Related ArticlesAccidental Interaction between PDZ Domains and Diclofenac Revealed by NMR-Assisted Virtual Screening.
Molecules. 2013;18(8):9567-81
Authors: Tenno T, Goda N, Umetsu Y, Ota M, Kinoshita K, Hiroaki H
Abstract
In silico approaches have become indispensable for drug discovery as well as drug repositioning and adverse effect prediction. We have developed the eF-seek program to predict protein-ligand interactions based on the surface structure of proteins using a clique search algorithm. We have also developed a special protein structure prediction pipeline and accumulated predicted 3D models in the Structural Atlas of the Human Genome (SAHG) database. Using this database, genome-wide prediction of non-peptide ligands for proteins in the human genome was performed, and a subset of predicted interactions including 14 PDZ domains was then confirmed by NMR titration. Surprisingly, diclofenac, a non-steroidal anti-inflammatory drug, was found to be a non-peptide PDZ domain ligand, which bound to 5 of 15 tested PDZ domains. The critical residues for the PDZ-diclofenac interaction were also determined. Pharmacological implications of the accidental PDZ-diclofenac interaction are further discussed.
[NMR paper] Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide.
Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Stable isotope-assisted NMR characterization of interaction between lipid A and sarcotoxin IA, a cecropin-type antibacterial peptide.
Biochem Biophys Res Commun. 2013 Feb 8;431(2):136-40
Authors: Yagi-Utsumi M, Yamaguchi Y, Boonsri P, Iguchi T, Okemoto K, Natori S, Kato K
...
nmrlearner
Journal club
0
08-21-2013 08:49 PM
[NMR paper] Molecular basis of the PED/PEA15 interaction with the C-terminal fragment of Phospholipase D1 revealed by NMR spectroscopy.
Molecular basis of the PED/PEA15 interaction with the C-terminal fragment of Phospholipase D1 revealed by NMR spectroscopy.
Related Articles Molecular basis of the PED/PEA15 interaction with the C-terminal fragment of Phospholipase D1 revealed by NMR spectroscopy.
Biochim Biophys Acta. 2013 Apr 19;
Authors: Farina B, Doti N, Pirone L, Malgieri G, Pedone EM, Ruvo M, Fattorusso R
Abstract
PED/PEA15 is a small protein involved in many protein-protein interactions that modulates the function of a number of key cellular effectors involved in...
nmrlearner
Journal club
0
04-24-2013 09:48 PM
[U. of Ottawa NMR Facility Blog] Virtual Coupling
Virtual Coupling
When the chemical shift difference between two J coupled nuclei is of the same order as the coupling constant, second order spectra are obtained. See this and this. One, often unrecognized, second order effect is virtual coupling which is often misinterpreted as first order weak coupling. In a three-spin system, virtual coupling occurs when the observed nucleus appears to be coupled to both of the other two nuclei even though it is only coupled to one of them. This arises in AA'X and ABX spin systems when X (the observed nucleus) is coupled to only one of the other two...
nmrlearner
News from NMR blogs
0
08-12-2011 02:30 AM
Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy.
Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy.
Interaction of a putative BH3 domain of clusterin with anti-apoptotic Bcl-2 family proteins as revealed by NMR spectroscopy.
Biochem Biophys Res Commun. 2011 Apr 19;
Authors: Lee DH, Ha JH, Kim Y, Bae KH, Park JY, Choi WS, Yoon HS, Park SG, Park BC, Yi GS, Chi SW
Clusterin (CLU) is a multifunctional glycoprotein that is overexpressed in prostate and breast cancers. Although CLU is known to be involved in the regulation...
nmrlearner
Journal club
0
04-30-2011 12:36 PM
[NMR paper] A NMR study of the interaction of a three-domain construct of ATP7A with copper(I) and copper(I)-HAH1: the interplay of domains.
A NMR study of the interaction of a three-domain construct of ATP7A with copper(I) and copper(I)-HAH1: the interplay of domains.
Related Articles A NMR study of the interaction of a three-domain construct of ATP7A with copper(I) and copper(I)-HAH1: the interplay of domains.
J Biol Chem. 2005 Nov 18;280(46):38259-63
Authors: Banci L, Bertini I, Cantini F, Chasapis CT, Hadjiliadis N, Rosato A
ATP7A is a P-type ATPase involved in copper(I) homeostasis in humans. It possesses a long N-terminal tail protruding into the cytosol and containing six...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] NMR fragment screening: tackling protein-protein interaction targets.
NMR fragment screening: tackling protein-protein interaction targets.
Related Articles NMR fragment screening: tackling protein-protein interaction targets.
Curr Opin Drug Discov Devel. 2005 May;8(3):365-73
Authors: Schade M, Oschkinat H
High-throughput screening of libraries containing compounds of 'drug-like' molecular weight has frequently resulted in no or poor drug candidates, especially when screening against demanding drug targets such as protein-protein interactions. Fragment-based lead discovery and optimization has evolved as a...
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[NMR paper] Expression screening, protein purification and NMR analysis of human protein domains
Expression screening, protein purification and NMR analysis of human protein domains for structural genomics.
Related Articles Expression screening, protein purification and NMR analysis of human protein domains for structural genomics.
J Struct Funct Genomics. 2004;5(1-2):119-31
Authors: Folkers GE, van Buuren BN, Kaptein R
Structural genomics, the determination of protein structures on a genome-wide scale, is still in its infancy for eukaryotes due to the number and size of their genes. Low protein expression and solubility of eukaryotic...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl d
Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl domain and E1 component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
Related Articles Protein-protein interaction revealed by NMR T(2) relaxation experiments: the lipoyl domain and E1 component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus.
J Mol Biol. 2000 Jan 28;295(4):1023-37
Authors: Howard MJ, Chauhan HJ, Domingo GJ, Fuller C, Perham RN
T(2) relaxation experiments in combination with...
Accidental Interaction between PDZ Domains and Diclofenac Revealed by NMR-Assisted Virtual Screening.
Linear Mode
