Protein Conformational Dynamics Underlie Selective Recognition of Thermophilic over Mesophilic Enzyme I by a Substrate Analogue.
Protein Conformational Dynamics Underlie Selective Recognition of Thermophilic over Mesophilic Enzyme I by a Substrate Analogue.
复制标题
DOI：
10.3390/biom13010160
复制
发表时间：
2023-01-12
期刊：
影响因子：
5.5
通讯作者：
中科院分区：
文献类型：
--
作者：
底物选择性是一个重要的预防措施，以减少酶和代谢产物之间的交叉相互作用的可能性，共享结构相似性。此外，了解确定对特定底物的选择性的机制增加了设计靶酶特异性抑制剂的知识基础。在这里，我们结合联合收割机NMR，分子动力学（MD）模拟，和蛋白质工程研究如何两个底物类似物，烯丙基膦酸酯（cPEP）和磺基烯醇丙酮酸（SEP），识别嗜温（eEIC）和嗜热（tEIC）的同源物的受体结构域的细菌酶I，这已被提出作为抗菌研究的目标。化学位移扰动（CSP）实验表明，cPEP和SEP识别tEIC超过嗜温同系物。半微秒长的MD模拟的组合主成分分析表明，eEIC-配体复合物中的呼吸运动的不完全淬灭使相互作用不稳定，并使所研究的底物类似物对嗜热酶具有选择性。我们的研究结果表明，残余蛋白运动时，需要仔细考虑优化EI的小分子抑制剂。在一般情况下，我们的工作表明，蛋白质构象动力学可以利用在合理的设计和优化抑制剂与亚家族的选择性。
Substrate selectivity is an important preventive measure to decrease the possibility of cross interactions between enzymes and metabolites that share structural similarities. In addition, understanding the mechanisms that determine selectivity towards a particular substrate increases the knowledge base for designing specific inhibitors for target enzymes. Here, we combine NMR, molecular dynamics (MD) simulations, and protein engineering to investigate how two substrate analogues, allylicphosphonate (cPEP) and sulfoenolpyruvate (SEP), recognize the mesophilic (eEIC) and thermophilic (tEIC) homologues of the receptor domain of bacterial Enzyme I, which has been proposed as a target for antimicrobial research. Chemical Shift Perturbation (CSP) experiments show that cPEP and SEP recognize tEIC over the mesophilic homologue. Combined Principal Component Analysis of half-microsecond-long MD simulations reveals that incomplete quenching of a breathing motion in the eEIC–ligand complex destabilizes the interaction and makes the investigated substrate analogues selective toward the thermophilic enzyme. Our results indicate that residual protein motions need to be considered carefully when optimizing small molecule inhibitors of EI. In general, our work demonstrates that protein conformational dynamics can be exploited in the rational design and optimization of inhibitors with subfamily selectivity.
登录
查看更多内容
影响因子：
14.8
作者：
Doucette, Christopher D.;Schwab, David J.;Wingreen, Ned S.;Rabinowitz, Joshua D.
通讯作者：
Rabinowitz, Joshua D.
影响因子：
6.4
作者：
Meza E;Becker J;Bolivar F;Gosset G;Wittmann C
通讯作者：
Wittmann C
影响因子：
2.7
作者：
LIU, DC;NOCEDAL, J
通讯作者：
NOCEDAL, J
影响因子：
2.9
作者：
Nguyen, Trang T.;Venditti, Vincenzo
通讯作者：
Venditti, Vincenzo
影响因子：
0.9
作者：
Dotas, Rochelle Rea;Venditti, Vincenzo
通讯作者：
Venditti, Vincenzo