Abstract：
:Many nucleic acids and proteins require divalent metal ions such as Mg(2+) and Ca(2+) for folding and function. The lipophilic alignment media frequently used as membrane mimetics also bind these divalent metals. Here we demonstrate the use of (31)P NMR spectrum of a metal ion chelator (deoxycytidine diphosphate) to measure the bound [Mg(2+)] and [Ca(2+)] in situ for several biological model systems at relatively high divalent ion concentrations (1-10 mM). This method represents a general approach to measuring divalent metal ion binding in NMR samples where the amount and type of metal ion added to the system is known.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Kozlyuk N,Sengupta S,Lupták A,Martin RWdoi
10.1007/s10858-016-0031-3subject
Has Abstractpub_date
2016-04-01 00:00:00pages
269-73issue
4eissn
0925-2738issn
1573-5001pii
10.1007/s10858-016-0031-3journal_volume
64pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1007/BF00211786
更新日期：1995-09-01 00:00:00
abstract：:NMR spectra of ubiquitin in the presence of bicelles at a concentration of 32% w/v have been recorded at 700 MHz under sample spinning conditions at the magic angle (54.7 degrees ) and at an angle of 45.5 degrees . At the magic angle, the 1H-15N HSQC spectrum of ubiquitin in bicelles is virtually indistinguishable fro...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-005-3210-1
更新日期：2005-11-01 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
pub_type： 杂志文章
doi：10.1007/s10858-015-9957-0
更新日期：2015-07-01 00:00:00
abstract：:Paramagnetic relaxation enhancement (PRE) measurements constitute a powerful approach for detecting both permanent and transient protein-protein interactions. Typical PRE experiments require an intrinsic or engineered paramagnetic site on one of the two interacting partners; while a second, diamagnetic binding partner...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0165-6
更新日期：2018-03-01 00:00:00
abstract：:Scalar coupling correlations across hydrogen bonds with carbonyl groups as acceptors have been observed in a variety of proteins, but not in nucleic acids. Here we present a pulse scheme that allows such an observation and quantification of trans-hydrogen bond 3hJ(NC)' correlations in nucleic acid base pairs, between ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008307115641
更新日期：2000-04-01 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
pub_type： 杂志文章
doi：10.1023/a:1026776721348
更新日期：2000-12-01 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
pub_type： 杂志文章
doi：10.1007/s10858-006-9089-7
更新日期：2006-12-01 00:00:00
abstract：:The use of pulsed field gradients in multiple-pulse NMR experiments has many advantages, including the possibility of obtaining excellent water suppression without the need for selective presaturation. In such gradient experiments the water magnetization is dephased deliberately; exchange between the saturated protons...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00211750
更新日期：1995-04-01 00:00:00
abstract：:The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023060720156
更新日期：2003-05-01 00:00:00
abstract：:We present a computational method for finding optimal labeling patterns for the backbone assignment of membrane proteins and other large proteins that cannot be assigned by conventional strategies. Following the approach of Kainosho and Tsuji (Biochemistry 21:6273-6279 (1982)), types of amino acids are labeled with (1...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-010-9462-4
更新日期：2011-02-01 00:00:00
abstract：:Three experiments are introduced to determine a complete set of coupling constants in RNA oligomers. In the HCCH-E.COSY experiment, the vicinal proton-proton coupling constants can be measured with high accuracy. In the P-FIDS-CT-HSQC experiment, vicinal proton-phosphorus and carbon-phosphorus couplings are measured t...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00404274
更新日期：1994-09-01 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
pub_type： 杂志文章
doi：10.1007/s10858-018-00223-3
更新日期：2019-02-01 00:00:00
abstract：:High amino acid coverage labeling of the mammalian G protein coupled receptors (GPCR) rhodopsin was established with 15N and 15N/13C isotopes. Rhodopsin was expressed at preparative scale in HEK293S cells and studied in full-length by NMR spectroscopy in detergent micelle solution. This resulted in the assignment and ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-007-9205-3
更新日期：2008-01-01 00:00:00
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
pub_type： 杂志文章
doi：10.1023/a:1024983029700
更新日期：2003-10-01 00:00:00
abstract：:A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章,评审
doi：10.1007/s10858-009-9365-4
更新日期：2010-01-01 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
pub_type： 杂志文章
doi：10.1007/BF00198369
更新日期：1993-11-01 00:00:00
abstract：:Novel alpha/beta-half-filter elements are proposed for the separation of the high-field and low-field component of 1JHC and 1JHN splittings into different subspectra. The alpha/beta-half-filter elements are of the same duration as the S3CT pulse sequence element and, like this, are less sensitive to cross talk between...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008239027287
更新日期：1998-10-01 00:00:00
abstract：:Recent efforts to reduce the measurement time for multidimensional NMR experiments have fostered the development of a variety of new procedures for sampling and data processing. We recently described concentric ring sampling for 3-D NMR experiments, which is superior to radial sampling as input for processing by a mul...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-008-9275-x
更新日期：2008-12-01 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
pub_type： 杂志文章
doi：10.1007/s10858-017-0142-5
更新日期：2017-10-01 00:00:00
abstract：:Hydroxyl protons on serine and threonine residues are not well characterized in protein structures determined by both NMR spectroscopy and X-ray crystallography. In the case of NMR spectroscopy, this is in large part because hydroxyl proton signals are usually hidden under crowded regions of (1)H-NMR spectra and remai...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-013-9799-6
更新日期：2014-01-01 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
pub_type： 杂志文章
doi：10.1007/BF02192797
更新日期：1992-01-01 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
pub_type： 杂志文章
doi：10.1007/s10858-005-8872-1
更新日期：2005-08-01 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
pub_type： 杂志文章
doi：10.1007/BF02192848
更新日期：1992-11-01 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
pub_type： 杂志文章
doi：10.1007/BF01874569
更新日期：1991-05-01 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
pub_type： 杂志文章
doi：10.1007/s10858-017-0141-6
更新日期：2017-10-01 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
pub_type： 杂志文章
doi：10.1007/BF00197809
更新日期：1995-11-01 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
pub_type： 杂志文章
doi：10.1007/s10858-015-9976-x
更新日期：2015-10-01 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
pub_type： 杂志文章
doi：10.1023/B:JNMR.0000019507.95667.3e
更新日期：2004-05-01 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
pub_type： 杂志文章
doi：10.1023/a:1008351128089
更新日期：2000-03-01 00:00:00
abstract：:Extensive spectral overlap presents a major problem for the NMR study of large RNAs. Here we present NMR techniques for resolution enhancement and spectral simplification of fully 13C labelled RNA. High-resolution 1H-13C correlation spectra are obtained by combining TROSY-type experiments with multiple-band-selective ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008340210079
更新日期：2001-02-01 00:00:00
