Molecular dynamics and free energy calculations applied to malic enzymes on structural stability

• Main Authors: Jia-Kai Zhou, 周佳楷
• Other Authors: Sheh-Yi Sheu
• Format: Others
• Language: en_US
• Published: 2007
• Online Access: http://ndltd.ncl.edu.tw/handle/38653860496202836839

碩士 === 國立陽明大學 === 醫學生物技術研究所 === 95 === Quaternary structures of proteins often involve in the regulation mechanisms. Human mitochondrial malic enzyme is a tetrameric enzyme which one malic enzyme monomer has 584 residues and the MW is about 66 kDa. Malic enzymes are widely distributed in every organism and it catalyzes the oxidative decarboxylation of L-malate to produce carbon dioxide and pyruvate in the concomitant reduction of NAD(P)+ to NAD(P)H. Low temperature, high ionic strength or acidic environment will induce the dissociations of tetrameric malic enzymes. One tetrameric malic enzyme will reversibly dissociate into two dimers and then one dimer dissociates into two monomers. The equilibrium of tetramer─dimer─monomer might be a mechanism of malic enzyme to regulate the catalysis rate. The Trp548 of pigeon liver malic enzyme has been found to be correlated with the structural stability of terameric malic enzyme. The corresponding residue of human mitochondrial malic enzyme, Trp572, hence is also believed to be correlated with the stability of the quaternary structure of malic enzyme. The traditional methods to judge how the substitution of certain amino acid affects the structural stability of protein have to pay for much in money and time. In this study, by the power of computers, we plan to use molecular dynamics simulations and calculate the difference of the binding free energy to investigate how the different substitutions of Trp572 affect the stability of quaternary structure of malic enzyme. The results shown in the present study reveal that the substitutions of Trp572 destabilize the quaternary structures of malic enzymes and the destabilizations are more strikingly at pH 4.5. These results respond to the previous studies which the acdic environment will induce the dissociations of tetrameric malic enzymes. Besides, these results also prove that Trp residue plays an important role in the protein-protein interactions and does not prefer to be substituted.