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Team:Goettingen/project overview/project drylab ZH
From 2014.igem.org
Project
理化模拟实验
同源建模
我们通过同源建模模拟了含肽支架(从金黄色葡萄球菌取出的 G 蛋白的 B1 区域) 的三维结构。我们使用了Modeller Library(建模库)这个软件去完成这项工作。因为 这个多肽链是由 20~25 个氨基酸链接而成的,它可以在 B1 区域支架内成环。而这个 B1 区域的支架 3D 模型能在蛋白数据库中找到。
图释:描述了同源建模的过程。所有的多肽都在骨架(金黄色葡萄球菌提取出的 G 蛋 白的 B1 区域)内被克隆。这些肽链足够短以至于他们能够通过循环优化的方法对这些 内部环进行建模。令人遗憾的是因为我们没有直接的晶体学数据所以它们仅仅能被看做 工作模型。A detailed procedure can be found in this link.
Results summary
We obtained working structural models for our peptides inside their scaffolds. The following table is a summary of them. Please note that these models are not definitive, since they were obtained by homology modeling and loop refinement. Their main purpose is to give us an idea if the calculated energy profile matches our assumption that the peptide is being exposed to the exterior of the scaffold.
| Peptide | PNG* | PDB | Peptide location | QMEAN score | Overall DOPE score | Energy profile |
|---|---|---|---|---|---|---|
| Prey 3 |  |
Download | K17-E42 | 0.512 | -7053.966797 | Download |
| Prey 4.1 |  |
Download | K17-E44 | 0.468 | -7246.956055 | Download |
| Prey 5 |  |
Download | K17-E44 | 0.495 | -7501.071777 | Download |
| Prey 13 |  |
Download | K17-E42 | 0.535 | -7729.056152 | Download |
| Prey 15 |  |
Download | K17-E42 | 0.447 | -7671.660156 | Download |
*The peptide is shown in red and the scaffold in blue.
This is peptide IGP4 that shows interaction with ssr1 protein from Candida glabrata
References
1. N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006.
2. M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
3. A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779-815, 1993.
4. A. Fiser, R.K. Do, & A. Sali. Modeling of loops in protein structures, Protein Science 9. 1753-1773, 2000.
