| The complex structure of protein and its ligand is important for clarifying the function and action mechanisms of protein and useful for drug design. Today, X-ray Diffraction, NMR, Two-Dimensionalal Electron Diffraction or Three-Dimensionalal Image Restructure techniques have been the most valuable tools for elucidating structure-function relationships of biological molecules. Although the application of these experimental methods is continually growing, they remain time-consuming and limited applicability due to difficulties of accurate experimental data. Molecular modeling not only can overcome the limiting of experimental tools effectively, but also can guide the experiment. Molecular modeling is widely applied in scientific research, its significance and advantage were acknowledged. Using Molecular Figure and Computational Chemistry, molecular modeling can build up, bring forth and analyze molecular structure, computing its characters. Using molecular modeling methods to study the interaction between small drug molecules and their target proteins can afford theoretical guide for drug design or structure modification of protein. Through contrasting the space structures of similar proteins, people find that the three-dimensional structures of proteins are more conservative than the sequences. If the amino acid sequences have 50% homology, the errors of 90% of Cα atoms will be no more than 0.3nm and the errors of share root also will be less than 0.1nm. The changes of amino acid residues often occur at two-double areas of protein surfaces or the protein main chains. The structure of de- hydrophilic core is unchanged under the aberrant sequences. The methods of Homology modeling not only can rapidly and accurately confirm the three-dimensional structure of amino acid sequence, but also do not fussily cultivate the single crystal. Therefore, it can be reliable to forecast the structure of target protein through the structure of similar protein. In mammals there are at least three isoforms of the glycolytic enzyme enolase encoded by three similar genes: α,β and γ. They are the different functional role of multiple enzyme isoforms and have different regulatory mechanisms for developmental and tissue expression. Three distant isoforms of the enzyme, referred to as α or non-neuronal enolase, β or muscle-specific enolase and γ or neuron-specific enolase are present in both avian and mammalian tissues. While the γ isoform is mainly detected in cell of nenuronal origin and the β isoform is found in adult skeletal muscle, the α isoform is widely distributed among different tissues and is the major form of enolase present in the early stage of embryonic development.Although the isoenzymes have been studied for many years and a substantial body of information on their biochemical, kinetic, and immunological properties has been detected, the α isoform still only has its amino acid sequence and has not its three-dimensional structure. It is unknown for us about the mechanism of the α isoform and its ligand. In this thesis, we use the new molecular modeling technology to study the α isoform. The main results of the thesis are as follows:⑴ By means of Homology modeling module in Insight II programs, we construct reliable three-dimensional structure of the α isoform. We blast high homology sequences in NCBI, and construct enolase by the crystallograms in PDB. Under CVFF force field, we optimize the full molecule by means of steepest descent and conjugate gradient. Through molecular mechanism and molecular dynamics simulation, we perfectly model the enolase's three- dimensional structure. There are sixteen of helices, thirteen of sheets, and nineteen of anormal turns in enolase. ⑵ By means of Affinity, we dock PGA to ENOLASE, then using flexible docking method gain the reasonable complex structure. The complexes structure of PGA-ENOLASE and interaction between PGA and ENOLASE show that it is mainly by the Van der Waals interaction. Hydrogen bonds are also the main forces between PGA... |
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