College of Physics, Jilin University , Changchun, Jilin 130012, People's Republic of China.
State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences , Changchun, Jilin 130022, People's Republic of China.
J Phys Chem B. 2018 Feb 15;122(6):1885-1897. doi: 10.1021/acs.jpcb.7b12562. Epub 2018 Feb 6.
HPPK (6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase) is a monomeric protein with 158 residues, which undergoes large-scale conformational changes between apo, open, and holo states responding to ligand binding for its function. It has been explored widely as an excellent target for potential antibacterial drug development. However, little is known about how conformational dynamics between the native states influences the substrate recognition and the functionality of enzymatic catalysis. Here, we report a coarse-grained triple-basin structure-based model upon ligand binding to describe such multiple-state system by the molecular dynamics simulation. With our model, we have made theoretical predictions that are in good agreement with the experimental measurements. Our results revealed the intrinsic conformational fluctuations between apo and open states without ligand binding. We found that HPPK can switch to the activated holo state upon the ordered binding of the two ligands (ATP and HP). We uncovered the underlying mechanism by which major induced fit and minor population shift pathways coexist upon ligand binding by quantitative flux analysis. Additionally, we pointed out the structural origin for the conformational changes and identified the key residues as well as contact interactions. We further explored the temperature effect on the conformational distributions and pathway weights. It gave strong support that higher temperatures promote population shift, while the induced fit pathway is always the predominant activation route of the HPPK system. These findings will provide significant insights of the mechanisms of the multistate conformational dynamics of HPPK upon ligand binding.
HPPK（6-羟甲基-7,8-二氢蝶呤磷酸激酶）是一种单体蛋白，由 158 个残基组成，在apo、开放和全酶状态之间发生大规模构象变化，以响应配体结合以发挥其功能。它已被广泛探索作为潜在抗菌药物开发的优秀靶标。然而，对于天然状态之间的构象动力学如何影响底物识别和酶催化功能，人们知之甚少。在这里，我们报告了一个基于配体结合的粗粒度三池结构模型，通过分子动力学模拟来描述这种多态系统。通过我们的模型，我们进行了理论预测，这些预测与实验测量结果非常吻合。我们的结果揭示了apo 和开放状态之间没有配体结合时的固有构象波动。我们发现 HPPK 可以在两个配体（ATP 和 HP）有序结合的情况下切换到激活的全酶状态。通过定量通量分析，我们揭示了配体结合时主要诱导契合和次要种群转移途径共存的潜在机制。此外，我们指出了构象变化的结构起源，并确定了关键残基和接触相互作用。我们进一步研究了温度对构象分布和途径权重的影响。这有力地支持了更高的温度促进种群转移，而诱导契合途径始终是 HPPK 系统的主要激活途径。这些发现将为 HPPK 在配体结合时的多态构象动力学的机制提供重要的见解。
