Molecular dynamics simulation of ß2-microglobulin in denaturing and stabilizing conditions.

ß2-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of ß2-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 ß2-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of ß2-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 ß2-microglobulin provides details of the binding modes of the drug and a rationale for its effect.

Static friction scaling of physisorbed islands: the key is in the edge.

The static friction preventing the free sliding of nanosized rare gas solid islands physisorbed on incommensurate crystalline surfaces is not completely understood. Simulations modeled on Kr/Pb(111) highlight the importance and the scaling behavior of the island's edge contribution to static friction.