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 biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
journal_name
J Biomol NMRjournal_title
Journal of biomolecular NMRauthors
Keiffer S,Carneiro MG,Hollander J,Kobayashi M,Pogoryelev D,Ab E,Theisgen S,Müller G,Siegal Gdoi
10.1007/s10858-020-00343-9subject
Has Abstractpub_date
2020-11-01 00:00:00pages
521-529issue
10-11eissn
0925-2738issn
1573-5001pii
10.1007/s10858-020-00343-9journal_volume
74pub_type
杂志文章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::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::Detection of (15)N in multidimensional NMR experiments of proteins has sparsely been utilized because of the low gyromagnetic ratio (γ) of nitrogen and the presumed low sensitivity of such experiments. Here we show that selecting the TROSY components of proton-attached (15)N nuclei (TROSY (15)NH) yields high quality s...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9991-y
更新日期:2015-12-01 00:00:00
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
更新日期:2008-12-01 00:00:00
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
更新日期:2008-05-01 00:00:00
abstract::Sparse sampling in biomolecular multidimensional NMR offers increased acquisition speed and resolution and, if appropriate conditions are met, an increase in sensitivity. Sparse sampling of indirectly detected time domains combined with the direct truly multidimensional Fourier transform has elicited particular attent...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-011-9584-3
更新日期:2012-01-01 00:00:00
abstract::We present NMRlib, a suite of jython-based tools designed for Bruker spectrometers (TopSpin versions 3.2-4.0) that allow easy setup, management, and exchange of NMR experiments. A NMR experiment can be set up and executed in a few clicks by navigating through the NMRlib GUI tree structure, without any further paramete...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-019-00249-1
更新日期:2019-05-01 00:00:00
abstract::NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00404272
更新日期:1994-09-01 00:00:00
abstract::The greatly improved sensitivity resulting from the use of TROSY during 15N evolution and amide proton acquisition enables the recording of HNCA spectra of large proteins with constant-time 13C alpha evolution. In [13C]-ct-[15N,1H]-TROSY-HNCA experiments with a 2H/13C/15N-labeled 110 kDa protein, 7,8-dihydroneopterin ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008346931993
更新日期:1999-05-01 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 NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] 13C-filtered NOESY experiment that empl...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1011296112710
更新日期:2001-03-01 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::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::The use of dipolar shifts as important constraints in refining molecular structure of paramagnetic metalloproteins by solution NMR is now well established. A crucial initial step in this procedure is the determination of the orientation. of the anisotropic paramagnetic susceptibility tensor in the molecular frame whic...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008309121949
更新日期:2000-06-01 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::Hydroxyl protons on serine and threonine residues are not well characterized in protein structures determined by both NMR spectroscopy and X-ray crystallography. In the case of NMR spectroscopy, this is in large part because hydroxyl proton signals are usually hidden under crowded regions of (1)H-NMR spectra and remai...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-013-9799-6
更新日期:2014-01-01 00:00:00
abstract::The binding site and backbone dynamics of a bioactive complex formed by the acidic fibroblast growth factor (FGF-1) and a specifically designed heparin hexasaccharide has been investigated by HSQC and relaxation NMR methods. The comparison of the relaxation data for the free and bound states has allowed showing that t...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-006-9024-y
更新日期:2006-08-01 00:00:00
abstract::For larger proteins, and proteins not amenable to expression in bacterial hosts, it is difficult to deduce structures using NMR methods based on uniform (13)C, (15)N isotopic labeling and observation of just nuclear Overhauser effects (NOEs). In these cases, sparse labeling with selected (15)N enriched amino acids and...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-007-9159-5
更新日期:2007-07-01 00:00:00
abstract::Three different conformations of proline rings in a protein in solution, Up, Down and Twist, have been distinguished, and stereospecific assignments of the pyrrolidine beta-, gamma- and delta-hydrogens have been made on the basis of 1H-1H vicinal coupling constant patterns and intraresidue NOEs. For all three conforma...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/BF00211775
更新日期:1995-09-01 00:00:00
abstract::Adiabatic pulses have been widely used for broadband decoupling and spin inversion at high magnetic fields. In this paper we propose adiabatic pulses and supercycles that can be used at high magnetic fields like 800 or 900 MHz to obtain broadband TOCSY sequences with C,C or H,H J-transfer. The new mixing sequences are...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1026785725363
更新日期:2000-11-01 00:00:00
abstract::A method is proposed to determine the conformational equilibrium of flexible polypeptides in solution, using the data provided by NMR spectroscopy and theoretical conformational calculations. The algorithm consists of the following three steps: (i) search of the conformational space in order to find conformations with...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008349424452
更新日期:1999-12-01 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::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::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::Cytochrome c552 from the thermophilic bacterium Hydrogenobacter thermophilus is a typical c-type cytochrome which binds heme covalently via two thioether bonds between the two heme vinyl groups and two cysteine thiol groups in a CXXCH sequence motif. This protein was converted to a b-type cytochrome by substitution of...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-015-9938-3
更新日期:2015-06-01 00:00:00
abstract::Activated dynamics plays a central role in protein function, where transitions between distinct conformations often underlie the switching between active and inactive states. The characteristic time scales of these transitions typically fall in the microsecond to millisecond range, which is amenable to investigations ...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-013-9764-4
更新日期:2013-09-01 00:00:00
abstract::The assignment of protein backbone and side-chain NMR chemical shifts is the first step towards the characterization of protein structure. The recent introduction of proton detection in combination with fast MAS has opened up novel opportunities for assignment experiments. However, typical 3D sequential-assignment exp...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1007/s10858-018-0207-0
更新日期:2018-10-01 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::One of the major bottlenecks in the determination of proteinstructures by NMR is in the evaluation of the data produced by theexperiments. An important step in this process is assignment, where thepeaks in the spectra are assigned to specific spins within specificresidues. In this paper, we discuss a spin system assig...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/A:1018329420659
更新日期:1997-10-01 00:00:00
abstract::The systematic difference between T2 values obtained from CPMG and T1p experiments was observed for backbone 15N nuclei of bacterial ribonuclease barnase. Theoretical consideration suggests that the observed difference is caused by off-resonance effects of 180 degree pulses of the CPMG pulse train. Namely, at off-reso...
journal_title:Journal of biomolecular NMR
pub_type: 杂志文章
doi:10.1023/a:1008348827208
更新日期:2000-07-01 00:00:00