Studying the unfolding kinetics of proteins under pressure using long molecular dynamic simulation runs

CHARA OSVALDO; MCCARTHY ANDRÉS NORMAN; GRIGERA JOSÉ RAÚL

Montevideo

Congreso; 5th Southern Cone Biophysics Congress. 6th International Conference of Biological Physics.; 2007

IUPAP - SAB

The usefulness of computational methods such as molecular dynamic simulation has been extensively established for studying systems inequilibrium. Nevertheless, its application on complex non-equilibrium biological processes, such as protein unfolding, has been generallyregarded as producing results which cannot be interpreted straightforwardly.In the present study we present results for the kinetics of unfolding of apomyoglobin, based on the analysis of long simulation runs of thisprotein in solution at 3kbar (1 atm = 1.01325 bar = 101 325 Pa). We hereby demonstrate that the analysis of the data collected within asimulated time span of 0.18μs suffices for producing results which coincide remarkably with the available unfolding kinetics experimentaldata. This not only validates molecular dynamic simulation as a valuable alternative for studying non equilibrium processes, but also enablesfor a detailed analysis of the actual structural mechanism which underlies the unfolding process of proteins under elusive denaturingconditions such as high pressure.Methods: All the simulations were done using GROMACS package. All-atoms (ff2gmx) force field was used for the minimization processand molecular dynamics and kept all protein bond lengths constrained (LINCS algorithm). Water molecules (SPC/E model) wereconstrained using the SETTLE algorithm. For the electrostatic forces we applied the Reaction Field method. Lennard-Jones interactionswere calculated within a cut-off radius of 1.4nm. The unfolding kinetics was followed by adjusting the Radius of Gyration (Rg) to a two statesaturable kinetic model.