Molecular Dynamics of Subtilisin Carlsberg in Aqueous and Nonaqueous Solutions
C'rystul .striictiircs huvc recently appeared ,fir the enzyme suhtilisin Carlsberg in anhydrous ut~t~[onitril~~ und in wuter. To guin u mechanistic undcmtanding ofhow the solvent environmmt Uffi'cts protein .striictiir~ und djmunics, we have performed molecular dynamics simulations on siihtilisin Carlshrrg in water and acetonitrile. W e describe a 480 p s simulation of suhtilisin in ucvtonitrile soliition and a 450 p s simiilation of'siibtilisin in water. Each simulation employed tlw ull-atom AMBER f k r .field. The calculated rms deviations, ,from their respective x-ray striictiiri's, \tvre .similar in each simulation, biit -0.5 A" higher in the ucetonitrile simulation.
Only in thc ucetonitrilc simulution does one helix iindergt, a reversihlepartial unwinding, which lastvd,fOr ahoiit 100 ps. The other secondary striictiire elements remain inlact or undergo modst, fliictiiutions. In thr aqiieoiis simiilation, the calculated and experimental temperature factors ugrw vrrj-~~4 1 .
In thc acetonitrile simulation, however, the calciilated temperature factors are miich higlwr than tlie cxperimental values. The larger rms deviation and thermal fluctuations notid in tlic acc'tonitrile simulation are consistent with the requirement,for protein cross-linking in this crwtul and a recim two-dimensional NH-exchange nmr study on horse heart cytochrome c in nonaqiieoits sollition.