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M. Brunori - How proteins recognize their biochemical partners: ligand binding and folding pathways of PDZ domains
states of two homologous three-state proteins, PSD-
95 PDZ3 and PTP-BL PDZ2 (33% sequence identity).
The analysis was carried out by Φ-value analysis,
a powerful experimental method to obtain structural
information about transition states. In this technique
residue-specific structural information is inferred by
comparing the kinetics of folding of the wild-type
protein with a series of conservative single mutants.
The structural information provided by the measurement
of Φ-values was used to build models of the
transition state structures.
Our results demonstrate that for the PDZ proteins
the late folding transition states (TS2) are more
similar to each other than the early transition
states (TS1) (Fig. 1). Thus, taking two snapshots
along each folding pathway illustrates the presence
of a weak native bias at the early stages of the
process, which results in alternative folding events.
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By contrast approaching the native conformation
the folding pathway is essentially dictated by the
native topology. This result, which reflects the funnelling
of the free energy landscape toward the
native state, opens the way to new results on the
structure of transition states and intermediates in
the circular permutants, and to the definition of
the role of topology in determining on-pathway or
off-pathway misfolded intermediates.
Selected publications
Calosci N, Chi CN, Richter B, Camilloni C,
Engström A, Eklund L, Travaglini-Allocatelli C,
Gianni S, Vendruscolo M, Jemth P. Comparison of
successive transition states for folding reveals alternative
early folding pathways of two homologous
proteins. Proc Natl Acad Sci USA 2008, 105:19240-5.
Fig. 1 - Representative structures of early (TS1) and late (TS2) transition states in the folding of two PDZ domains as obtained by - value
analysis and restrained molecular dynamics simulations.
(left) A representative structure of TS1 of PSD-95 PDZ3. (right) Superposition of representative structures of TS2 of PSD-95 PDZ3 and PTP-BL
PDZ2. The TS1 structures of the two proteins were too different to be superimposed.