posted on 2021-01-20, 12:34authored byJennifer Fischer, Aurel Radulescu, Peter Falus, Dieter Richter, Ralf Biehl
Disordered regions
as found in intrinsically disordered proteins
(IDP) or during protein folding define response time to stimuli and
protein folding times. Neutron spin-echo spectroscopy is a powerful
tool to directly access the collective motions of the unfolded chain
to enlighten the physical origin of basic conformational relaxation.
During the thermal unfolding of native ribonuclease A, we examine
the structure and dynamics of the disordered state within a two-state
transition model using polymer models, including internal friction,
to describe the chain dynamics. The presence of four disulfide bonds
alters the disordered configuration to a more compact configuration
compared to a Gaussian chain that is defined by the additional links,
as demonstrated by coarse-grained simulation. The dynamics of the
disordered chain is described by Zimm dynamics with internal friction
(ZIF) between neighboring amino acids. Relaxation times are dominated
by mode-independent internal friction. Internal friction relaxation
times show an Arrhenius-like behavior with an activation energy of
33 kJ/mol. The Zimm dynamics is dominated by internal friction and
suggest that the characteristic motions correspond to overdamped elastic
modes similar to the motions observed for folded proteins but within
a pool of disordered configurations spanning the configurational space.
For IDP, internal friction dominates while solvent friction and hydrodynamic
interactions are smaller corrections.