Related ArticlesProbing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics.
Nat Catal. 2019 Aug;2(8):726-734
Authors: Stiller JB, Kerns SJ, Hoemberger M, Cho YJ, Otten R, Hagan MF, Kern D
Abstract
Protein conformational changes are frequently essential for enzyme catalysis, and in several cases, shown to be the limiting factor for overall catalytic speed. However, a structural understanding of corresponding transition states, needed to rationalize the kinetics, remains obscure due to their fleeting nature. Here, we determine the transition-state ensemble of the rate-limiting conformational transition in the enzyme adenylate kinase, by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations. By comparing homologous kinases evolved under ambient or high pressure in the deep-sea, we detail transition state ensembles that differ in solvation as directly measured by the pressure dependence of catalysis. Capturing transition-state ensembles begins to complete the catalytic energy landscape that is generally characterized by structures of all intermediates and frequencies of transitions among them.
[NMR paper] High-pressure NMR techniques for the study of protein dynamics, folding and aggregation.
High-pressure NMR techniques for the study of protein dynamics, folding and aggregation.
Related Articles High-pressure NMR techniques for the study of protein dynamics, folding and aggregation.
J Magn Reson. 2017 Apr;277:179-185
Authors: Nguyen LM, Roche J
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins and dissociate protein complexes or aggregates. The heterogeneity of the response to pressure offers a unique opportunity to dissect the thermodynamic contributions to protein...
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04-02-2017 11:43 AM
High-pressure NMR techniques for the study of protein dynamics, folding and aggregation
High-pressure NMR techniques for the study of protein dynamics, folding and aggregation
Publication date: April 2017
Source:Journal of Magnetic Resonance, Volume 277</br>
Author(s): Luan M. Nguyen, Julien Roche</br>
High-pressure is a well-known perturbation method used to destabilize globular proteins and dissociate protein complexes or aggregates. The heterogeneity of the response to pressure offers a unique opportunity to dissect the thermodynamic contributions to protein stability. In addition, pressure perturbation is generally reversible, which is essential...
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03-30-2017 06:42 PM
[NMR paper] Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Related Articles Pressure-induced structural transition of mature HIV-1 Protease from a combined NMR/MD simulation approach.
Proteins. 2015 Sep 18;
Authors: Roche J, Louis JM, Bax A, Best RB
Abstract
We investigate the pressure-induced structural changes in the mature human immunodeficiency virus type 1 protease dimer (HIV-1 PR), using residual dipolar coupling (RDC) measurements in a weakly oriented solution. (1) DNH RDCs...
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09-20-2015 12:56 PM
[NMR paper] Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme.
Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme.
Cavity as a Source of Conformational Fluctuation and High-Energy State: High-Pressure NMR Study of a Cavity-Enlarged Mutant of T4Lysozyme.
Biophys J. 2015 Jan 6;108(1):133-145
Authors: Maeno A, Sindhikara D, Hirata F, Otten R, Dahlquist FW, Yokoyama S, Akasaka K, Mulder FA, Kitahara R
Abstract
Although the structure, function, conformational dynamics, and controlled thermodynamics of proteins...
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01-08-2015 01:29 PM
[NMR paper] Solution and high-pressure NMR studies of the structure, dynamics and stability of the cross-reactive allergenic cod parvalbumin Gad m 1.
Solution and high-pressure NMR studies of the structure, dynamics and stability of the cross-reactive allergenic cod parvalbumin Gad m 1.
Related Articles Solution and high-pressure NMR studies of the structure, dynamics and stability of the cross-reactive allergenic cod parvalbumin Gad m 1.
Proteins. 2014 Aug 12;
Authors: Moraes AH, Ackerbauer D, Kostadinova M, Bublin M, de Oliveira GA, Ferreira F, Almeida FC, Breiteneder H, Valente AP
Abstract
Beta-parvalbumins from different fish species have been identified as the main...
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08-15-2014 12:53 PM
[NMR paper] Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein.
Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein.
Related Articles Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein.
Chembiochem. 2013 Jun 28;
Authors: Roche J, Ying J, Maltsev AS, Bax A
Abstract
The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated ?-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close...
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07-03-2013 01:46 PM
Probing alanine transaminase catalysis with hyperpolarized 13CD3-pyruvate
From the The DNP-NMR Blog:
Probing alanine transaminase catalysis with hyperpolarized 13CD3-pyruvate
Barb, A.W., et al., Probing alanine transaminase catalysis with hyperpolarized 13CD3-pyruvate. J. Magn. Reson., 2013. 228(0): p. 59-65.
http://dx.doi.org/10.1016/j.jmr.2012.12.013
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04-15-2013 08:52 AM
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A
A Delicate Interplay of Structure, Dynamics, and Thermodynamics for Function: A High Pressure NMR Study of Outer Surface Protein A
22 February 2012
Publication year: 2012
Source:Biophysical Journal, Volume 102, Issue 4</br>
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Outer surface protein A (OspA) is a crucial protein in the infection of Borrelia burgdorferi causing Lyme disease. We studied conformational fluctuations of OspA with high-pressure 15N/1H two-dimensional NMR along with high-pressure fluorescence spectroscopy. We found evidence within folded, native OspA for rapid local fluctuations of the...
Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics.
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