Simulations of hairpin formation in spherical pores using distributed computing

We report the thermodynamics and kinetics of an o lattice Go model hairpin from immunoglobulin binding protein con ned to an inert spherical pore Con nement enhances the stability of the hairpin due to the decrease in the entropy of the unfolded state Compared to its value in the bulk the rates of hairpin formation increase in the spherical pore Surprisingly the dependence of the rates on the pore radius Rs is non monotonic The rates reach a maximum at Rs R b g N where R b g N is the radius of gy ration of the hairpin in the bulk The denatured state ensemble DSE of the encapsulated hairpin is highly structured even at substantially ele vated temperatures Remarkably profound e ect of con nement is evident even when hairpin occupies less than a tenth of the sphere volume i e Rs R b g N Our calculations show that the emergence of substantial structure in denatured state of proteins in inert pores is a consequence of con nement In contrast the structure of the bulk DSE depends dramatically on the extent of denaturation