b2-Microglobulin has been a model system for the study
of fibril formation for 20 years. The experimental study
of b2-microglobulin structure, dynamics, and thermodynamics
in solution, at atomic detail, along the pathway
leading to fibril formation is difficult because the onset
of disorder and aggregation prevents signal resolution
in Nuclear Magnetic Resonance experiments. Moreover,
it is difficult to characterize conformers in exchange
equilibrium. To gain insight (at atomic level) on processes
for which experimental information is available at
molecular or supramolecular level, molecular dynamics
simulations have been widely used in the last decade.
Here, we use molecular dynamics to address three key
aspects of b2-microglobulin, which are known to be relevant
to amyloid formation: (1) 60 ns molecular dynamics
simulations of b2-microglobulin in trifluoroethanol
and in conditions mimicking low pH are used to study
the behavior of the protein in environmental conditions
that are able to trigger amyloid formation; (2) adaptive
biasing force molecular dynamics simulation is used to
force cis-trans isomerization at Proline 32 and to calculate
the relative free energy in the folded and unfolded
state. The native-like trans-conformer (known as intermediate
2 and determining the slow phase of refolding),
is simulated for 10 ns, detailing the possible link
between cis-trans isomerization and conformational disorder;
(3) molecular dynamics simulation of highly concentrated
doxycycline (a molecule able to suppress fibril
formation) in the presence of b2-microglobulin provides
details of the binding modes of the drug and a rationale
for its effect.
