Dynamics connect substrate recognition to catalysis in protein kinase A

Masterson, Larry R.; Cheng, Cecilia Y.; Yu, Tao; Tonelli, Marco; Kornev, Alexandr P.; Taylor, Susan S.; Veglia, Gianluigi

doi:10.1038/nchembio.452

Cited by 191 publications

(315 citation statements)

References 50 publications

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“…The role of conformational dynamics in a receptor-ligand interaction has been the subject of intensive studies 3,9,10,12,[16][17][18] . The receptor-ligand interaction process comprises two fundamental steps, namely, the binding and dissociation of a ligand.…”

Section: Discussionmentioning

confidence: 99%

Protein conformational dynamics dictate the binding affinity for a ligand

et al. 2014

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Interactions between a protein and a ligand are essential to all biological processes. Binding and dissociation are the two fundamental steps of ligand-protein interactions, and determine the binding affinity. Intrinsic conformational dynamics of proteins have been suggested to play crucial roles in ligand binding and dissociation. Here, we demonstrate how protein dynamics dictate the binding and dissociation of a ligand through a single-molecule kinetic analysis for a series of maltose-binding protein mutants that have different intrinsic conformational dynamics and dissociation constants for maltose. Our results provide direct evidence that the ligand dissociation is determined by the intrinsic opening rate of the protein.

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Section: Discussionmentioning

confidence: 99%

Protein conformational dynamics dictate the binding affinity for a ligand

et al. 2014

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“…While this approach is useful, it is important to recall that both of these reference states can also be involved in various exchange processes that may complicate the analysis. Nevertheless, analyses of chemical shifts have provided significant insights into several systems and chemical shifts are often used as a measure of a reaction coordinate between the active and inactive states of proteins (Ådén et al 2012;Ådén & Wolf-Watz, 2007;Li et al 2008;Masterson et al 2010Masterson et al , 2011bOlsson & Wolf-Watz, 2010;Volkman et al 2001). An alternative approach for quantification of chemical shifts is the projection analysis (Selvaratnam et al 2012).…”

Section: Chemical Shiftsmentioning

confidence: 99%

Protein dynamics and function from solution state NMR spectroscopy

Kovermann

Rogne

Wolf‐Watz

2016

Quart. Rev. Biophys.

148

122

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Abstract. It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

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“…A major structural rearrangement has to occur for the enzyme to adopt the active conformational state, where the active site is accessible and catalysis may occur. 4,21,47 Indeed, the existence of discrete active and inactive conformational states has been documented for multiple monomeric regulated enzymes. 4,21,35,47 However, to date there is limited knowledge whether effectors simply redistribute the equilibrium of preexisting conformational states, 35,47,48 introduce a new conformational state, 49 or a convolution of the above.…”

Section: ■ Conclusionmentioning

confidence: 99%

Single Enzyme Studies Reveal the Existence of Discrete Functional States for Monomeric Enzymes and How They Are “Selected” upon Allosteric Regulation

Hatzakis¹,

Li²,

Jørgensen³

et al. 2012

J. Am. Chem. Soc.

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Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.

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Dynamics connect substrate recognition to catalysis in protein kinase A

Cited by 191 publications

References 50 publications

Protein conformational dynamics dictate the binding affinity for a ligand

Protein conformational dynamics dictate the binding affinity for a ligand

Protein dynamics and function from solution state NMR spectroscopy

Single Enzyme Studies Reveal the Existence of Discrete Functional States for Monomeric Enzymes and How They Are “Selected” upon Allosteric Regulation

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