Chemical shifts and three-dimensional protein structures.

Abstract:

:During the past three years it has become possible to compute ab initio the 13C, 15N and 19F NMR chemical shifts of many sites in native proteins. Chemical shifts are beginning to become a useful supplement to more established methods of solution structure determination, and may find utility in solid-state analysis as well. From 13C NMR, information on phi, psi and chi torsions can be obtained, permitting both assignment verification, and structure refinement and prediction. For 15N, both torsional and hydrogen-bonding effects are important, while for 19F, chemical shifts are primarily indicators of the local charge field. Chemical shift calculations are still slow, but shielding hypersurfaces - the shift as a function of the dihedral angles that define the molecular conformation - are becoming accessible. Over the next few years, theoretical and computer hardware improvements will enable more routine use of chemical shifts in structural studies, including the study of metal-ligand interactions, the analysis of drug and substrate binding and catalysis, the study of folding/unfolding pathways, as well as the characterization of conformational substates. Rather than simply being a necessary prerequisite for multidimensional NMR, chemical shifts and chemical shift non-equivalence due to folding are now beginning to be useful for structural characterization.

journal_name

J Biomol NMR

authors

Oldfield E

doi

10.1007/BF00211749

subject

Has Abstract

pub_date

1995-04-01 00:00:00

pages

217-25

issue

3

eissn

0925-2738

issn

1573-5001

journal_volume

5

pub_type

杂志文章,评审
  • Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H, 13C, 31P triple resonance experiment: HCP-CCH-TOCSY.

    abstract::A three-dimensional 1H, 13C, 31P triple resonance experiment, HCP-CCH-TOCSY, is presented which provides unambiguous through-bond correlation of all 1H ribose protons on the 5' and 3' sides of the intervening phosphorus along the backbone bonding network in 13C-labeled RNA oligonucleotides. The correlation of the comp...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00227473

    authors: Marino JP,Schwalbe H,Anklin C,Bermel W,Crothers DM,Griesinger C

    更新日期:1995-01-01 00:00:00

  • Comparison of amide proton exchange in reduced and oxidized Rhodobacter capsulatus cytochrome c2: a 1H-15N NMR study.

    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

    authors: Gooley PR,Zhao D,MacKenzie NE

    更新日期:1991-07-01 00:00:00

  • Trans-hydrogen bond deuterium isotope effects of A:T base pairs in DNA.

    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

    authors: Vakonakis I,LiWang AC

    更新日期:2004-05-01 00:00:00

  • Triple resonance ¹⁵Ν NMR relaxation experiments for studies of intrinsically disordered proteins.

    abstract::Description of protein dynamics is known to be essential in understanding their function. Studies based on a well established [Formula: see text] NMR relaxation methodology have been applied to a large number of systems. However, the low dispersion of [Formula: see text] chemical shifts very often observed within intr...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-017-0138-1

    authors: Srb P,Nováček J,Kadeřávek P,Rabatinová A,Krásný L,Žídková J,Bobálová J,Sklenář V,Žídek L

    更新日期:2017-11-01 00:00:00

  • High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN.

    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

    authors: Coggins BE,Zhou P

    更新日期:2008-12-01 00:00:00

  • Determination of molecular alignment tensors without backbone resonance assignment: Aid to rapid analysis of protein-protein interactions.

    abstract::Based on high-resolution structures of the free molecules accurate determination of structures of protein complexes by NMR spectroscopy is possible using residual dipolar couplings. In order, however, to be able to apply these methods, protein backbone resonances have to be assigned first. This NMR assignment process ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1024768328860

    authors: Zweckstetter M

    更新日期:2003-09-01 00:00:00

  • A solubility-enhancement tag (SET) for NMR studies of poorly behaving proteins.

    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

    authors: Zhou P,Lugovskoy AA,Wagner G

    更新日期:2001-05-01 00:00:00

  • Practical considerations over spectral quality in solid state NMR spectroscopy of soluble proteins.

    abstract::Great theoretical and methodological advances are pushing the limits of resolution and sensitivity in solid state NMR (SSNMR). However, sample preparation remains a critical issue for the success of an experiment. The factors affecting spectral quality in SSNMR samples are discussed, examining cases encountered in the...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-013-9776-0

    authors: Fragai M,Luchinat C,Parigi G,Ravera E

    更新日期:2013-10-01 00:00:00

  • Methyl groups as probes of supra-molecular structure, dynamics and function.

    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

    authors: Ruschak AM,Kay LE

    更新日期:2010-01-01 00:00:00

  • Improved photo-CIDNP methods for studying protein structure and folding.

    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

    authors: Maeda K,Lyon CE,Lopez JJ,Cemazar M,Dobson CM,Hore PJ

    更新日期:2000-03-01 00:00:00

  • (1)H, (13)C and (15)N NMR backbone assignments of the 269-residue serine protease PB92 from Bacillus alcalophilus.

    abstract::The (1)H, (13)C and (15)N NMR resonances of the backbone of serine protease PB92 have been assigned. This 269-residue protein is one of the largest monomeric proteins assigned so far. The amount and quality of information available suggest that even larger proteins could be assigned with present methods. Measured chem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00178340

    authors: Fogh RH,Schipper D,Boelens R,Kaptein R

    更新日期:1994-01-01 00:00:00

  • An asymmetric deuterium labeling strategy to identify interprotomer and intraprotomer NOEs in oligomeric proteins.

    abstract::A major difficulty in determining the structure of an oligomeric protein by NMR is the problem of distinguishing inter- from intraprotomer NOEs. In order to address this issue in studies of the 27 kD compact trimeric domain of the MHC class II-associated invariant chain, we compared the 13C NOESY-HSQC spectrum of a un...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1008285512845

    authors: Jasanoff A

    更新日期:1998-08-01 00:00:00

  • Magic-angle spinning solid-state NMR of a 144 kDa membrane protein complex: E. coli cytochrome bo3 oxidase.

    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

    authors: Frericks HL,Zhou DH,Yap LL,Gennis RB,Rienstra CM

    更新日期:2006-09-01 00:00:00

  • Conformational analysis of alpha-D-Fuc-(1-->4)-beta-D-GlcNAc-OMe. One-dimensional transient NOE experiments and Metropolis Monte Carlo simulations.

    abstract::One-dimensional transient NOE build-up curves were measured for the synthetic disaccharide alpha-D-Fuc-(1-->4)-beta-D-GlcNAc 1 utilizing Gaussian shaped pulses. Simulated build-up curves from Metropolis Monte Carlo simulations were compared to the experimental data. Disaccharide 1 is structurally related to methyl bet...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00176007

    authors: Weimar T,Meyer B,Peters T

    更新日期:1993-07-01 00:00:00

  • MTH187 from Methanobacterium thermoautotrophicum has three HEAT-like repeats.

    abstract::With the completion of genome sequencing projects, there are a large number of proteins for which we have little or no functional information. Since protein function is closely related to three-dimensional conformation, structural proteomics is one avenue where the role of proteins with unknown function can be investi...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-006-0029-3

    authors: Julien O,Gignac I,Hutton A,Yee A,Arrowsmith CH,Gagné SM

    更新日期:2006-06-01 00:00:00

  • NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

    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

    authors: Delaglio F,Grzesiek S,Vuister GW,Zhu G,Pfeifer J,Bax A

    更新日期:1995-11-01 00:00:00

  • Application of virus-like particles (VLP) to NMR characterization of viral membrane protein interactions.

    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

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

    更新日期:2016-03-01 00:00:00

  • Efficient and generalized processing of multidimensional NUS NMR data: the NESTA algorithm and comparison of regularization terms.

    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

    authors: Sun S,Gill M,Li Y,Huang M,Byrd RA

    更新日期:2015-05-01 00:00:00

  • Metropolis Monte Carlo calculations of DNA structure using internal coordinates and NMR distance restraints: an alternative method for generating a high-resolution solution structure.

    abstract::A new method, a restrained Monte Carlo (rMC) calculation, is demonstrated for generating high-resolution structures of DNA oligonucleotides in solution from interproton distance restraints and bounds derived from complete relaxation matrix analysis of two-dimensional nuclear Overhauser effect (NOE) spectral peak inten...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/BF00174609

    authors: Ulyanov NB,Schmitz U,James TL

    更新日期:1993-09-01 00:00:00

  • Measuring hydrogen exchange in proteins by selective water saturation in (1)H- (15)N SOFAST/BEST-type experiments: advantages and limitations.

    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

    authors: Rennella E,Solyom Z,Brutscher B

    更新日期:2014-11-01 00:00:00

  • Narrow carbonyl resonances in proton-diluted proteins facilitate NMR assignments in the solid-state.

    abstract::HNCO/HNCACO type correlation experiments are an alternative for assignment of backbone resonances in extensively deuterated proteins in the solid-state, given the fact that line widths on the order of 14-17 Hz are achieved in the carbonyl dimension without the need of high power decoupling. The achieved resolution dem...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-010-9404-1

    authors: Linser R,Fink U,Reif B

    更新日期:2010-05-01 00:00:00

  • The NMR structure of the domain II of a chloroplastic NifU-like protein OsNifU1A.

    abstract::NifU-like proteins are a highly conserved protein that serves as the scaffold for assembly of Fe-S clusters. Chloroplastic NifU-like proteins have tandem NifU like domains, named domain I and domain II. Although the amino acid sequences of these domains are very similar to each other, the predicted functional region f...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-007-9155-9

    authors: Kumeta H,Ogura K,Asayama M,Katoh S,Katoh E,Teshima K,Inagaki F

    更新日期:2007-06-01 00:00:00

  • MAS dependent sensitivity of different isotopomers in selectively methyl protonated protein samples in solid state NMR.

    abstract::Sensitivity and resolution together determine the quality of NMR spectra in biological solids. For high-resolution structure determination with solid-state NMR, proton-detection emerged as an attractive strategy in the last few years. Recent progress in probe technology has extended the range of available MAS frequenc...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-019-00274-0

    authors: Xue K,Sarkar R,Tosner Z,Lalli D,Motz C,Koch B,Pintacuda G,Reif B

    更新日期:2019-11-01 00:00:00

  • Peptide self-association in aqueous trifluoroethanol monitored by pulsed field gradient NMR diffusion measurements.

    abstract::Defining the self-association state of a molecule in solution can be an important step in NMR-based structure determination. This is particularly true of peptides, where there can be a relatively small number of long-range interactions and misinterpretation of an intermolecular NOE as an intramolecular contact can hav...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1023/a:1008382624724

    authors: Yao S,Howlett GJ,Norton RS

    更新日期:2000-02-01 00:00:00

  • Understanding and solving abnormal peak splitting in 3D HCCH-TOCSY and HCC(CO)NH-TOCSY.

    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

    pub_type: 杂志文章

    doi:10.1007/s10858-020-00310-4

    authors: Xia Y,Yuwen T,Rossi P

    更新日期:2020-05-01 00:00:00

  • Improved 3D gd-HCACO and gd-(H)CACO-TOCSY experiments for isotopically enriched proteins dissolved in H2O.

    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

    authors: Zhang W,Gmeiner WH

    更新日期:1996-05-01 00:00:00

  • Advances towards resonance assignments for uniformly--13C, 15N enriched bacteriorhodopsin at 18.8 T in purple membranes.

    abstract::Solid state NMR spectra from uniformly (13)C, (15)N enriched bacteriorhodospin (bR) purified from H. salinarium were acquired at 18.8 T using magic angle spinning methods. Isolated resonances of 2D (13)C-(13)C spectra exhibited 0.50-0.55 ppm line-widths. Several amino acid types could be assigned, and at least 12 out ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-008-9235-5

    authors: Varga K,Aslimovska L,Watts A

    更新日期:2008-05-01 00:00:00

  • Proton, carbon, and nitrogen chemical shifts accurately delineate differences and similarities in secondary structure between the homologous proteins IRAP and IL-1 beta.

    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

    authors: Stockman BJ,Scahill TA,Strakalaitis NA,Brunner DP,Yem AW,Deibel MR Jr

    更新日期:1992-11-01 00:00:00

  • Perspective: revisiting the field dependence of TROSY sensitivity.

    abstract::The discovery of the TROSY effect (Pervushin et al. in Proc Natl Acad Sci USA 94:12366-12371, 1997) for reducing transverse relaxation and line sharpening through selecting pathways in which dipole-dipole and CSA Hamiltonians partially cancel each other had a tremendous impact on solution NMR studies of macromolecules...

    journal_title:Journal of biomolecular NMR

    pub_type: 信件

    doi:10.1007/s10858-016-0075-4

    authors: Takeuchi K,Arthanari H,Wagner G

    更新日期:2016-12-01 00:00:00

  • TSAR: a program for automatic resonance assignment using 2D cross-sections of high dimensionality, high-resolution spectra.

    abstract::While NMR studies of proteins typically aim at structure, dynamics or interactions, resonance assignments represent in almost all cases the initial step of the analysis. With increasing complexity of the NMR spectra, for example due to decreasing extent of ordered structure, this task often becomes both difficult and ...

    journal_title:Journal of biomolecular NMR

    pub_type: 杂志文章

    doi:10.1007/s10858-012-9652-3

    authors: Zawadzka-Kazimierczuk A,Koźmiński W,Billeter M

    更新日期:2012-09-01 00:00:00