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 abundance (13)C in 50% H(2)O, 50% D(2)O solvent mixtures yielded an average trans-hydrogen bond isotope effect, (2h)Delta(13)C2, of -47 ppb. The data suggest that stronger hydrogen bonds have more negative (2h)Delta(13)C2 values, which means that A:T N1.H3 hydrogen bonds increase the anharmonicity of the effective vibrational potential of H3. However, (2h)Delta(13)C2 values do not correlate with intra-residue (2)Delta(13)C4 values of thymidine observed here and earlier (Vakonakis et al., 2003), which suggests that (2h)Delta(13)C2 is not determined entirely by hydrogen bond strength. Instead, the variations observed in (2h)Delta(13)C2 values suggest that they may also be sensitive to base pair geometry.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Vakonakis I,LiWang ACdoi
10.1023/B:JNMR.0000019507.95667.3esubject
Has Abstractpub_date
2004-05-01 00:00:00pages
65-72issue
1eissn
0925-2738issn
1573-5001pii
5264833journal_volume
29pub_type
杂志文章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::Chitosan interaction with chitosanase was examined through analysis of spectral line shapes in the NMR HSQC titration experiments. We established that the substrate, chitosan hexamer, binds to the enzyme through the three-state induced-fit mechanism with fast formation of the encounter complex followed by slow isomeri...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-017-0109-6
更新日期:2017-04-01 00:00:00
abstract::In our previous work, we proposed a new way to represent protein native states, using ensembles of a small number of conformations with relative Populations, or ESP in short. Using Ubiquitin as an example, we showed that using a small number of conformations could greatly reduce the potential of overfitting and assign...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9993-9
更新日期:2015-12-01 00:00:00
abstract::Protein expression in E. coli grown in shaker flasks is a routine and pivotal tool in many research laboratories. To maximize protein yields, cells are normally induced in the middle of the linear growth phase, typically at an OD600 of ≤ 1 for cells grown in Luria-Bertani (LB) medium at 37 °C. We recently showed that ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-019-00285-x
更新日期:2019-12-01 00:00:00
abstract::A method, based on linewidth measurements, is described which permits the rapid and facile determination of JHNH alpha coupling constants from 15N labeled proteins. Using appropriately processed HMQC-J data, we have found that a simple linear relationship exists between the half-height linewidth (delta nu1/2) of 15N-1...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008202230140
更新日期:1998-04-01 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 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::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::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::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
doi:10.1007/s10858-006-9047-4
更新日期:2006-10-01 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::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::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::For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simul...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9534-0
更新日期:2011-11-01 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::As part of efforts to develop improved methods for NMR protein sample preparation and structure determination, the Northeast Structural Genomics Consortium (NESG) has implemented an NMR screening pipeline for protein target selection, construct optimization, and buffer optimization, incorporating efficient microscale ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-009-9386-z
更新日期:2010-01-01 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::Artifacts associated with the measurement of methyl (1)H single quantum CPMG-based relaxation dispersion profiles are described. These artifacts arise due to the combination of cross-correlated spin relaxation effects involving intra-methyl (1)H-(1)H dipolar interactions and imperfections in (1)H refocusing pulses tha...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-005-2468-7
更新日期:2005-04-01 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::Simple pulse schemes are presented for the measurement of methyl (13)C and (1)H CSA values from (1)H-(13)C dipole/(13)C CSA and (1)H-(13)C dipole/(1)H CSA cross-correlated relaxation. The methodology is applied to protein L and malate synthase G. Average (13)C CSA values are considerably smaller for Ile than Leu/Val (...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-004-4349-x
更新日期:2004-12-01 00:00:00
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
更新日期:2015-05-01 00:00:00
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
更新日期:1992-11-01 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::The arrival of very high field magnets and cryogenic circuitries, and the development of relaxation-optimized pulse sequences have added powerful tools for increasing sensitivity and resolution in NMR studies of biomacromolecules. The potential of these advances is not fully realized in practice, however, since curren...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章,评审
doi:10.1023/B:JNMR.0000042946.04002.19
更新日期:2004-09-01 00:00:00
abstract::The human alpha 3-chain type VI collagen C-terminal Kunitz domain fragment (alpha 3(VI)) has been studied by two dimensional 1H-1H and 1H-13C NMR spectroscopy at 303 K. It is shown that the secondary structure of the protein is strikingly similar to that of BPTI, and a number of unusual H alpha chemical shifts, which ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00228142
更新日期:1996-12-01 00:00:00
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 ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00178334
更新日期:1994-01-01 00:00:00
abstract::We report site-resolved observation of hydrogen exchange in the micro-crystalline protein Crh. Our approach is based on the use of proton T2' -selective 1H-13C-13C correlation spectra for site-specific assignments of carbons nearby labile protein protons. We compare the proton T2' selective scheme to frequency selecti...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-005-8073-y
更新日期:2005-07-01 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::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::In order to understand the role of the glycans in glycoproteins in solution, structural information obtained by NMR spectroscopy is obviously required. However, the assignment of the NMR signals from the glycans in larger glycoproteins is still difficult, mainly due to the lack of appropriate methods for the assignmen...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1026776721348
更新日期:2000-12-01 00:00:00