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 between the Ca(2+)-bound form of calmodulin (CaM) and non-cognate proteins in Escherichia coli lysate are explored using Ile, Leu, Val and Met methyl probes. Changes in CaM methyl chemical shifts as a function of added E. coli lysate are measured to determine a minimum 'average' dissociation constant for interactions between Ca(2+)-CaM and E. coli lysate proteins. (2)H R 2 and (13)C R 1 spin relaxation rates report on the binding reaction as well. Our results further highlight the power of methyl containing side-chains for characterizing biomolecular interactions, even in complex in-cell like environments.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Latham MP,Kay LEdoi
10.1007/s10858-013-9705-2subject
Has Abstractpub_date
2013-03-01 00:00:00pages
239-47issue
3eissn
0925-2738issn
1573-5001journal_volume
55pub_type
杂志文章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：: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
doi：10.1007/s10858-008-9261-3
更新日期：2008-09-01 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：:The program EASY supports the spectral analysis of biomacromolecular two-dimensional (2D) nuclear magnetic resonance (NMR) data. It provides a user-friendly, window-based environment in which to view spectra for interactive interpretation. In addition, it includes a number of automated routines for peak-picking, spin-...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF01877224
更新日期：1991-07-01 00:00:00
abstract：:The first reconstitution of an Fe2S2 ferredoxin with a diamagnetic prosthetic group was recently described [Kazanis et al. (1995) J. Am. Chem. Soc., 117, 6625-6626]. The replacement of the iron-sulfur cluster of the bacterial ferredoxin putidaredoxin (Pdx) by gallium (Ga3+) renders the protein diamagnetic and permits ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1018369721091
更新日期：1997-06-01 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：:To evaluate sequential nearest-neighbor effects on quantum-chemical calculations of (13)C(alpha) chemical shifts, we selected the structure of the nucleic acid binding (NAB) protein from the SARS coronavirus determined by NMR in solution (PDB id 2K87). NAB is a 116-residue alpha/beta protein, which contains 9 prolines...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-010-9435-7
更新日期：2010-09-01 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
abstract：:Prerequisite for chemical shift (CS) and CS tensor calculations are highly refined structures defining the molecular surroundings of the nuclei under study. Here, we present geometry optimizations with 13C and 15N CS constraints for large bio-molecules like peptides and proteins. The method discussed here provides bot...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00284-y
更新日期：2019-12-01 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：:Two-dimensional versions of HNCA and HNCO experiments are described, which provide essentially the same information as the 3D sequence. A multiple-quantum coherence involving either 15N and 13C alpha or 15N and 13CO is created. One of the two frequencies is given by the middle point between the two cross peaks (zero- ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00179343
更新日期：1994-05-01 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：:Temperature coefficients have been measured for backbone amide (1)H and (15)N nuclei in the B1 domain of protein G (GB1), using temperatures in the range 283-313 K, and pH values from 2.0 to 9.0. Many nuclei display pH-dependent coefficients, which were fitted to one or two pK(a) values. (1)H coefficients showed the e...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-011-9583-4
更新日期：2012-01-01 00:00:00
abstract：:Proton chemical shifts of a series of disordered linear peptides (H-Gly-Gly-X-Gly-Gly-OH, with X being one of the 20 naturally occurring amino acids) have been obtained using 1D and 2D 1H NMR at pH 5.0 as a function of temperature and solvent composition. The use of 2D methods has allowed some ambiguities in side-chai...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/BF00227466
更新日期：1995-01-01 00:00:00
abstract：:NMR spectroscopy provides a powerful approach for the characterisation of chemical exchange and molecular interactions by analysis of series of experiments acquired over the course of a titration measurement. The appearance of NMR resonances undergoing chemical exchange depends on the frequency difference relative to ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-019-00297-7
更新日期：2020-01-01 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
abstract：:Coherences were observed between 15N3 of cytosine and its trans amino proton (H42) using a modified gradient-based heteronuclear single quantum coherence (HSQC) pulse sequence optimized for three-bond proton-nitrogen couplings. The method is demonstrated with a 22-nucleotide RNA fragment of the P5abc region of a group...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1008359723515
更新日期：1999-10-01 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：:Three methods for calculating nuclear magnetic resonance cross-relaxation rates from molecular dynamics simulations of small flexible molecules have been compared in terms of their ability to reproduce relaxation data obtained experimentally and to produce consistent descriptions of the system. The importance of the a...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1019854626147
更新日期：2002-07-01 00:00:00
abstract：:The ability to simultaneously measure many long-range distances is critical to efficient and accurate determination of protein structures by solid-state NMR (SSNMR). So far, the most common distance constraints for proteins are 13C-15N distances, which are usually measured using the rotational-echo double-resonance (R...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0187-0
更新日期：2018-05-01 00:00:00
abstract：:Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-016-0024-2
更新日期：2016-03-01 00:00:00
abstract：:Understanding of the molecular mechanisms of protein function requires detailed insight into the conformational landscape accessible to the protein. Conformational changes can be crucial for biological processes, such as ligand binding, protein folding, and catalysis. NMR spectroscopy is exquisitely sensitive to such ...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-018-0193-2
更新日期：2018-06-01 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：: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：: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：:The importance of protein chemical shift values for the determination of three-dimensional protein structure has increased in recent years because of the large databases of protein structures with assigned chemical shift data. These databases have allowed the investigation of the quantitative relationship between chem...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/a:1023060720156
更新日期：2003-05-01 00:00:00
abstract：:Complex mixtures are at the heart of biology, and biomacromolecules almost always exhibit their function in a mixture, e.g., the mode of action for a spider venom is typically dependent on a cocktail of compounds, not just the protein. Information about diseases is encoded in body fluids such as urine and plasma in th...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1007/s10858-013-9752-8
更新日期：2014-04-01 00:00:00
abstract：:This paper presents new methods designed for quantitative analysis of chemical shift perturbation NMR spectra. The methods automatically trace the displacements of cross peaks between a perturbed test spectrum and the reference spectrum (or among a series of titration spectra), and measure the changes of chemical shif...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/B:JNMR.0000034351.37982.9e
更新日期：2004-08-01 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
abstract：:The question is addressed of how maximal structural NOE data on double labelled proteins can be acquired with a minimal set of NOESY experiments. Two 3D-NOESY spectra are reported which, in concert with other commonly used spectra, provide a convenient strategy for NOE assignment. The 3D CNH-NOESY and 3D NCH-NOESY pro...
journal_title：Journal of biomolecular NMR
pub_type： 杂志文章
doi：10.1023/A:1008367912535
更新日期：1999-10-01 00:00:00
