Residue-specific contributions to the energetics of the catalytic cycle of PGK

生物分子通过多个弱键相互作用，这决定了相互作用的特异性和亲和力。人们会期望这种相互作用的总强度等于孤立的所有弱键的总和。然而，事实并非如此，交互作用往往比预期的更弱或更强（称为协作性）。这通常与分子的功能相对应。大多数功能性生物分子是蛋白质，由DNA编码的大分子。与稀有营养物质（生物素或铁）或高度不稳定结构（化学反应的速率决定中间体）结合的蛋白质比预期的更紧密，而其他蛋白质结合并释放大量分子的速度更快（例如生化反应的反应物和产物，如葡萄糖或乳酸），但仍然必须特异性结合。这在酶中表现得最为明显，酶通过结合化学反应的速率决定中间体（过渡态）来加速生化反应。它们还必须与反应的反应物和产物结合，这在化学上与过渡态非常相似，但它们的结合要弱得多。本研究的重点是酶如何在其反应周期中结合这两种结合模式，以及它们如何利用其固有的灵活性来实现这一目标。我们希望测试结构性紧缩是否提供了实现这种区别的机制。核磁共振可以测量大分子中单个原子的性质，但是可以研究的分子的大小是有限制的。随着时间的推移，随着技术的进步，这种尺寸限制也在增加，现在可以研究像磷酸甘油酸激酶（PGK）这样的大型酶。这个项目将使用这种技术来确定这种酶内不同原子对它催化的反应的过渡态结合的贡献，使用类似于它的稳定化学物质（称为过渡态类似物）。该结论应广泛适用于其他酶。了解这一过程对于设计用作治疗剂（药物）的酶抑制剂以及在生物环境之外使用酶的技术（例如生物修复）至关重要。这也将有助于从理论上理解重要的生物分子是如何工作的。

Biological molecules interact through multiple weak bonds, which define the specificity and the affinity of the interaction. One would expect that the total strength of this interaction would equal the sum of all the contributing weak bonds in isolation. However this is not the case, and interactions are often much weaker or stronger than expected (known as cooperativity). This often corresponds with the function of the molecules. The majority of functional biological molecules are proteins, the large macromolecules that are encoded by DNA. Proteins that bind to rare nutrients (biotin or iron) or highly unstable structures (rate-defining intermediates of chemical reactions) bind more tightly than expected, whereas other proteins bind and release abundant molecules quickly (for example the reactants and products of biochemical reactions, like glucose or lactate), but must still bind specifically. This is most striking in enzymes, which speed up biochemical reactions by binding to rate-defining intermediates of chemical reactions (transition states). They must also bind to the reactants and products of the reactions, which are very similar in chemistry to the transition state, but must be bound much more weakly. The focus of this study is how enzymes combine these two modes of binding in their reaction cycles, and how they use their intrinsic flexibility to do so. We wish to test whether structural tightening provides a mechanism of achieving this discrimination. NMR allows the measurement of the properties of individual atoms within large molecules, but there is a size limit to the size of molecules that can be studied. Over time this size limit is increasing as technology improves and is now at a stage where large enzymes like phosphoglycerate kinase (PGK) can be studied. This project will use this technology to determine the contributions that different atoms within this enzyme make to the binding of the transition state of the reaction it catalyses, using stable chemicals that resemble it (called transition state analogues). The conclusions should be broadly applicable to other enzymes. An understanding of this process is vital to the design inhibitors of enzymes for use as therapeutic agents (drugs) and to technologies that use enzymes out of their biological context, for example bioremediation. It will also help the theoretical understanding of how important biological molecules work.