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Protein Folding at Atomic Resolution: Analysis of Autonomously Folding Supersecondary Structure Motifs by Nuclear Magnetic Resonance

Protocol
First Online:
Part of the Methods in Molecular Biology book series (MIMB, volume 932)

Abstract

The study of protein folding has been conventionally hampered by the assumption that all single-domain proteins fold by an all-or-none process (two-state folding) that makes it impossible to resolve folding mechanisms experimentally. Here we describe an experimental method for the thermodynamic analysis of protein folding at atomic resolution using nuclear magnetic resonance (NMR). The method is specifically developed for the study of small proteins that fold autonomously into basic supersecondary structure motifs, and that do so in the sub-millisecond timescale (folding archetypes). From the NMR experiments we obtain hundreds of atomic unfolding curves that are subsequently analyzed leading to the determination of the characteristic network of folding interactions. The application of this approach to a comprehensive catalog of elementary folding archetypes holds the promise of becoming the first experimental approach capable of unraveling the basic rules connecting protein structure and folding mechanism.

Key words

Protein structure Protein stability Protein folding Folding mechanisms Folding interaction networks Nuclear magnetic resonance 
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Notes

Acknowledgments

This work was supported by the Marie Curie Excellence Award MEXT-CT-2006-042334, and the grants BFU2008-03237, BFU2008-03278 and CONSOLIDER CSD2009-00088 from the Spanish Ministry of Science and Innovation (MICINN).

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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
  2. 2.Department of Chemistry and BiochemistryUniversity of MarylandCollege ParkUSA

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