Abstract
本文所實驗的目的，為重新設計bab以及babab之超二級蛋白結構。bab以及babab座標檔來源是由Protein Data Bank中之PDB --1HYH所截取出來的。Michael Rossmann首次發現了許多去氫□(Oxidoreductase)的NAD-binding domain 都有著相似的三維結構-babab motif，稱為Rossmann folds或是單核甘酸結合構形。其整個分子為一個對稱的四聚體(Tetramer)，我們則選取其中一單體(Monomer)的殘基，其中22-52殘基具有bab的構形而22-82則具有babab的構形。 利用分子模擬軟體InsightII的輔助，我們對選取的□□片段bab以及babab進行重新設計，在考量residue propensity的親疏水性、巨偶極效應以及鹽橋等等因素後，替換掉片段中位置不適合的殘基，以能量最小化模組進行最佳化，期使能找到獨立存在，且保留bab 以及babab等相同構形的胺基酸序列。The bab and babab template coordinates are derived fromLatate dehydrogenase of the Protein Data Bank with the search IDcode 1HYH. Michael Rossmann had first found that the NAD-binding domain of the dehydro-genase all with the same bababbinding motif. It had now to be said as Rossmann motif ormononucleotide binding motif. The 1HYH protein is tetramerwith four symmmetry monomer. We choose any one monomer anddetermine the bab and babab motif by using rasmol with thefunction of cartoon ribbon.After checking the motif location,weget the 22-52 and 22-82 residue number of the protein as bab andbabab motif coordinate .Considering about the macro dipole,helix propensity,hydrophobicity and salt bridge, we had manycombination of the bab and babab structure motif.With the helpof molecular modeling program InsightII,we can design a moststable structurethat can still keep the bab and babab motif.