Theoretical Studies On The Structures And Reaction Mechanisms Of Several Important Proteins

In recently years, along with the rapid development of computer technology and computational chemistry, molecule mechanics, molecular dynamics and quantum mechanics theories play an important role in life sciences. The molecular simulations of proteins have already become a very important and active research field. By the theoretical simulation, the three dimension (3D) structure, the interactions between receptor and lingand, and protein biochemistry mechanism can be obtained. In our thesis, molecular mechanics, molecular dynamics and quantum mechanics were used to theoretically study the 3D models of four proteins and investigate their structure properties in detail. The main results are summarized as follows:1. Homology modeling and docking studies of human acid mammalian chitinaseChitinases are endo-β-1,4-N-acetylglucosaminidases that can fragment chitin and have been identified in several organisms varying from bacteria to humans. Human chitinase (hAMCase) is a functional chitinase and the experiment showed that hAMCase contributes to Th2-mediated inflammation through IL-13-dependent mechanism, and inhibition of AMCase decreases airway inflammation and airway hyper-responsiveness. Thus, hAMCase is a potential therapeutic target for anti-inflammatory therapy in Th2-mediated diseases such as asthma.By means of the homology modeling and molecular dynamics methods, the 3D structure of hAMCase is created and refined. With this model, a flexible docking study is performed and the results indicate that allosamidin is a more preferred inhibitor than NAG2, which is in good agree with the experimental facts by Yi-Te et al. From the docking studies, the important residues for binding were identified.Glu49 and Glu276 may be the key amino acids residues interacting with the substrates, and Asp192 and Trp10 may help allosamidin steadily interact with hAMCase. These results will offer further experimental studies of structure-function relationships.2. Theoretical study of human serine racemaseD-Serine occurs at high levels in the mammalian brain, higher than even some common amino acids, and it has been shown to be an endogenous ligand for the"glycine site"of N-methyl-D-aspartate (NMDA) receptors. These receptors play central roles in excitatory neurotransmission, neuronal plasticity, and learning and memory. Over activation of the NMDA receptor is proposed to be responsible for the cell death that occurs in strokes. Other studies suggest that D-serine and NMDA receptor dysfunction play a role in the pathophysiology of Alzheimer's disease. The enzyme serine racemase has been shown to be responsible for the physiological conversion of L-serine to D-serine. The involvement of D-serine in this breadth of pathophysiological processes makes serine racemase an excellent drug target.The three dimensional structure of human serine racemase (hSR) was modeled and refined using homology modeling and molecular dynamics simulation. The binding pattern predicted by docking studies revealed that important residues interacted with the peptide inhibitors, which are Asn148, His76, Glu130 and Lys235. The module provided further refinement of the hSR/inhibitor binding interaction that may be used as a basis for new structure based design efforts.3. Homology modeling and inhibitors binding study of human fatty acid amide hydrodaseFatty acid amide hydrolase (FAAH) is responsible for the hydrolysis of the fatty acid amide class of lipid transmitters which include the endogenous cannabinoid N-arachidonoyl ethanolamine, sleep-inducing agent oleamide, anorexigenic agent N-oleoyl ethanolamide and anti-inflammatory agent N-palmitoyl ethanolamide. Studies of FAAH inactivation suggest that this enzyme could be an attractive target for the treatment of pain, inflammatory, or sleep disorders.With the aid of homology modeling and molecular dynamics methods, the 3D model of hFAAH is constructed. The docking study is performed on the basis of propofol and its structural analogs. The results indicate the residues Phe192, Ile238, Thr377, Leu380, Phe381, Phe388 and Leu404 in hFAAH are seven important determinant residues in binding as they have strong van der Waals interactions with the inhibitors.4. Theoretical studies on the reaction mechanism catalyzed by SirtuinsSirtuins comprise a broadly conserved family of NAD+-dependent protein deacetylases and mono ADP-ribosyltransferases whose functionis crucial to the apoptosis and cell survival, transcriptional silencing, neurodegeneration and calorie restriction. As a key player in a broad variety of biological processes, sirtuins may be attractive targets for treatment of cardiovascular disease, diabetes, cancers and the aging. A thorough understanding of the catalytic mechanism of these enzymes will facilitate the development specific, mechanism-based regulators of sirtuins activity in order to treat the diseases related with these enzymes.Using molecular mechanism and quantum mechanism methods, the reaction mechanism catalyzed by Sirtuins were theoretically studied. The calculated results indicate that the fist step take places in a concerted SN2 step. The second step of the catalytic mechanism was further explored and confirmed that subsequent proton is abstracted from 2' hydroxyl of N-ribose to His116 coupled with proton transferred from 2' hydroxyl to 3' hydroxyl, which is concerted reaction. In addition, we also examine the role of Phe33 in the protein structure, and the results of the calculations confirm that the Phe33 plays an important role in the first step of catalytic mechanism, which positions above the ribose oxygen adjacent to the ribose C1' position to prevent nicotinamide exchange reaction.