Structural insights into the two sequential folding transition states of the PB1 domain of NBR1 from Φ value analysis and biased molecular dynamics simulations.

Abstract:

:The PB1 domain of NBR1 folds via a single pathway mechanism involving two sequential energy barriers separated by a high-energy intermediate. The structural ensemble representing each of the two transition states (TS1 and TS2) has been calculated using experimental Φ values and biased molecular dynamics simulations. Both TS1 and TS2 represent compact states (β(TS1) = 0.71, and β(TS2) = 0.93) but are defined by quite different distributions of Φ values, degrees of structural heterogeneity, and nativelike secondary structure. TS1 forms a heterogeneous ensemble of dynamic structures, representing a global collapse of the polypeptide chain around a set of weak nativelike contacts. In contrast, TS2 has a high proportion of nativelike secondary structure, which is reflected in an extensive distribution of high Φ values. Two snapshots along the folding pathway of the PB1 domain reveal insights into the malleability, the solvent accessibility, and the timing of nativelike core packing that stabilizes the folded state.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Chen P,Evans CL,Hirst JD,Searle MS

doi

10.1021/bi1016793

subject

Has Abstract

pub_date

2011-01-11 00:00:00

pages

125-35

issue

1

eissn

0006-2960

issn

1520-4995

journal_volume

50

pub_type

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