Abstract：
:For biomolecular NMR structures typically only a poor correspondence is observed between statistics derived from the experimental input data and structural quality indicators obtained from the structure ensembles. Here, we investigate the relationship between the amount of available NMR data and structure quality. By generating datasets with a predetermined information content and evaluating the quality of the resulting structure ensembles we show that there is, in contrast to previous findings, a linear relation between the information contained in experimental data and structural quality. From this relation, a new quality parameter is derived that provides direct insight, on a per-residue basis, into the extent to which structural quality is governed by the experimental input data.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Nabuurs SB,Krieger E,Spronk CA,Nederveen AJ,Vriend G,Vuister GWdoi
10.1007/s10858-005-2826-5subject
Has Abstractpub_date
2005-10-01 00:00:00pages
123-34issue
2eissn
0925-2738issn
1573-5001journal_volume
33pub_type
杂志文章abstract：:The exchange broadening of backbone amide proton resonances of a 23-mer fusion peptide of the transmembrane subunit of HIV-1 envelope glycoprotein gp41, gp41-FP, was investigated at pH 5 and 7 at room temperature in perdeuterated sodium dodecyl sulfate (SDS) micellar solution. Comparison of resonance peaks for these p...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008399304450
更新日期：1998-11-01 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：: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
pub_type： 杂志文章
doi：10.1023/B:JNMR.0000019248.48726.ff
更新日期：2004-06-01 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
pub_type： 杂志文章
doi：10.1023/a:1018602220061
更新日期：1997-02-01 00:00:00
abstract：:We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further paramete...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00249-1
更新日期：2019-05-01 00:00:00
abstract：:Nearly complete backbone 1H, 15N and 13C signal assignments are reported for beta-hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although 15N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experimen...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00200435
更新日期：1996-06-01 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
pub_type： 杂志文章
doi：10.1023/a:1011208109853
更新日期：2001-07-01 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：:Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-008-9228-4
更新日期：2008-04-01 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
pub_type： 杂志文章
doi：10.1007/BF00176010
更新日期：1993-07-01 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：:A theoretical framework for the prediction of nuclear magnetic resonance (NMR) residual dipolar couplings (RDCs) in unfolded proteins under weakly aligning conditions is presented. The unfolded polypeptide chain is modeled as a random flight chain while the alignment medium is represented by a set of regularly arrange...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-007-9169-3
更新日期：2007-09-01 00:00:00
abstract：:G-matrix FT projection NMR spectroscopy was employed for resonance assignment of the 79-residue subunit c of the Escherichia coli F(1)F(0) ATP synthase embedded in micelles formed by lyso palmitoyl phosphatidyl glycerol (LPPG). Five GFT NMR experiments, that is, (3,2)D HNNCO, L-(4,3)D HNNC (alphabeta) C (alpha), L-(4,...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-008-9224-8
更新日期：2008-03-01 00:00:00
abstract：:A method is proposed to determine the conformational equilibrium of flexible polypeptides in solution, using the data provided by NMR spectroscopy and theoretical conformational calculations. The algorithm consists of the following three steps: (i) search of the conformational space in order to find conformations with...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008349424452
更新日期：1999-12-01 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
pub_type： 杂志文章
doi：10.1007/s10858-018-0197-y
更新日期：2018-06-01 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
pub_type： 杂志文章
doi：10.1007/s10858-020-00315-z
更新日期：2020-07-01 00:00:00
abstract：:15N-C alpha and 15N-C' J couplings were measured for the backbone of staphylococcal nuclease, uniformly enriched with 15N and 13C. It is found that the 1JC'N coupling is similar for beta-sheet, J = 14.8 +/- 0.5 and for alpha-helix, J = 14.8 +/- 0.4 but tends to be larger for the unstructured N- and C-terminal ends of ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF02192865
更新日期：1991-11-01 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
pub_type： 杂志文章
doi：10.1007/s10858-012-9683-9
更新日期：2013-01-01 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
pub_type： 杂志文章
doi：10.1007/s10858-017-0109-6
更新日期：2017-04-01 00:00:00
abstract：:We describe a general computational approach to site-specific resonance assignments in multidimensional NMR studies of uniformly (15)N,(13)C-labeled biopolymers, based on a simple Monte Carlo/simulated annealing (MCSA) algorithm contained in the program MCASSIGN2. Input to MCASSIGN2 includes lists of multidimensional ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9517-1
更新日期：2011-07-01 00:00:00
abstract：:The development of new protein labeling strategies, along with optimized experiments that exploit the label, have significantly impacted on the types of biochemical problems that can now be addressed by solution NMR spectroscopy. Here we describe how methyl labeling of key residues in a highly deuterated protein backg...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章,评审
doi：10.1007/s10858-009-9376-1
更新日期：2010-01-01 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
pub_type： 杂志文章
doi：10.1023/a:1014929925008
更新日期：2002-04-01 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
pub_type： 杂志文章
doi：10.1007/s10858-007-9215-1
更新日期：2008-02-01 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
pub_type： 杂志文章
doi：10.1007/s10858-016-0038-9
更新日期：2016-06-01 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
pub_type： 杂志文章
doi：10.1023/A:1018329420659
更新日期：1997-10-01 00:00:00
abstract：:Two-dimensional (2D) 1H NMR experiments using deuterium labeling have been carried out to investigate the solution of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), which consists of 155 amino acids. To simplify the 1H NMR spectra, two fully deuterated enzymes bearing several protonated amino acids were p...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF01875525
更新日期：1992-03-01 00:00:00
abstract：:Considerable excitement has been aroused by recent new methods for speeding up multidimensional NMR experiments by radically modifying the normal time-domain sampling protocols. These new schemes include the filter diagonalization method, GFT-NMR, the single-scan two-dimensional technique, Hadamard spectroscopy, and a...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1024960302926
更新日期：2003-10-01 00:00:00
abstract：:Selective water excitation schemes are provided which rely on the radiation damping effect in probeheads characterized by high quality factors. The schemes are implemented in homonuclear NOE and ROE experiments, designed for the selective observation of water-protein cross peaks and their assignment using standard pro...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00182286
更新日期：1995-06-01 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：: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
pub_type： 杂志文章
doi：10.1007/s10858-006-9070-5
更新日期：2006-09-01 00:00:00
