A nuclear magnetic resonance (NMR)-based method is described in which small organic molecules that bind to proximal subsites of a protein are identified, optimized, and linked together to produce high-affinity ligands. The approach is called "SAR by NMR" because structure-activity relationships (SAR) are obtained from NMR. With this technique, compounds with nanomolar affinities for the FK506 binding protein were rapidly discovered by tethering two ligands with micromolar affinities. The method reduces the amount of chemical synthesis and time required for the discovery of high-affinity ligands and appears particularly useful in target-directed drug research.
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field
High resolution NMR spectroscopy of nanocrystalline proteins at ultra-high magnetic field
Abstract Magic-angle spinning (MAS) solid-state NMR (SSNMR) spectroscopy of uniformly-13C,15N labeled protein samples provides insight into atomic-resolution chemistry and structure. Data collection efficiency has advanced remarkably in the last decade; however, the study of larger proteins is still challenged by relatively low resolution in comparison to solution NMR. In this study, we present a systematic analysis of SSNMR protein spectra acquired at 11.7, 17.6 and 21.1 Tesla (1H frequencies of...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
[NMR paper] Competition STD NMR for the detection of high-affinity ligands and NMR-based screenin
Competition STD NMR for the detection of high-affinity ligands and NMR-based screening.
Related Articles Competition STD NMR for the detection of high-affinity ligands and NMR-based screening.
Magn Reson Chem. 2004 Jun;42(6):485-9
Authors: Wang YS, Liu D, Wyss DF
The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing...
nmrlearner
Journal club
0
11-24-2010 09:51 PM
[NMR paper] NMR probing of protein-protein interactions using reporter ligands and affinity tags.
NMR probing of protein-protein interactions using reporter ligands and affinity tags.
Related Articles NMR probing of protein-protein interactions using reporter ligands and affinity tags.
J Am Chem Soc. 2004 Feb 18;126(6):1636-7
Authors: Ludwiczek ML, Baminger B, Konrat R
A novel method is proposed for the detection and quantification of protein-protein interactions in solution. In this approach, one protein binding partner is tagged with a ligand binding domain, and protein-protein interaction is monitored via changes in the NMR relaxation...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12.
Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12.
Related Articles Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12.
J Mol Biol. 2002 Dec 13;324(5):1003-14
Authors: Inman KG, Yang R, Rustandi RR, Miller KE, Baldisseri DM, Weber DJ
The solution NMR structure is reported for Ca(2+)-loaded S100B bound to a 12-residue peptide, TRTK-12, from the actin capping protein CapZ (alpha1 or alpha2 subunit, residues 265-276: TRTKIDWNKILS). This peptide was discovered by Dimlich and co-workers...
nmrlearner
Journal club
0
11-24-2010 08:58 PM
[NMR paper] MS/NMR: a structure-based approach for discovering protein ligands and for drug desig
MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy.
Related Articles MS/NMR: a structure-based approach for discovering protein ligands and for drug design by coupling size exclusion chromatography, mass spectrometry, and nuclear magnetic resonance spectroscopy.
Anal Chem. 2001 Feb 1;73(3):571-81
Authors: Moy FJ, Haraki K, Mobilio D, Walker G, Powers R, Tabei K, Tong H, Siegel MM
A protocol is described...
nmrlearner
Journal club
0
11-19-2010 08:32 PM
[NMR paper] Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-
Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-LTR by high resolution 2D-NMR.
Related Articles Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-LTR by high resolution 2D-NMR.
J Biomol Struct Dyn. 1995 Dec;13(3):553-64
Authors: Singh MP, Pon RT, Lown JW
The understanding of early events in the expression of genes has vastly improved in recent years with the identification of a variety of gene- and sequence-specific DNA binding transcription factors. One such protein, Sp1,...
Discovering high-affinity ligands for proteins: SAR by NMR.
Linear Mode
