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Protein folding transition states probed by loop extension
Author(s) -
Sánchez Ignacio Enrique
Publication year - 2008
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.073217708
Subject(s) - protein folding , loop (graph theory) , downhill folding , folding (dsp implementation) , sh3 domain , phi value analysis , chemistry , thermodynamics , physics , chemical physics , crystallography , statistical physics , mathematics , biochemistry , kinase , combinatorics , electrical engineering , engineering , proto oncogene tyrosine protein kinase src
We propose a new way to characterize protein folding transition states by (1) insertion of one or more residues into an unstructured protein loop, (2) measurement of the effect on protein folding kinetics and thermodynamics, and (3) analysis of the results in terms of a rate‐equilibrium free energy relationship, α Loop . α Loop reports on the fraction of molecules that form the perturbed loop in the transition state. Interpretation of the changes in equilibrium free energy using standard polymer theory can help detect residual structure in the unfolded state. We illustrate our approach with data for the model proteins CI2 and the alpha spectrin SH3 domain.