The Folding of a Family of Three- Helix Bundle Proteins: Spectrin R15 Has a Robust Folding Nucleus, Unlike Its Homologous Neighbours J. Mol. Biol. (2014) Lee Gyan Kwa Department of Chemistry, University of Cambridge, UK presented by Chao Wang

Abstract

A seminal study of the three-helix-bundle homeodomain family allowed Fersht, Daggett and co-workers to propose that there is continuum of folding mechanisms between diffusion-collision and nucleation-condensation folding mechanisms. This continuum has proved a useful framework for understanding both folding mechanism and pathway. They showed that the principal determinant of mechanism lies in the balance between secondary structure propensity and tertiary contacts. Where secondary structure (helical) propensity is high, early local structure formation is favoured, but where helical propensity is low, formation of longrange tertiary interactions is concomitant with secondary structure formation.

Phi-value analysis Phi value analysis is an experimental protein engineering method used to study the structure of the folding transition state in small protein domains that fold in a two-state manner. Since the folding transition state is by definition a transient and partially unstructured state, its structure is difficult to determine by traditional methods such as protein NMR or X-ray crystallography. In phi-value analysis, the folding kinetics and conformational folding stability of the wild-type protein are compared with those of one or more point mutants. This comparison yields a phi value (defined below) that seeks to measure the mutated residue's energetic contribution to the folding transition state (and thus the degree of native structure around the mutated residue in the transition state) from the relative free energies of the unfolded state, the folded state and the transition state for the wild-type and mutant proteins.

What can we learn? For me: –Evidence of A1A4/5, F18-I22, I22-V25, V25- L29 –Remote anti-charged pair, E18-K25 –Hydrophobic interaction dominates folding, even for charged amino acids For Haicang: –Evidence of core interaction Discussion –Beta-branched residue propensity