| Abstract | In this thesis, all-atom classical molecular dynamics simulations were used to study two proteins of interest : 14-3-3 and PTP-PEST. Two mutagenesis studies were performed on 14-3-3 zeta protein, wherein D124 and E131 were mutated with Alanine. Observations were made on on the effects of each mutation on the conformational dynamics and implications on binding of phosphopeptide to the dimeric protein and the results were correlated with the experimental observations made by our collaborators. In the case of D124A , it was observed that the pocket becomes wider and change in the charged interactions in the pocket may lead to reduction/complete loss of binding affinity of the phosphopeptide to the protein. In the case of E131A, both monomers show different effects on the residue-level changes due to the mutation. In M1, the effects seems to be very minimal on the binding pocket while in M2, the effects seem to be very similar to D124A which may lead to reduced binding in this case as well. But docking studies show that although the structural effects are similar to D124A, the binding energy is slightly increased compared to WT. Phosphorylation studies were performed on PTP-PEST in two parts. In the first study, Y64 in PEST was phosphorylated and its effect on stability of AMPK-PEST complex was checked and the implications on binding of AMPK to PEST was deduced. It was observed that stronger interactions are present in AMPK-PEST complex after pY64 , hinting towards change in electrostatic network in complex upon phosphorylation. New interactions pop up after Y64 phosphorylation and conformational changes at the interface , all led to the inference that the phosphorylation led to stronger binding of AMPK to PTP-PEST. In the second study, the effect of phosphorylation of chosen tyrosines on structure and dynamics of PTP-PEST was studied. The results show that tyrosine phosphorylation can impact structural dynamics, potentially influencing substrate recognition and binding. |