Lamothe Gilles, Malliavin Thérèse E
Unité de Bioinformatique Structurale, UMR CNRS 3528 and Institut Pasteur, Paris, France.
Université Denis Diderot Paris 7, Paris, France.
BMC Struct Biol. 2018 Apr 3;18(1):4. doi: 10.1186/s12900-018-0083-6.
Analysis of preferred binding regions of a ligand on a protein is important for detecting cryptic binding pockets and improving the ligand selectivity.
The enhanced sampling approach TAMD has been adapted to allow a ligand to unbind from its native binding site and explore the protein surface. This so-called re-TAMD procedure was then used to explore the interaction between the N terminal peptide of histone H3 and the YEATS domain. Depending on the length of the peptide, several regions of the protein surface were explored. The peptide conformations sampled during the re-TAMD correspond to peptide free diffusion around the protein surface.
The re-TAMD approach permitted to get information on the relative influence of different regions of the N terminal peptide of H3 on the interaction between H3 and YEATS.
分析配体在蛋白质上的优先结合区域对于检测隐藏的结合口袋和提高配体选择性很重要。
增强采样方法TAMD已被调整，以允许配体从其天然结合位点解离并探索蛋白质表面。然后使用这种所谓的重新TAMD程序来探索组蛋白H3的N端肽与YEATS结构域之间的相互作用。根据肽的长度，探索了蛋白质表面的几个区域。在重新TAMD过程中采样的肽构象对应于肽在蛋白质表面周围的自由扩散。
重新TAMD方法能够获得有关H3的N端肽不同区域对H3与YEATS之间相互作用的相对影响的信息。
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