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 pHs revealed an insignificant change in exchange rate between pH 5 and 7 for amide protons of residues 4 through 14, while the exchange rate increase at neutral pH was more prominent for amide protons of the remaining residues, with peaks from some protons becoming undetectable. The relative insensitivity to pH of the exchange for the amide protons of residues 4 through 14 is attributable to the drastic reduction in [OH-] in the micellar interior, leading to a decreased exchange rate. The A15-G16 segment represents a transition between these two regimes. The data are thus consistent with the notion that the peptide inserts into the hydrophobic core of a membrane-like structure and the A15-G16 dipeptide is located at the micellar-aqueous boundary.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Chang DK,Cheng SFdoi
10.1023/a:1008399304450subject
Has Abstractpub_date
1998-11-01 00:00:00pages
549-52issue
4eissn
0925-2738issn
1573-5001journal_volume
12pub_type
杂志文章abstract::Model-membrane systems composed of liquid-crystalline bicellar phases can be uniaxially oriented with respect to a magnetic field, thereby facilitating structural and dynamics studies of membrane-associated proteins. Here we quantitatively characterize a method that allows the manipulation of the direction of this uni...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1022236217018
更新日期:2003-02-01 00:00:00
abstract::Active bandwidth and global quality factor are the two main metrics used to quantitatively compare the performance of TOCSY mixing sequences. Active bandwidth refers to the spectral region over which at least 50 % of the magnetization is transferred via a coupling. Global quality factor scores mixing sequences accordi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0051-z
更新日期:2016-09-01 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::Melittin is a naturally occurring hexacosa peptide which forms an amphiphilic helix in methanol, a random coil in water, and a tetramer of helices at basic pH or in the presence of a high salt concentration. The monomeric structure in methanol has been well characterized by proton NMR (Pastore et al. (1989) Eur. Bioph...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00198369
更新日期:1993-11-01 00:00:00
abstract::Laboratories often repeatedly determine the structure of a given protein under a variety of conditions, mutations, modifications, or in a number of states. This approach can be cumbersome and tedious. Given then a database of structures, identifiers, and corresponding (1)H,(15)N-HSQC NMR spectra for homologous protein...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9546-9
更新日期:2011-09-01 00:00:00
abstract::The P1 adhesin (aka Antigen I/II or PAc) of the cariogenic bacterium Streptococcus mutans is a cell surface-localized protein involved in sucrose-independent adhesion and colonization of the tooth surface. The immunoreactive and adhesive properties of S. mutans suggest an unusual functional quaternary ultrastructure c...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0017-1
更新日期:2016-02-01 00:00:00
abstract::A new homonuclear Hartmann-Hahn-type mixing scheme is introduced that effects coherence transfer between resonances in two separated frequency bands. The mixing scheme relies on the irradiation of two-band selective shaped pulses that are expanded in an MLEV-16 supercycle. Similar to heteronuclear Hartmann-Hahn experi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00211162
更新日期:1996-09-01 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::A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue 'i' with that of residues 'i-1' and 'i+1' in ((13)C, (15)N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploi...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9976-x
更新日期:2015-10-01 00:00:00
abstract::Protein structure determination of low affinity complexes of interacting macromolecules is often hampered by a lack of observable NOEs between the binding partners. Covalent linkage offers a way to shift the equilibrium of the interaction partners to the bound state. Here we show that a single-chain protein containing...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1024983029700
更新日期:2003-10-01 00:00:00
abstract::The cryogenic temperatures at which dynamic nuclear polarization (DNP) solid-state NMR experiments need to be carried out cause line-broadening, an effect that is especially detrimental for crowded protein spectra. By increasing the magnetic field strength from 600 to 800 MHz, the resolution of DNP spectra of type III...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-016-0044-y
更新日期:2016-08-01 00:00:00
abstract::A new protocol is described for obtaining intraresidual and sequential correlations between carbonyl carbons and amide (1)H and (15)N resonances of amino acids. Frequency labeling of (13)CO spins occurs during a period required for the (13)C(α)-(15)N polarization transfer, leading to an optimized transfer efficiency. ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00211783
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::13CHD2 methyl isotopomers are particularly useful to study methyl dynamics in proteins because, as compared with other methyl isotopomers, the 13C relaxation mechanism for this isotopomer is straightforward. However, in the case of proteins, where (omega tau)2 > 1, the refocused INEPT pulse sequence does not completel...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1012482426306
更新日期:2001-10-01 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::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::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::We report the determination of the global fold of human ubiquitin using protein backbone NMR residual dipolar coupling and long-range nuclear Overhauser effect (NOE) data as conformational restraints. Specifically, by use of a maximum of three backbone residual dipolar couplings per residue (Ni-H N i, Ni-C'(i-1), H N ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1021954812977
更新日期:2003-01-01 00:00:00
abstract::Mollib is a software framework for the analysis of molecular structures, properties and data with an emphasis on data collected by NMR. It uses an open source model and a plugin framework to promote community-driven development of new and enhanced features. Mollib includes tools for the automatic retrieval and caching...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-017-0142-5
更新日期:2017-10-01 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::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::An approach for the efficient implementation of RN(n)(nu) symmetry-based pulse schemes that are often employed for recoupling and decoupling of nuclear spin interactions in biological solid state NMR investigations is demonstrated at high magic-angle spinning frequencies. RF pulse sequences belonging to the RN(n)(nu) ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-009-9335-x
更新日期:2009-08-01 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::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::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::TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-017-0133-6
更新日期:2017-09-01 00:00:00
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::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