Bogacheva E N, Gol'danskii V I, Shishkov A V, Galkin A V, Baratova L A
Semenov Institute of Chemical Physics, Russian Academy of Sciences, Moscow, 117977, Russia.
Proc Natl Acad Sci U S A. 1998 Mar 17;95(6):2790-4. doi: 10.1073/pnas.95.6.2790.
The method of tritium planigraphy, which provides comprehensive information on the accessible surface of macromolecules, allows an attempt at reconstructing the three-dimensional structure of a protein from the experimental data on residue accessibility for labeling. The semiempirical algorithm proposed for globular proteins involves (i) predicting theoretically the secondary structure elements (SSEs), (ii) experimentally determining the residue-accessibility profile by bombarding the whole protein with a beam of hot tritium atoms, (iii) generating the residue-accessibility profiles for isolated SSEs by computer simulation, (iv) locating the contacts between SSEs by collating the experimental and simulated accessibility profiles, and (v) assembling the SSEs into a compact model via these contact regions in accordance with certain rules. For sperm whale myoglobin, carp and pike parvalbumins, the lambda cro repressor, and hen egg lysozyme, this algorithm yields the most realistic models when SSEs are assembled sequentially from the amino to the carboxyl end of the protein chain.
氚平面成像方法能够提供关于大分子可及表面的全面信息，从而可以尝试根据标记残基可及性的实验数据重建蛋白质的三维结构。针对球状蛋白质提出的半经验算法包括：（i）从理论上预测二级结构元件（SSE）；（ii）通过用热氚原子束轰击整个蛋白质，实验确定残基可及性图谱；（iii）通过计算机模拟生成孤立SSE的残基可及性图谱；（iv）通过对比实验和模拟的可及性图谱来确定SSE之间的接触点；（v）根据特定规则，通过这些接触区域将SSE组装成一个紧凑模型。对于抹香鲸肌红蛋白、鲤鱼和梭子鱼小清蛋白、λ噬菌体cro阻遏蛋白以及鸡蛋清溶菌酶而言，当从蛋白质链的氨基端到羧基端依次组装SSE时，该算法能得出最逼真的模型。
