SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs

There is a paramount need to develop new techniques and
tools that
will extract as much information as possible from the ever growing
repository of protein 3D structures. We report here on the development
of a software tool for the multiple superimposition of large sets
of protein structural motifs. Our superimposition methodology performs
a systematic search for the atom pairing that provides the best fit.
During this search, the RMSD values for all chemically relevant pairings
are calculated by quaternion algebra. The number of evaluated pairings
is markedly decreased by using PDB annotations for atoms. This approach
guarantees that the best fit will be found and can be applied even
when sequence similarity is low or does not exist at all. We have
implemented this methodology in the Web application SiteBinder, which
is able to process up to thousands of protein structural motifs in
a very short time, and which provides an intuitive and user-friendly
interface. Our benchmarking analysis has shown the robustness, efficiency,
and versatility of our methodology and its implementation by the
successful superimposition of 1000 experimentally determined structures
for each of 32 eukaryotic linear motifs. We also demonstrate the applicability
of SiteBinder using three case studies. We first compared the structures
of 61 PA-IIL sugar binding sites containing nine different sugars,
and we found that the sugar binding sites of PA-IIL and its mutants
have a conserved structure despite their binding different sugars.
We then superimposed over 300 zinc finger central motifs and revealed
that the molecular structure in the vicinity of the Zn atom is highly
conserved. Finally, we superimposed 12 BH3 domains from pro-apoptotic
proteins. Our findings come to support the hypothesis that there is
a structural basis for the functional segregation of BH3-only proteins
into activators and enablers.

当前亟需开发新型技术与工具，以从持续增长的蛋白质三维结构库中尽可能多地提取有效信息。本文报道一款用于大规模蛋白质结构基序多重叠合的软件工具的开发工作。该叠合方法会系统性搜索能实现最优匹配的原子配对方案。在搜索过程中，通过四元数代数计算所有化学相关原子配对的均方根偏差（Root Mean Square Deviation, RMSD）值。通过为原子标注蛋白质数据库（Protein Data Bank, PDB）注释信息，可显著减少需评估的原子配对数量。该方法可确保找到最优匹配方案，且即使序列相似性较低或完全不存在序列相似性时仍可适用。我们已将该方法集成至Web应用程序SiteBinder中，该工具可在极短时间内处理多达数千个蛋白质结构基序，并提供直观友好的用户界面。通过对32种真核线性基序各1000个实验测定结构的成功叠合，我们的基准测试分析验证了该方法及其实现方案的稳健性、高效性与通用性。我们还通过三个案例研究验证了SiteBinder的适用性。首先，我们比对了包含9种不同糖类的61个PA-IIL糖结合位点的结构，发现尽管PA-IIL及其突变体结合的糖类各异，但其糖结合位点的结构具有保守性。随后，我们对超过300个锌指核心基序进行了叠合分析，发现锌原子（Zinc, Zn）周边的分子结构具有高度保守性。最后，我们对来自促凋亡蛋白的12个BH3结构域（BH3 domain）进行了叠合分析。我们的研究结果支持这一假说：仅含BH3结构域的蛋白可分为激活剂与辅助剂两类，其功能分化具有结构基础。