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The Folding of a Family of ThreeHelix 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, V25L29
– 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