH, HCA(CO)N, HNCO, HN(CO)CA, HN(COCA)HA, and CBCA(CO...

journal_title：Journal of biomolecular NMR

authors： Lukin JA,Gove AP,Talukdar SN,Ho C

更新日期：1997-02-01 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：: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：:Staphylococcus aureus hibernation promoting factor (SaHPF) is a 22,2 kDa protein which plays a crucial role in 100S Staphylococcus aureus ribosome formation during stress. SaHPF consists of N-terminal domain (NTD) that prevents proteins synthesis by binding to the 30S subunit at the P- and A-sites, connected through a...

journal_title：Journal of biomolecular NMR

authors： Usachev KS,Validov SZ,Khusainov IS,Varfolomeev AA,Klochkov VV,Aganov AV,Yusupov MM

更新日期：2019-05-01 00:00:00

abstract：:The 3D HCCH-TOCSY and HCC(CO)NH-TOCSY experiments provide through bond connectivity and are used for side-chain chemical shift assignment by solution-state NMR. Careful design and implementation of the pulse sequence are key to the successful application of the technique particularly when trying to extract the maximum...

journal_title：Journal of biomolecular NMR

authors： Xia Y,Yuwen T,Rossi P

更新日期：2020-05-01 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

abstract：:As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale ...

journal_title：Journal of biomolecular NMR

authors： Rossi P,Swapna GV,Huang YJ,Aramini JM,Anklin C,Conover K,Hamilton K,Xiao R,Acton TB,Ertekin A,Everett JK,Montelione GT

更新日期：2010-01-01 00:00:00

abstract：:Sample solubility is essential for structural studies of proteins by solution NMR. Attachment of a solubility enhancement tag, such as GB1, MBP and thioredoxin, to a target protein has been used for this purpose. However, signal overlap of the tag with the target protein often made the spectral analysis difficult. Her...

journal_title：Journal of biomolecular NMR

authors： Kobashigawa Y,Kumeta H,Ogura K,Inagaki F

更新日期：2009-03-01 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：:Methyl (13)CHD(2) isotopomers of all methyl-containing amino-acids can be observed in residually protonated samples of large proteins obtained from [U-(13)C,(1)H]-glucose/D(2)O-based bacterial media, with sensitivity sufficient for a number of NMR applications. Selective detection of some subsets of methyl groups (Ala...

journal_title：Journal of biomolecular NMR

authors： Guo C,Tugarinov V

更新日期：2010-02-01 00:00:00

abstract：:Senktide is a highly specific and potent analog of neurokinin B, the natural ligand of the tachykinin receptor NK-3. The membrane-bound conformation of senktide, interacting with negatively charged membrane vesicles composed of perdeuterated phosphatidylcholine and phosphatidylglycerol (70:30), has been investigated u...

journal_title：Journal of biomolecular NMR

authors： Bersch B,Koehl P,Nakatani Y,Ourisson G,Milon A

更新日期：1993-07-01 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：:High-pressure NMR spectroscopy has emerged as a complementary approach for investigating various structural and thermodynamic properties of macromolecules. Noticeably absent from the array of experimental restraints that have been employed to characterize protein structures at high hydrostatic pressure is the residual...

journal_title：Journal of biomolecular NMR

authors： Fu Y,Wand AJ

更新日期：2013-08-01 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 solution structure of the SH3 domain of human p56 Lck tyrosine kinase (Lck-SH3) has been determined by multidimensional heteronuclear NMR spectroscopy. The structure was calculated from a total of 935 experimental restraints comprising 785 distance restraints derived from 1017 assigned NOE cross peaks and 150 dihe...

journal_title：Journal of biomolecular NMR

authors： Hiroaki H,Klaus W,Senn H

更新日期：1996-09-01 00:00:00

abstract：:13CHD2 methyl isotopomers are particularly useful to study methyl dynamics in proteins because, as compared with other methyl isotopomers, the 13C relaxation mechanism for this isotopomer is straightforward. However, in the case of proteins, where (omega tau)2 > 1, the refocused INEPT pulse sequence does not completel...

journal_title：Journal of biomolecular NMR

authors： Ishima R,Louis JM,Torchia DA

更新日期：2001-10-01 00:00:00