pH Sensitivity of the SERF1a Conformational Ensemble

The MOAG-4/SERF class
of proteins is a positive regulator of the
aggregate formation of amyloid proteins that play an important role
in the origin of numerous age-related diseases. In this class of proteins,
previous structural studies showed that SERF1a is a very flexible
protein, containing at least one α-helical region. The present
work proposes the first description of the conformational space of
SERF1a at two pH values (6 and 6.8) using nuclear magnetic resonance
(NMR) and small-angle X-ray scattering (SAXS). SERF1a NMR conformations
have been generated using the CYANA-FLYA procedure as well as the
TAiBP (Threading-Augmented interval Branch-and-Prune) procedure, based
on the systematic enumeration of protein conformations within an original
distance geometry scheme. The generated conformations were filtered
using Pepsi-SAXS by fitting small-angle X-ray experiments based on
size exclusion chromatography (SEC-SAXS). At pH 6.8, a good fit of
the SEC-SAXS curves was obtained for the CYANA and TAiBP NMR conformations,
while at pH 6, analysis of the NMR conformations and the SEC-SAXS
curves indicated that there could be a conformational exchange between
a compact conformation displaying long-range nuclear Overhauser effects
(NOEs) between residues LYS-13 and THR-32, and slightly more extended
conformations. The shortening of the C-terminal α-helix, as
well as the destabilization of the N-terminal α-helix at acidic
pH, may be related to the physiological function of SERF1a in the
nucleoli. Interestingly, the N-terminal region of SERF1a displays
numerous possible binding pockets, particularly in the region interacting
with α-synuclein, detected by chemical shift perturbations.
In general, the TAiBP procedure allows for a more expanded exploration
of the SERF1a conformational space as well as for a description of
the internal dynamics of SERF1a in agreement with NMR relaxation and
with predictions from the protein primary sequence.