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 histogram method (EHM) is presented which extracts these parameters more effectively from dipolar coupling data. The method exploits the correlated nature of RDCs for structural elements of planar geometry, such as the one-bond (13)C'(i)-(13)C(i)(alpha), (13)C'(i)-(15)N(i+1), and (15)N(i+1)-(1)H(N)(i+1) couplings in peptide bonds of proteins, or suitably chosen combinations of (1) D (C1'H1'), (1) D (C2'H2'), (1) D (C1'C2'), (2) D (C2'H1'), (2) D (C1'H2'), and (3) D (H1'H2') couplings in nucleic acids, to generate an arbitrarily large number of synthetic RDCs. These synthetic couplings result in substantially improved histograms and resulting values of D (a) and R, compared with histograms generated solely from the original sets of correlated RDCs, particularly when the number of planar fragments for which couplings are available is small. An alternative method, complementary to the EHM, is also described, which uses a systematic grid search procedure, based on least-squares fitting of sets of correlated RDCs to structural elements of known geometry, and provides an unambiguous lower limit for the degree of molecular alignment.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Bryce DL,Bax Adoi
10.1023/B:JNMR.0000013701.16162.0csubject
Has Abstractpub_date
2004-03-01 00:00:00pages
273-87issue
3eissn
0925-2738issn
1573-5001pii
5253167journal_volume
28pub_type
杂志文章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
pub_type: 杂志文章
doi:10.1007/s10858-014-9857-8
更新日期:2014-11-01 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::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
pub_type: 杂志文章
doi:10.1007/s10858-016-0025-1
更新日期:2016-03-01 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
pub_type: 杂志文章
doi:10.1007/BF00211158
更新日期:1996-09-01 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
pub_type: 杂志文章
doi:10.1023/a:1008308128050
更新日期:1999-06-01 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::We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T2' -selective 1H-13C-13C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T2' selective scheme to frequency selecti...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-005-8073-y
更新日期:2005-07-01 00:00:00
abstract::We present heteronuclear three-dimensional gradient-NMR techniques for the resonanceassignment of exchangeable (-OH and -NH) protons in uniformly 13C isotopically enrichedoligosaccharides and for the measurement of 1H-1H nuclear Overhauser enhancementsinvolving these protons. These techniques are derived from conventi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/A:1018671517876
更新日期:1997-01-01 00:00:00
abstract::Two methods for the measurement of homonuclear 3J(HNH)alpha coupling constants are described. Both HSQC- and HMQC-type experiments employ 'quantitative J-correlation', in which the coupling constant of interest is obtained from the intensity ratio of cross peaks of two spectra. The first spectrum is acquired with 3J(H...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008343926502
更新日期:2000-01-01 00:00:00
abstract::The voltage-dependent anion channel (VDAC) is the most abundant protein of the outer mitochondrial membrane and constitutes the major pathway for the transport of ADP, ATP, and other metabolites. In this multidisciplinary study we combined solid-state NMR, electrophysiology, and molecular dynamics simulations, to stud...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-014-9876-5
更新日期:2015-04-01 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
pub_type: 杂志文章
doi:10.1007/s10858-007-9149-7
更新日期:2007-05-01 00:00:00
abstract::The systematic difference between T2 values obtained from CPMG and T1p experiments was observed for backbone 15N nuclei of bacterial ribonuclease barnase. Theoretical consideration suggests that the observed difference is caused by off-resonance effects of 180 degree pulses of the CPMG pulse train. Namely, at off-reso...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008348827208
更新日期:2000-07-01 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
pub_type: 杂志文章
doi:10.1023/B:JNMR.0000034351.37982.9e
更新日期:2004-08-01 00:00:00
abstract::It is proposed to obtain effective Lipari-Szabo order parameters and local correlation times for relaxation vectors of protein (13)CO nuclei by carrying out a (13)CO-R(1) auto relaxation experiment, a transverse (13)CO CSA/13CO-13Calpha CSA/dipolar cross correlation and a transverse (13)CO CSA/(13)CO-(15)N CSA/dipolar...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-006-9047-4
更新日期:2006-10-01 00:00:00
abstract::We demonstrate a novel sparse (13)C labelling approach for methylotrophic yeast P. pastoris expression system, towards solid-state NMR studies of eukaryotic membrane proteins. The labelling scheme was achieved by co-utilizing natural abundance methanol and specifically (13)C labelled glycerol as carbon sources in the ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0033-1
更新日期:2016-05-01 00:00:00
abstract::The conformation of chymotryptic fragment C2 of bacteriohodopsin (residues 1-71) was studied by 2D 1H NMR. The fragment was solubilized in a mixture of chloroform/methanol (1:1), 0.1 M LiClO4. Most of the resonances in 1H NMR spectra of fragment C2 were assigned using phase-sensitive DQF-COSY, TOCSY, and NOESY techniq...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF01875527
更新日期:1992-03-01 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
pub_type: 杂志文章
doi:10.1007/s10858-004-6729-7
更新日期:2005-02-01 00:00:00
abstract::Dynamics of large-amplitude conformational motions in proteins are complex and less understood, although these processes are intimately associated with structure, folding, stability, and function of proteins. Here, we use a large set of spectra obtained by cross-relaxation suppressed exchange NMR spectroscopy (EXSY) t...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-007-9186-2
更新日期:2007-11-01 00:00:00
abstract::Intramolecular correlations among the (18)O-labels of metabolic oligophosphates, mapped by J-decoupled (31)P NMR 2D chemical shift correlation spectroscopy, impart stringent constraints to the (18)O-isotope distributions over the whole oligophosphate moiety. The multiple deduced correlations of isotopic labels enable ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9515-3
更新日期:2011-07-01 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
pub_type: 杂志文章
doi:10.1007/s10858-018-0197-y
更新日期:2018-06-01 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
pub_type: 杂志文章
doi:10.1007/BF00211786
更新日期:1995-09-01 00:00:00
abstract::NMR relaxometry plays crucial role in studies of protein dynamics. The measurement of longitudinal and transverse relaxation rates of [Formula: see text]N is the main source of information on backbone motions. However, even the most basic approach exploiting a series of [Formula: see text]N HSQC spectra can require se...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-017-0115-8
更新日期:2017-06-01 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
pub_type: 杂志文章
doi:10.1007/s10858-013-9754-6
更新日期:2013-08-01 00:00:00
abstract::Backbone assignments for the isolated α-subunit of Salmonella typhimurium tryptophan synthase (TS) are reported based on triple resonance solution-state NMR experiments on a uniformly 2H,13C,15N-labeled sample. From the backbone chemical shifts, secondary structure and random coil index order parameters (RCI-S2) are p...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-020-00320-2
更新日期:2020-07-01 00:00:00
abstract::The advantages of non-uniform sampling (NUS) in offering time savings and resolution enhancement in NMR experiments have been increasingly recognized. The possibility of sensitivity gain by NUS has also been demonstrated. Application of NUS to multidimensional NMR experiments requires the selection of a sampling schem...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9923-x
更新日期:2015-05-01 00:00:00
abstract::Recently we have shown that HMQC spectra of protonated methyl groups in high molecular weight, highly deuterated proteins have large enhancements in sensitivity and resolution relative to HSQC-generated data sets. These enhancements derive from a TROSY effect in which complete cancellation of intra-methyl (1)H-(1)H an...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/B:JNMR.0000013824.93994.1f
更新日期:2004-02-01 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
pub_type: 杂志文章
doi:10.1007/s10858-020-00354-6
更新日期:2021-01-27 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
pub_type: 杂志文章
doi:10.1007/s10858-014-9841-3
更新日期:2014-08-01 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::Although the order of the time steps in which the non-uniform sampling (NUS) schedule is implemented when acquiring multi-dimensional NMR spectra is of limited importance when sample conditions remain unchanged over the course of the experiment, it is shown to have major impact when samples are unstable. In the latter...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-019-00235-7
更新日期:2019-09-01 00:00:00