Mapping allostery through the covariance analysis of NMR chemical shifts

Rajeevan Selvaratnam, Somenath Chowdhury, Bryan VanSchouwena, Giuseppe Melacini

Research output: Contribution to journalArticle

139 Citations (Scopus)

Abstract

Allostery is a fundamental mechanism of regulation in biology. The residues at the end points of long-range allosteric perturbations are commonly identified by the comparative analyses of structures and dynamics in apo and effector-bound states. However, the networks of interactions mediating the propagation of allosteric signals between the end points often remain elusive. Here we show that the covariance analysis of NMR chemical shift changes caused by a set of covalently modified analogs of the allosteric effector (i.e., agonists and antagonists) reveals extended networks of coupled residues. Unexpectedly, such networks reach not only sites subject to effector-dependent structural variations, but also regions that are controlled by dynamically driven allostery. In these regions the allosteric signal is propagated mainly by dynamic rather than structural modulations, which result in subtle but highly correlated chemical shift variations. The proposed chemical shift covariance analysis (CHESCA) identifies interresidue correlations based on the combination of agglomerative clustering (AC) and singular value decomposition (SVD). AC results in dendrograms that define functional clusters of coupled residues, while SVD generates score plots that provide a residue-specific dissection of the contributions to binding and allostery. The CHESCA approach was validated by applying it to the cAMP-binding domain of the exchange protein directly activated by cAMP (EPAC) and the CHESCA results are in full agreement with independent mutational data on EPAC activation. Overall, CHESCA is a generally applicable method that utilizes a selected chemical library of effector analogs to quantitatively decode the binding and allosteric information content embedded in chemical shift changes.

Original languageEnglish (US)
Pages (from-to)6133-6138
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume108
Issue number15
DOIs
StatePublished - Apr 12 2011

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Small Molecule Libraries
Dissection
Proteins
Protein Domains

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Mapping allostery through the covariance analysis of NMR chemical shifts. / Selvaratnam, Rajeevan; Chowdhury, Somenath; VanSchouwena, Bryan; Melacini, Giuseppe.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 108, No. 15, 12.04.2011, p. 6133-6138.

Research output: Contribution to journalArticle

Selvaratnam, Rajeevan ; Chowdhury, Somenath ; VanSchouwena, Bryan ; Melacini, Giuseppe. / Mapping allostery through the covariance analysis of NMR chemical shifts. In: Proceedings of the National Academy of Sciences of the United States of America. 2011 ; Vol. 108, No. 15. pp. 6133-6138.
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