Determination of stable structure for Tr yptophan cage usin g Molecular dyna mics simulation

Understanding pr otein foldin g is critical in molecula r biology. M olecular dynamic simulation (MD) performed from simple lattice models with no solvent to all atom mo dels with im plicit continum solvent and explici t solvent mo del are used to supple ment experi ments. In im plicit solven t model folded structure kineticall y may trap in high energy minimu m [۱-۳]. We have suggested a way to avoid this problem. Here MD simulation has been used t o study folding of Trypt ophan cage (TC۵B)a mini protein from its full y extended c onformation. The meas uring of main-chin root mean squa re deviation (rmsd) is criterion to determine th e stable structure. The final structure has beenproduced with ۱.۶ǖrmsd r elated to N MR native structure.

کلیدواژه ها:

Folding ، Molecu lar dynamic ، Tryptophan cage ، Rmsd ،