Saponaro Andrea, Maione Vincenzo, Bonvin Alexandre M J J, Cantini Francesca
Department of Biosciences, University of Milan, Milan, Italy.
Department of Chemistry, University of Florence, Florence, Italy.
Bio Protoc. 2020 Oct 20;10(20):e3793. doi: 10.21769/BioProtoc.3793.
This protocol illustrates the modelling of a protein-peptide complex using the synergic combination of analysis and experimental results. To this end, we use the integrative modelling software HADDOCK, which possesses the powerful ability to incorporate experimental data, such as NMR Chemical Shift Perturbations and biochemical protein-peptide interaction data, as restraints to guide the docking process. Based on the modelling results, a rational mutagenesis approach is used to validate the generated models. The experimental results allow to select a final structural model best representing the protein-peptide complex. The described protocol can also be applied to model protein-protein complexes. There is no size limit for the macromolecular complexes that can be characterized by HADDOCK as long as the 3D structures of the individual components are available.
本方案阐述了利用分析与实验结果的协同组合对蛋白质 - 肽复合物进行建模的方法。为此，我们使用了整合建模软件HADDOCK，它具有强大的能力，能够将诸如核磁共振化学位移扰动和生化蛋白质 - 肽相互作用数据等实验数据作为约束条件纳入，以指导对接过程。基于建模结果，采用合理的诱变方法来验证生成的模型。实验结果有助于选择最能代表蛋白质 - 肽复合物的最终结构模型。所描述的方案也可应用于蛋白质 - 蛋白质复合物的建模。只要各个组分的三维结构可用，HADDOCK可表征的大分子复合物就没有尺寸限制。
