Sarkar Aurijit, Desai Umesh R
Institute for Structural Biology, Drug Discovery & Development and Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America.
PLoS One. 2015 Oct 21;10(10):e0141127. doi: 10.1371/journal.pone.0141127. eCollection 2015.
Glycosaminoglycans (GAGs) affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS) on proteins that in turn helps predict high specific GAG-protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an unusual constellation of ionic and non-ionic residues in the binding site leads to specificity. Nature engineers the local environment of Asn45 of antithrombin, Gln255 of 3-O-sulfotransferase 3, Gln163 and Asn167 of 3-O-sulfotransferase 1 and Asn27 of basic fibroblast growth factor in the respective GBSs to induce specificity. Such residues are distinct from other uncharged residues on the same protein structure in possessing a significantly higher electrostatic potential, resultant from the local topology. In contrast, uncharged residues on nonspecific GBSs such as thrombin and serum albumin possess a diffuse spread of electrostatic potential. Our findings also contradict the paradigm that GAG-binding sites are simply a collection of contiguous Arg/Lys residues. Our work demonstrates the basis for discovering specifically interacting and druggable GAG-protein systems based on the structure of protein alone, without requiring access to any structure-function relationship data.
糖胺聚糖（GAGs）通过调节500多种蛋白质来影响人体生理和病理过程。一般认为GAG与蛋白质的相互作用是离子性且非特异性的，但特异性相互作用确实存在。在此，我们提出一种简单方法来鉴定蛋白质上的GAG结合位点（GBS），这反过来有助于预测高特异性的GAG-蛋白质系统。与当代观点相反，我们发现碱性精氨酸和赖氨酸残基处的静电势既不能始终如一地识别GBS，也无法确定其特异性。通过考虑中性氢键供体（如天冬酰胺或谷氨酰胺侧链）处的电势，能更好地识别GBS。我们的研究还表明，结合位点中离子性和非离子性残基的异常组合导致了特异性。在各自的GBS中，抗凝血酶的Asn45、3-O-磺基转移酶3的Gln255、3-O-磺基转移酶1的Gln163和Asn167以及碱性成纤维细胞生长因子的Asn27的局部环境经自然设计以诱导特异性。这些残基与同一蛋白质结构上的其他不带电残基不同，因其局部拓扑结构导致具有显著更高的静电势。相比之下,凝血酶和血清白蛋白等非特异性GBS上的不带电残基具有分散的静电势分布。我们的发现也与GBS只是相邻Arg/Lys残基集合的范式相矛盾。我们的工作证明了仅基于蛋白质结构就能发现特异性相互作用且可成药的GAG-蛋白质系统的基础，而无需获取任何结构-功能关系数据。
