Insights on Protein Structure and Dynamics from Temperature-Dependent Molecular Dynamics and Normal Mode Analysis
Rehman, Habib ur
AdvisorGwaltney, Steven R.
CommitteeLewis, Edwin A.
Emerson, Joseph P.
In this thesis we have employed two computational approaches, temperature-dependent molecular dynamics (MD) and normal mode analysis (NMA), to gain insights into the structure-function relationships between three structurally-related proteins, each possessing a central alpha/beta core. The three proteins studied here are: pnbCE from Bacillus subtilis, cutinase from Fusarium solani - both belong to the serine hydrolase family - and TTHA1554, from the thermophile Thermus thermophilus. Mutations at the gate residue 362, located at the side-door of the pnbCE enzyme, are known to alter the catalytic activity of this enzyme. In this work the modifications induced by mutating LEU362 on the structural and dynamical properties of pnbCE are also explored. From MD simulations at several temperatures, we propose a mechanism by which mutations at position 362 of pnbCE affect the stability and functionality of this enzyme. We have identified two coil residues, SER218 and GLN276, whose interactions with residue 362 in wild-type and mutant pnbCE enzymes control the dynamics of the side-door domain of pnbCE. A hydrogen bond between the GLN276 and ARG362 residues in the arginine substituted (L362R) pnbCE mutant enzyme appears to be responsible for locking the sidedoor domain region of the L362R enzyme, thus lowering the catalytic rates of the L362R mutant pnbCE enzyme compared to the wild-type. Similarly, a hydrogen bond formed between SER218 and ARG362 in L362R provides thermal stability to the arginine substituted mutant enzyme. This hydrogen bond is not as prevalent in the wild-type or other mutated pnbCEs, making them prone to structural fluctuations upon increasing temperature. The predominant low-frequency mode, obtained from normal mode analysis, reveals a collective scissor-like motion of residues surrounding the openings to the active site that validates the results of MD simulations on pnbCE systems. The collective motion of large loops also appear in the low-frequency modes of cutinase and TTHA1554, which correspond to particularly mobile regions in these proteins. An attempt to locate a putative active site of the thermophilic protein TTHA1554 was inconclusive. In general, useful comparisons of the flexibility, stability, and dynamic changes were calculated for the three selected proteins.