Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany.
Acta Crystallogr D Struct Biol. 2021 Sep 1;77(Pt 9):1116-1126. doi: 10.1107/S2059798321007907. Epub 2021 Aug 24.
Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure using HHpred, internal repeats using HHrepID, coiled coils using PCOILS and DeepCoil, and transmembrane segments using Quick2D are focused on.
生化和生物物理实验对于揭示感兴趣的蛋白质的三维结构和生物学功能至关重要。然而，基于进化相关性，从研究充分的蛋白质向未阐明的蛋白质转移知识的生物信息学资源也可以进行有意义的预测。这些预测有助于制定具体的假设来指导湿实验室实验。常用的生物信息学资源包括识别和预测保守序列基序、蛋白质结构域、跨膜片段、信号序列以及二级和三级结构的方法。这里描述了通过 MPI 生物信息学工具包（https://toolkit.tuebingen.mpg.de）提供的几种此类方法，以及如何结合使用这些方法可以为未知功能的蛋白质提供有意义的信息。特别关注使用 HHpred 识别已知结构的同源物、使用 HHrepID 识别内部重复、使用 PCOILS 和 DeepCoil 识别卷曲螺旋以及使用 Quick2D 识别跨膜片段。
