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Structure-Based, In Silico Approaches for the Development of Novel cAMP FRET Reporters

  • Matías Machado
  • Sergio PantanoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1294)

Abstract

A significant contribution to the research in cAMP signaling has been made by the development of genetically encoded FRET sensors that allow detection of local concentrations of second messengers in living cells. Nowadays, the availability of a number of 3D structures of cyclic nucleotide-binding domains (CNBD) undergoing conformational transitions upon cAMP binding, along with computational tools, can be exploited for the design of novel or improved sensors. In this chapter we will overview some coarse-grained geometrical considerations on fluorescent proteins, CNBD, and linker peptides to draw simple qualitative rules that may aid the design of novel sensors. Finally, we will illustrate how the application of these simple rules can be used to describe the mechanistic basis of cAMP sensors reported in the literature.

Keywords

Fluorescent protein Allosteric mechanism CNBD Rational design Protein engineering Coarse grain SIRAH 

Notes

Acknowledgments

This work was partially funded by FOCEM (MERCOSUR Structural Convergence Fund), COF 03/11, and Intramural Transversal Program 2013, Institut Pasteur de Montevideo. M.M and S.P are members of the SNI, ANII, Uruguay.

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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Group of Biomolecular SimulationsInstitut Pasteur de MontevideoMontevideoUruguay

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