NMR spectroscopy was used to characterize the hepatitis C virus (HCV) NS3 protease in a complex with the 24 residue peptide cofactor from NS4A and a boronic acid inhibitor, Ac-Asp-Glu-Val-Val-Pro-boroAlg-OH. Secondary-structure information, NOE constraints between protease and cofactor, and hydrogen-deuterium exchange rates revealed that the cofactor was an integral strand in the N-terminal beta-sheet of the complex as observed in X-ray crystal structures. Based upon chemical-shift perturbations, inhibitor-protein NOEs, and the protonation state of the catalytic histidine, the boronic acid inhibitor was bound in the substrate binding site as a transition state mimic. In the absence of cofactor, the inhibitor had a lower affinity for the protease. Although the inhibitor binds in the same location, differences were observed at the catalytic site of the protease.
Combined X-ray, NMR and kinetic analyses reveal uncommon binding characteristics of the HCV NS3-NS4A protease inhibitor BI 201335.
Combined X-ray, NMR and kinetic analyses reveal uncommon binding characteristics of the HCV NS3-NS4A protease inhibitor BI 201335.
Combined X-ray, NMR and kinetic analyses reveal uncommon binding characteristics of the HCV NS3-NS4A protease inhibitor BI 201335.
J Biol Chem. 2011 Jan 26;
Authors: Lemke CT, Goudreau N, Zhao S, Hucke O, Thibeault D, Llinás-Brunet M, White PW
Hepatitis C virus (HCV) infection, a major cause of liver disease world-wide, is curable but currently approved therapies have suboptimal efficacy. Supplementing these therapies...
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01-29-2011 12:35 PM
[NMR paper] Determining the optimal size of small molecule mixtures for high throughput NMR scree
Determining the optimal size of small molecule mixtures for high throughput NMR screening.
Related Articles Determining the optimal size of small molecule mixtures for high throughput NMR screening.
J Biomol NMR. 2005 Mar;31(3):243-58
Authors: Mercier KA, Powers R
High-throughput screening (HTS) using NMR spectroscopy has become a common component of the drug discovery effort and is widely used throughout the pharmaceutical industry. NMR provides additional information about the nature of small molecule-protein interactions compared to...
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11-24-2010 11:14 PM
[NMR paper] Cofactor fingerprinting with STD NMR to characterize proteins of unknown function: id
Cofactor fingerprinting with STD NMR to characterize proteins of unknown function: identification of a rare cCMP cofactor preference.
Related Articles Cofactor fingerprinting with STD NMR to characterize proteins of unknown function: identification of a rare cCMP cofactor preference.
FEBS Lett. 2005 Jan 31;579(3):661-6
Authors: Yao H, Sem DS
Proteomics efforts have created a need for better strategies to functionally categorize newly discovered proteins. To this end, we have employed saturation transfer difference NMR with pools of closely...
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11-24-2010 11:14 PM
[NMR paper] The design of a potent inhibitor of the hepatitis C virus NS3 protease: BILN 2061--fr
The design of a potent inhibitor of the hepatitis C virus NS3 protease: BILN 2061--from the NMR tube to the clinic.
Related Articles The design of a potent inhibitor of the hepatitis C virus NS3 protease: BILN 2061--from the NMR tube to the clinic.
Biopolymers. 2004;76(4):309-23
Authors: Tsantrizos YS
The virally encoded serine protease NS3/NS4A is essential to the life cycle of the hepatitis C virus (HCV), an important human pathogen causing chronic hepatitis, cirrhosis of the liver, and hepatocellular carcinoma. Until very recently, the...
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11-24-2010 09:25 PM
[NMR paper] NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (
NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (type 1) Rev.
Related Articles NMR solution structure of the RNA-binding peptide from human immunodeficiency virus (type 1) Rev.
Biochemistry. 1995 Jul 4;34(26):8242-9
Authors: Scanlon MJ, Fairlie DP, Craik DJ, Englebretsen DR, West ML
NMR spectroscopy has been used to solve the three-dimensional solution structure of a minimal RNA-binding domain of the Rev protein from the human immunodeficiency virus (type 1), an essential regulatory protein for viral...
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08-22-2010 03:50 AM
[Question from NMRWiki Q&A forum] What is the optimal sample length with Shigemi tubes?
What is the optimal sample length with Shigemi tubes?
Our coil area length is 16 mm. Should we be making samples exactly 16 mm long in the Shigemi tubes for the best sensitivity (assuming that we are limited on amount of material)?
For example, we use D2O matched shigemi tubes for samples in 90/10 H2O/D2O. Is susceptibility matching affected by switch from D2O to H2O?
Thanks!
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08-22-2010 02:30 AM
NMR structure and ion channel activity of the p7 protein from hepatitis C virus.
NMR structure and ion channel activity of the p7 protein from hepatitis C virus.
Related Articles NMR structure and ion channel activity of the p7 protein from hepatitis C virus.
J Biol Chem. 2010 Jul 28;
Authors: Montserret R, Saint N, Vanbelle C, Salvay AG, Simorre JP, Ebel C, Sapay N, Renisio JG, Bockmann A, Steinmann E, Pietschmann T, Dubuisson J, Chipot C, Penin F
The small membrane protein p7 of hepatitis C virus forms oligomers and exhibits ion channel activity essential for virus infectivity. These viroporin features render p7 an...
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08-17-2010 03:36 AM
Optimal methyl labeling for studies of supra-molecular systems
Abstract Selective methyl labeling combined with HMQC spectroscopy that exploits a TROSY effect in 13CH3 spin systems has significantly extended the utility of solution NMR spectroscopy in studies of high molecular weight particles. Herein we compare the utility of 13CH3- versus 13CHD2-labeling of Ile, Leu, Val probes in supra-molecular systems through quantification of relative signal-to-noise ratios in optimized spectra of highly deuterated, 13CH3- and 13CHD2-labeled samples of the half proteasome (α7α7, 360 kDa). It is shown that the sensitivity of spectra recorded on Ile, Leu, Val...
Hepatitis C virus NS3 protease requires its NS4A cofactor peptide for optimal binding
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