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NMR reveals novel mechanisms of protein activity regulation

Charalampos G. Kalodimos
- 01 May 2011 - 
- Vol. 20, Iss: 5, pp 773-782
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TLDR
A summary of mechanisms underpinning protein activity regulation revealed by the application of NMR spectroscopy in a number of biological systems studied in the lab is provided.
Abstract
NMR spectroscopy is one of the most powerful tools for the characterization of biomolecular systems. A unique aspect of NMR is its capacity to provide an integrated insight into both the structure and intrinsic dynamics of biomolecules. In addition, NMR can provide site-resolved information about the conformation entropy of binding, as well as about energetically excited conformational states. Recent advances have enabled the application of NMR for the characterization of supramolecular systems. A summary of mechanisms underpinning protein activity regulation revealed by the application of NMR spectroscopy in a number of biological systems studied in the lab is provided.

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Dynamic allostery: linkers are not merely flexible.

TL;DR: It is proposed that successive conformational states along major allosteric propagation pathways are pre-encoded in linker sequences where each state is encoded by the previous one, achieving faster timescales even for large conformational changes.
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Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle

TL;DR: These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.
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Solution NMR Spectroscopy for the Study of Enzyme Allostery

TL;DR: NMR spectroscopy is unequaled in its ability to detect structural and dynamical changes in biomolecules, and the case studies presented herein demonstrate the range of insights to be gained from this valuable method.
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The design of covalent allosteric drugs.

TL;DR: In a recent promising step in therapeutic drug development, allosteric, disulfide-tethered fragments successfully modulated the activity of a protein kinase and K-Ras.
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Advances in NMR Methods To Map Allosteric Sites: From Models to Translation

TL;DR: It is clear that NMR plays a central role not only in experimentally validating transformative theories of allostery, but also in tapping the full translational potential of allosteric systems.
References
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Journal ArticleDOI

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TL;DR: Experimental evidence supports a new molecular recognition paradigm for processes as diverse as signaling, catalysis, gene regulation and protein aggregation in disease, which has the potential to significantly impact views and strategies in drug design, biomolecular engineering and molecular evolution.
Journal ArticleDOI

The Conformational Plasticity of Protein Kinases

TL;DR: Crystal structures of inactive kinases have revealed a remarkable plasticity in the kinase domain that allows the adoption of distinct conformations in response to interactions with specific regulatory domains or proteins.
Journal ArticleDOI

Intrinsic dynamics of an enzyme underlies catalysis

TL;DR: It is shown that the intrinsic plasticity of the protein is a key characteristic of catalysis, and the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergy pressure between structure and dynamics.
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