title: Molecular dynamics simulation of β₂-microglobulin in denaturing and stabilizing conditions.
abstract: β₂-Microglobulin has been a model system for the study of fibril formation for 20 years. The experimental study of β₂-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 β₂-microglobulin, which are known to be relevant to amyloid formation: (1) 60 ns molecular dynamics simulations of β₂-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 β₂-microglobulin provides details of the binding modes of the drug and a rationale for its effect.
authors.affiliation: Dipartimento di Scienze e Tecnologie Biomediche, Universita' di Udine, Piazzale Kolbe 4, 33100 Udine, Italy. federico.fogolari@uniud.it
authors.forename: Federico
authors.initials: F
authors.lastname: Fogolari
authors.forename: Alessandra
authors.initials: A
authors.lastname: Corazza
authors.forename: Nicola
authors.initials: N
authors.lastname: Varini
authors.forename: Matteo
authors.initials: M
authors.lastname: Rotter
authors.forename: Devrim
authors.initials: D
authors.lastname: Gumral
authors.forename: Luca
authors.initials: L
authors.lastname: Codutti
authors.forename: Enrico
authors.initials: E
authors.lastname: Rennella
authors.forename: Paolo
authors.initials: P
authors.lastname: Viglino
authors.forename: Vittorio
authors.initials: V
authors.lastname: Bellotti
authors.forename: Gennaro
authors.initials: G
authors.lastname: Esposito
mesh_terms: D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011489:Protein Denaturation; D001613:beta 2-Microglobulin / Q000737:chemistry*
chemical_list: D001613:beta 2-Microglobulin