Related ArticlesBinding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR.
Proc Natl Acad Sci U S A. 2017 11 14;114(46):E9855-E9862
Authors: Deshmukh L, Tugarinov V, Louis JM, Clore GM
Abstract
The conversion of immature noninfectious HIV-1 particles to infectious virions is dependent upon the sequential cleavage of the precursor group-specific antigen (Gag) polyprotein by HIV-1 protease. The precise mechanism whereby protease recognizes distinct Gag cleavage sites, located in the intrinsically disordered linkers connecting the globular domains of Gag, remains unclear. Here, we probe the dynamics of the interaction of large fragments of Gag and various variants of protease (including a drug resistant construct) using Carr-Purcell-Meiboom-Gill relaxation dispersion and chemical exchange saturation transfer NMR experiments. We show that the conformational dynamics within the flaps of HIV-1 protease that form the lid over the catalytic cleft play a significant role in substrate specificity and ordered Gag processing. Rapid interconversion between closed and open protease flap conformations facilitates the formation of a transient, sparsely populated productive complex between protease and Gag substrates. Flap closure traps the Gag cleavage sites within the catalytic cleft of protease. Modulation of flap opening through protease-Gag interactions fine-tunes the lifetime of the productive complex and hence the likelihood of Gag proteolysis. A productive complex can also be formed in the presence of a noncognate substrate but is short-lived owing to lack of optimal complementarity between the active site cleft of protease and the substrate, resulting in rapid flap opening and substrate release, thereby allowing protease to differentiate between cognate and noncognate substrates.
Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR [Biophysics and Computational Biology]
Binding kinetics and substrate selectivity in HIV-1 protease-Gag interactions probed at atomic resolution by chemical exchange NMR
Lalit Deshmukh, Vitali Tugarinov, John M. Louis, G. Marius Clore...
Date: 2017-11-14
The conversion of immature noninfectious HIV-1 particles to infectious virions is dependent upon the sequential cleavage of the precursor group-specific antigen (Gag) polyprotein by HIV-1 protease. The precise mechanism whereby protease recognizes distinct Gag cleavage sites, located in the intrinsically disordered linkers connecting the globular domains of Gag, remains...
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11-15-2017 08:36 AM
[NMR paper] Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry.
Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry.
Related Articles Substrate and Cofactor Dynamics on Guanosine Monophosphate Reductase Probed by High Resolution Field Cycling 31P NMR Relaxometry.
J Biol Chem. 2016 Sep 9;
Authors: Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L
Abstract
Guanosine-5'-monophosphate reductase (GMPR) catalyzes the reduction of GMP to IMP and ammonia with concomitant oxidation of NADPH. Here we investigated the structure...
[NMR paper] The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.
The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.
Related Articles The H/D-exchange Kinetics of the Escherichia coli Co-chaperonin GroES Studied by 2D-NMR and DMSO-Quenched Exchange Methods.
J Mol Biol. 2013 Apr 11;
Authors: Chandak MS, Nakamura T, Makabe K, Takenaka T, Mukaiyama A, Chaudhuri TK, Kato K, Kuwajima K
Abstract
We studied hydrogen/deuterium-exchange reactions of peptide amide protons of GroES using two different techniques: (1) two-dimensional (1)H-(15)N...
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04-16-2013 07:46 PM
[NMR paper] Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy.
Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy.
Probing Slow Chemical Exchange at Carbonyl Sites in Proteins by Chemical Exchange Saturation Transfer NMR Spectroscopy.
Angew Chem Int Ed Engl. 2013 Feb 28;
Authors: Vallurupalli P, Kay LE
Abstract
Seeing the invisible: A 13 CO NMR chemical exchange saturation transfer (CEST) experiment for the study of "invisible" excited protein states with lifetimes on the order of 5-50 ms has been developed. The 13 CO chemical...
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03-02-2013 11:45 AM
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study
Nonnative Interactions in the FF Domain Folding Pathway from an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study
Dmitry M. Korzhnev, Robert M. Vernon, Tomasz L. Religa, Alexandar L. Hansen, David Baker, Alan R. Fersht and Lewis E. Kay
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja203686t/aop/images/medium/ja-2011-03686t_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja203686t
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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06-29-2011 04:45 AM
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study.
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study.
Non-Native Interactions in the FF Domain Folding Pathway From an Atomic Resolution Structure of a Sparsely Populated Intermediate: An NMR Relaxation Dispersion Study.
J Am Chem Soc. 2011 Jun 6;
Authors: Korzhnev DM, Vernon RM, Religa TL, Hansen AL, Baker D, Fersht AR, Kay LE
Several all-helical single-domain proteins have been shown to fold rapidly (us timescale) to a compact...