Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States.
J Phys Chem B. 2013 Aug 22;117(33):9591-7. doi: 10.1021/jp4030443. Epub 2013 Aug 8.
Transition-state analogues of bacterial 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases (MTANs) disrupt quorum-sensing pathways in Escherichia coli and Vibrio cholerae, demonstrating the potential to limit pathogenicity without placing bacteria under intense selective pressure that leads to antibiotic resistance. Despite the similarity of the crystal structures of E. coli MTAN (EcMTAN) and V. cholerae MTAN (VcMTAN) bound to DADMe-Immucillin-A transition-state (TS) analogues, EcMTAN demonstrates femtomolar affinity for BuT-DADMe-Immucillin-A (BDIA) whereas VcMTAN possesses only picomolar affinity. Protein dynamic interactions are therefore implicated in this inhibitor affinity difference. We conducted molecular dynamics simulations of both EcMTAN and VcMTAN in complex with BDIA to explore differences in protein dynamic architecture. Simulations revealed that electrostatic and hydrophobic interactions with BDIA are similar for both enzymes and thus unlikely to account for the difference in inhibitor affinity. The EcMTAN-BDIA complex reveals a greater flexibility and conformational freedom of catalytically important atoms. We propose that conserved motions related to the EcMTAN transition state correlate with the increased affinity of BDIA for EcMTAN. Transition-state analogues permitting protein motion related to formation of the transition state are better mimics of the enzymatic transition state and can bind more tightly than those immobilizing catalytic site dynamics.
细菌 5'-甲基硫代腺苷/S-腺苷同型半胱氨酸核苷酶（MTANs）的过渡态类似物可破坏大肠杆菌和霍乱弧菌的群体感应途径，这表明有可能在不使细菌承受导致抗生素耐药性的强烈选择性压力的情况下限制致病性。尽管与 DADMe-Immucillin-A 过渡态（TS）类似物结合的大肠杆菌 MTAN（EcMTAN）和霍乱弧菌 MTAN（VcMTAN）的晶体结构相似，但 EcMTAN 对 BuT-DADMe-Immucillin-A（BDIA）表现出毫微微摩尔亲和力，而 VcMTAN 仅具有微微摩尔亲和力。因此，蛋白质动态相互作用与此抑制剂亲和力差异有关。我们对与 BDIA 结合的 EcMTAN 和 VcMTAN 进行了分子动力学模拟，以探索蛋白质动态结构的差异。模拟表明，两种酶与 BDIA 的静电和疏水相互作用相似，因此不太可能解释抑制剂亲和力的差异。EcMTAN-BDIA 复合物显示出催化重要原子更大的灵活性和构象自由度。我们提出与 EcMTAN 过渡态相关的保守运动与 BDIA 对 EcMTAN 增加的亲和力相关。允许与形成过渡态相关的蛋白质运动的过渡态类似物更好地模拟酶过渡态，并且可以比固定催化位点动力学的类似物更紧密地结合。
