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 E. coli ACP and a similar secondary structure. The output unit corresponding to the correct amino acid is one of the four most activated units in 83% of the spin systems tested. The utility of this information is illustrated by a second network which uses a constraint satisfaction algorithm to find the best fit of the spin systems to the amino acid sequence. Application to a stretch of 20 amino acids in spinach ACP results in 75% correct sequential assignment. Since the output of the amino acid type identification network can be coupled with a variety of sequential assignment strategies, the approach offers substantial potential for expediting assignment of protein NMR spectra.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Hare BJ,Prestegard JHdoi
10.1007/BF00178334subject
Has Abstractpub_date
1994-01-01 00:00:00pages
35-46issue
1eissn
0925-2738issn
1573-5001journal_volume
4pub_type
杂志文章abstract：:The hydrogen-deuterium exchange rates of the reduced and oxidized forms of Rhodobacter capsulatus cytochrome c2 were studied by 1H-15N homonuclear multiple quantum correlation spectroscopy. Minimal differences were observed for the N- and C-terminal helices on changing redox state suggesting that although these helice...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF01877226
更新日期：1991-07-01 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：: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：:We discuss the optimum experimental conditions to obtain assignment spectra for solid proteins at magic-angle spinning (MAS) frequencies around 100 kHz. We present a systematic examination of the MAS dependence of the amide proton T 2' times and a site-specific comparison of T 2' at 93 kHz versus 60 kHz MAS frequency....
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9975-y
更新日期：2015-10-01 00:00:00
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
pub_type： 杂志文章
doi：10.1007/s10858-011-9490-8
更新日期：2011-04-01 00:00:00
abstract：:Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and a...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1012927325963
更新日期：2001-11-01 00:00:00
abstract：:A simple constant-time 3D heteronuclear NMR pulse sequence has been developed to quantitatively determine the heteronuclear three-bond couplings 3J(HN,C') and 3J(H beta,C') in uniformly 13C-enriched proteins. The protocols for measuring accurate coupling constants are based on 1H,13C-heteronuclear relayed E.COSY [Schm...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00203824
更新日期：1996-03-01 00:00:00
abstract：:Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-015-9938-3
更新日期：2015-06-01 00:00:00
abstract：:Protein-fusion constructs have been used with great success for enhancing expression of soluble recombinant protein and as tags for affinity purification. Unfortunately the most popular tags, such as GST and MBP, are large, which hinders direct NMR studies of the fusion proteins. Cleavage of the fusion proteins often ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1011258906244
更新日期：2001-05-01 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：: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
pub_type： 杂志文章
doi：10.1007/s10858-013-9705-2
更新日期：2013-03-01 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 nuclear magnetic resonance (NMR) methods are described for the measurement of cross-correlation rates of zero- and double-quantum coherences involving two nitrogen nuclei belonging to successive amino acids in proteins and peptides. Rates due to the concerted fluctuations of two NH(N) dipole-dipole interactions an...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023076212536
更新日期：2003-04-01 00:00:00
abstract：:Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramag...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9532-2
更新日期：2011-11-01 00:00:00
abstract：:In aqueous solution, exchanging peptide NH protons experience two environments, that of the peptide itself with a relatively slow diffusion coefficient and that of the water solvent with a faster diffusion coefficient. Although in slow exchange on the NMR chemical shift timescale, the magnetic field gradient dependenc...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/A:1008393202076
更新日期：1999-01-01 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
pub_type： 杂志文章
doi：10.1023/a:1018615400129
更新日期：1997-01-01 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
pub_type： 杂志文章
doi：10.1007/s10858-014-9845-z
更新日期：2014-08-01 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
pub_type： 杂志文章
doi：10.1007/BF00190455
更新日期：1996-01-01 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
pub_type： 杂志文章
doi：10.1023/a:1021662423490
更新日期：2002-11-01 00:00:00
abstract：:Simultaneous data acquisition in time-sharing (TS) multi-dimensional NMR experiments has been shown an effective means to reduce experimental time, and thus to accelerate structure determination of proteins. This has been accomplished by spin evolution time-sharing of the X and Y heteronuclei, such as (15)N and (13)C,...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1025407905478
更新日期：2003-11-01 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：:Pulsed field gradients were incorporated into the HCACO experiment for acquiring spectra on isotopically enriched protein samples dissolved in H2O. Excellent water suppression and spectral quality were achieved using the modified pulse sequence (gd-HCACO), as demonstrated for a 13C-/15N-labeled sample of the SH2 domai...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00202041
更新日期：1996-05-01 00:00:00
abstract：:Relaxation measurements of side-chain 13CH2-groups of uniformly 13C labeled human ubiquitin were performed at 600 MHz and 800 MHz magnetic field strength at 30 degrees C. Dipole-dipole cross-correlated relaxation effects in T1 experiments were suppressed by the combination of radio-frequency pulses and pulsed field gr...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023833407515
更新日期：2003-07-01 00:00:00
abstract：:We present reduced dimensionality (RD) 3D HN(CA)NH for efficient sequential assignment in proteins. The experiment correlates the (15)N and (1)H chemical shift of a residue ('i') with those of its immediate N-terminal (i - 1) and C-terminal (i + 1) neighbors and provides four-dimensional chemical shift correlations ra...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9598-x
更新日期：2012-02-01 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
pub_type： 杂志文章
doi：10.1023/a:1024078926886
更新日期：2003-08-01 00:00:00
abstract：:An 'isotopomer-selected NOE' (ISNOE) method for the unequivocal identification of mutually hydrogen-bond-linked hydroxyl groups is described. It relies on the fact that the OH group's signal patterns obtained for a partially deuterated sample originate from both isotopomers of the 'partner' hydroxyl, whereas a NOE for...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/A:1008237308320
更新日期：1998-07-01 00:00:00
abstract：:Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR experiments are extremely powerful for characterizing millisecond time-scale conformational exchange processes in biomolecules. A large number of such CPMG experiments have now emerged for measuring protein backbone chemical shifts of sparsely populated (>0.5%...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-009-9310-6
更新日期：2009-09-01 00:00:00
abstract：:No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophy...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-020-00343-9
更新日期：2020-11-01 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：: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
