Mazzolari Angelica, Coppa Crescenzo, Altomare Alessandra, Degani Genny, Vistoli Giulio
Department of Biosciences, University of Milan, Via Celoria 26, I-20133 Milan, Italy.
Dept. Pharmaceutical Sciences, University of Milan, Via Mangiagalli, 25, I-20133 Milan, Italy.
Data Brief. 2017 May 6;12:656-661. doi: 10.1016/j.dib.2017.05.009. eCollection 2017 Jun.
This data article contains the results of docking simulations performed in order to develop a suitable in silico strategy able to assess the stability of the putative complexes between RAGE and MDA induced adducts on human albumin as experimentally determined doi: 10.1016/j.redox.2016.12.017, (Degani et al., 2017) [1]. The docking simulations involved different approaches to give a simplified yet realistic representation of the protein adducts and their environment. With increasing complexity, simulations involved the corresponding albumin tripeptides and pentapeptides with the modified residue in the central position as well as pseudo-structures which were generated by collecting the albumin residues around the adducted residue within a sphere of 7.5 Å and 5 Å radius. The reliability of the tested approaches was assessed by monitoring the score differences between adducted and unmodified residues. The obtained results revealed the greater predictive power of the spherical pseudo-structures compared to the simple tri- or pentapeptidic sequences thus suggesting that RAGE recognition involves residues which are spatially close to the modified residue even though not necessarily adjacent in the primary sequence.
本数据文章包含对接模拟的结果，该模拟旨在开发一种合适的计算机模拟策略，以评估RAGE与实验确定的人白蛋白上MDA诱导加合物之间假定复合物的稳定性（doi: 10.1016/j.redox.2016.12.017，(Degani等人，2017) [1]）。对接模拟采用了不同方法，以对蛋白质加合物及其环境进行简化但逼真的呈现。随着复杂度增加，模拟涉及相应的白蛋白三肽和五肽，其中修饰残基位于中心位置，以及通过收集加合残基周围半径为7.5 Å和5 Å球体内的白蛋白残基生成的伪结构。通过监测加合残基和未修饰残基之间的得分差异来评估所测试方法的可靠性。所得结果表明，与简单的三肽或五肽序列相比，球形伪结构具有更强的预测能力，这表明RAGE识别涉及在空间上靠近修饰残基的残基，即使在一级序列中不一定相邻。
