Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA.
J Phys Chem B. 2009 Dec 17;113(50):16197-208. doi: 10.1021/jp903861a.
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) catalyzes the transfer of pyrophosphate from ATP to HP (6-hydroxymethyl-7,8-dihydropterin). This first reaction in the folate biosynthetic pathway is a potential target for antimicrobial agents. A Hamiltonian replica exchange method (HREM) molecular dynamics (MD) approach is used, with the goal of improving conformational sampling, whereby multiple copies of the system are run without requiring a large number of system copies. For HPPK, the aim is to improve conformational sampling around the HP binding pocket and thereby find near-closed conformations (similar but not identical to the binding pocket of HP, as defined by the ternary crystal structure). Near-closed conformations may be better targets for the design of species-selective inhibitors. Well-populated, near-closed conformations of Escherichia coli HPPK (EcHPPK) and Yersinia pestis HPPK (YpHPPK) were found with HREM by focusing on the interactions involving loops 2 and 3 that are known to be the more flexible regions of HPPK. A small number of systems were found to be sufficient to enlarge the sample space substantially, on the basis of root-mean-square fluctuation measures, relative to the results of a conventional MD simulation. By clustering snapshots on the basis of some of the key residues that form the HP binding pocket, distinct HREM-generated conformations are found. Residue displacements mainly from loop 2 are responsible for the distinct conformers found, relative to the crystal structure, for both EcHPPK and YpHPPK. In contrast, the conventional MD simulations of EcHPPK and YpHPPK each lead essentially to one cluster, with use of the same clustering criterion as for the HREM. The shapes of the HREM near-closed binding pockets are qualitatively investigated and found to be different. Some of these conformations are distinguishable between EcHPPK and YpHPPK, indicating that there may be differing species-selective, near-closed conformations suited to HP binding.
HPPK（6-羟甲基-7,8-二氢蝶呤磷酸激酶）催化焦磷酸从 ATP 转移到 HP（6-羟甲基-7,8-二氢蝶呤）。该叶酸生物合成途径中的第一个反应是抗微生物药物的潜在靶标。使用哈密顿复制交换方法（HREM）分子动力学（MD）方法，目的是改善构象采样，从而无需大量系统副本即可运行多个系统副本。对于 HPPK，目标是改善 HP 结合口袋周围的构象采样，从而找到接近闭合的构象（与 HP 的结合口袋相似但不完全相同，如三元晶体结构所定义）。接近闭合的构象可能是设计物种选择性抑制剂的更好目标。通过重点关注已知 HPPK 更灵活的环 2 和 3 的相互作用，通过 HREM 找到了大肠杆菌 HPPK（EcHPPK）和鼠疫耶尔森氏菌 HPPK（YpHPPK）的充分占据、接近闭合的构象。基于均方根波动测量值，与常规 MD 模拟的结果相比，发现少量系统就足以大大扩大样本空间。基于形成 HP 结合口袋的一些关键残基对快照进行聚类，发现了明显的 HREM 生成的构象。与晶体结构相比，相对于 EcHPPK 和 YpHPPK，残基位移主要来自环 2，导致发现明显的构象。相比之下，使用与 HREM 相同的聚类标准，对 EcHPPK 和 YpHPPK 的常规 MD 模拟都导致基本上只有一个簇。定性研究了 HREM 近闭合结合口袋的形状，发现它们不同。这些构象中的一些在 EcHPPK 和 YpHPPK 之间是可区分的，表明可能存在不同的物种选择性、适合 HP 结合的近闭合构象。
