Gromiha M Michael, Veluraja K, Fukui Kazuhiko
Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
Protein Pept Lett. 2014;21(8):799-807. doi: 10.2174/09298665113209990055.
Protein-carbohydrate interactions play important roles in several biological processes in living organisms. Understanding the recognition mechanism of protein-carbohydrate complexes is a challenging task in molecular and computational biology. In this work, we have developed an energy based approach for identifying the binding sites and important residues for binding in protein-carbohydrate complexes. Our method identified 3.3% of residues as binding sites in protein- carbohydrate complexes whereas the binding site residues in protein-protein, protein-RNA and protein-DNA complexes are 10.8%, 7.6% and 8.7%, respectively. In all these complexes, binding site residues are accommodated in singleresidue segments so that the neighboring residues are not involved in binding. Binding propensity analysis indicates the dominance of Trp to interact with carbohydrates through aromatic-aromatic interactions. Further, the preference of residue pairs and tripeptides interacting with carbohydrates has been delineated. The information gained in the present study will be beneficial for understanding the recognition mechanism of protein-carbohydrate complexes and for predicting the binding sites in carbohydrate binding proteins.
蛋白质 - 碳水化合物相互作用在生物体的多个生物学过程中发挥着重要作用。理解蛋白质 - 碳水化合物复合物的识别机制是分子生物学和计算生物学中的一项具有挑战性的任务。在这项工作中，我们开发了一种基于能量的方法来识别蛋白质 - 碳水化合物复合物中的结合位点和结合的重要残基。我们的方法将蛋白质 - 碳水化合物复合物中3.3%的残基识别为结合位点，而蛋白质 - 蛋白质、蛋白质 - RNA和蛋白质 - DNA复合物中的结合位点残基分别为10.8%、7.6%和8.7%。在所有这些复合物中，结合位点残基位于单残基片段中，因此相邻残基不参与结合。结合倾向分析表明色氨酸通过芳香 - 芳香相互作用与碳水化合物相互作用占主导地位。此外，还描绘了与碳水化合物相互作用的残基对和三肽的偏好。本研究中获得的信息将有助于理解蛋白质 - 碳水化合物复合物的识别机制，并有助于预测碳水化合物结合蛋白中的结合位点。
