Abstract:
:A new pulse sequence is presented for the measurement of relaxation dispersion profiles quantifying millisecond time-scale exchange dynamics of side-chain carbonyl groups in uniformly (13)C labeled proteins. The methodology has been tested using the 87-residue colicin E7 immunity protein, Im7, which is known to fold via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. Comparison of exchange parameters extracted for this folding 'reaction' using the present methodology with those obtained from more 'traditional' (15)N and backbone carbonyl probes establishes the utility of the approach. The extracted excited state side-chain carbonyl chemical shifts indicate that the Asx/Glx side-chains are predominantly unstructured in the Im7 folding intermediate. However, several crucial salt-bridges that exist in the native structure appear to be already formed in the excited state, either in part or in full. This information, in concert with that obtained from existing backbone and side-chain methyl relaxation dispersion experiments, will ultimately facilitate a detailed description of the structure of the Im7 folding intermediate.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Hansen AL,Kay LEdoi
10.1007/s10858-011-9520-6subject
Has Abstractpub_date
2011-08-01 00:00:00pages
347-55issue
4eissn
0925-2738issn
1573-5001journal_volume
50pub_type
杂志文章abstract::The (13)C(alpha) chemical shifts for 16,299 residues from 213 conformations of four proteins (experimentally determined by X-ray crystallography and Nuclear Magnetic Resonance methods) were computed by using a combination of approaches that includes, but is not limited to, the use of density functional theory. Initial...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-007-9162-x
更新日期:2007-07-01 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
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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::Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H-15N correlation spectra in a few seconds of acquisition time ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-005-4425-x
更新日期:2005-12-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/b:jnmr.0000048948.66235.d9
更新日期:2004-10-01 00:00:00
abstract::2D 15N-1H correlation spectra are ideal for measuring backbone amide populations to determine amide exchange protection factors in studies of protein folding or other structural features. Most protein NMR spectroscopists use HSQC, which has been shown to be generally superior to HMQC in both resolution and sensitivity...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00182288
更新日期:1995-06-01 00:00:00
abstract::PG-1 adopts a dimeric structure in dodecylphosphocholine (DPC) micelles, and a channel is formed by the association of several dimers but the molecular mechanisms of the membrane damage by non-α-helical peptides are still unknown. The formation of the PG-1 dimer is important for pore formation in the lipid bilayer, si...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-014-9885-4
更新日期:2015-04-01 00:00:00
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
更新日期:1994-01-01 00:00:00
abstract::Lanthanide complexes based on the DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) cage are commonly used as phase contrast agents in magnetic resonance imaging, but can also be utilized in structural NMR applications due to their ability to induce either paramagnetic relaxation enhancement or a pseudoc...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0061-x
更新日期:2016-10-01 00:00:00
abstract::The transmembrane protein YuaF from B. subtilis is a member of the NfeD-like clan with a potential role in maintaining membrane integrity during conditions of cellular stress. nfeD-genes are primarily found in highly conserved operon structures together with the gene of another membrane protein belonging to the SPFH s...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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更新日期:2008-09-01 00:00:00
abstract::Pseudocontact shifts (PCS) induced by tags loaded with paramagnetic lanthanide ions provide powerful long-range structure information, provided the location of the metal ion relative to the target protein is known. Usually, the metal position is determined by fitting the magnetic susceptibility anisotropy (Δχ) tensor ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-0003-z
更新日期:2016-01-01 00:00:00
abstract::Strong solvent signals lead to a disappearance of weak protein signals close to the solvent resonance frequency and to base plane variations all over the spectrum. AUREMOL-SSA provides an automated approach for solvent artifact removal from multidimensional NMR protein spectra. Its core algorithm is based on singular ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-010-9414-z
更新日期:2010-06-01 00:00:00
abstract::Recent advances in the field of in-cell NMR spectroscopy have made it possible to study proteins in the context of bacterial or mammalian cell extracts or even entire cells. As most mammalian cells are part of a multi-cellular complex, there is a need to develop novel NMR approaches enabling the study of proteins with...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-020-00328-8
更新日期:2020-09-01 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::RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a sialic-acid-binding lectin purified from Rana catesbeiana (bullfrog) oocytes. This 111-amino acid protein exhibits cytotoxicity toward several tumor cell lines. In this paper we report the assignments of proton NMR resonances and the identification ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00410331
更新日期:1996-10-01 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::We have analyzed the relaxation properties of all (31)P nuclei in an RNA cUUCGg tetraloop model hairpin at proton magnetic field strengths of 300, 600 and 900 MHz in solution. Significant H, P dipolar contributions to R (1) and R (2) relaxation are observed in a protonated RNA sample at 600 MHz. These contributions ca...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-009-9343-x
更新日期:2009-09-01 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::In magic angle spinning solid state NMR experiments the potential of heteronuclear (1)H decoupling employing a continuous train of adiabatic inversion pulses has been assessed via numerical simulations and experimental measurements. It is shown that, with a (1)H RF field strength of approximately 100 kHz that is typic...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/B:JNMR.0000032614.79833.3d
更新日期:2004-07-01 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
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更新日期:2005-11-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章,评审
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更新日期:2010-01-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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更新日期:2015-02-01 00:00:00
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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::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::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::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::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
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更新日期:2017-06-01 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
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更新日期:2006-10-01 00:00:00
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journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
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更新日期:1991-07-01 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
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更新日期:2013-08-01 00:00:00