Defining the nature of thermal intermediate in 3 state folding proteins: apoflavodoxin, a study case.

ABSTRACT: The early stages of the thermal unfolding of apoflavodoxin have been determined by using atomistic multi microsecond-scale molecular dynamics (MD) simulations complemented with a variety of experimental techniques. Results strongly suggest that the intermediate is reached very early in the thermal unfolding process and that it has the properties of an "activated" form of the native state, where thermal fluctuations in the loops break loop-loop contacts. The unrestrained loops gain then kinetic energy corrupting short secondary structure elements without corrupting the core of the protein. The MD-derived ensembles agree with experimental observables and draw a picture of the intermediate state inconsistent with a well-defined structure and characteristic of a typical partially disordered pr

SUBMITTER: Garcia-Fandino R 

PROVIDER: S-EPMC3426563 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature