PDF(Pubmed)
Abstract：
Glucagon stands out as a pivotal peptide hormone, instrumental in controlling blood glucose levels and lipid metabolism. While the formation of glucagon amyloid fibrils has been documented, their biological functions remain enigmatic. Recently, we demonstrated experimentally that glucagon amyloid fibrils can act as catalysts in several biological reactions including esterolysis, lipid hydrolysis, and dephosphorylation. Herein, we present a multiscale quantum mechanics/molecular mechanics (QM/MM) simulation of the acylation step in the esterolysis of para-nitrophenyl acetate (p-NPA), catalyzed by native glucagon amyloid fibrils, serving as a model system to elucidate their catalytic function. This step entails a concerted mechanism, involving proton transfer from serine to histidine, followed by the nucleophilic attack of the serine oxy anion on the carbonyl carbon of p-NPA. We computed the binding energy and free-energy profiles of this reaction using the protein-dipole Langevin-dipole (PDLD) within the linear response approximation (LRA) framework (PDLD/S-LRA-2000) and the empirical valence bond (EVB) methods. This included simulations of the reaction in an aqueous environment and in the fibril, enabling us to estimate the catalytic effect of the fibril. Our EVB calculations obtained a barrier of 23.4 kcal mol-1 for the enzyme-catalyzed reaction compared to the experimental value of 21.9 kcal mol-1 (and a calculated catalytic effect of 3.2 kcal mol-1 compared to the observed effect of 4.7 kcal mol-1). This close agreement together with the barrier reduction when transitioning from the reference solution reaction to the amyloid fibril provides supporting evidence to the catalytic role of glucagon amyloid fibrils. Moreover, employing the PDLD/S-LRA-2000 approach further reinforced exclusively the enzyme\'s catalytic role. The results presented in this study contribute significantly to our understanding of the catalytic role of glucagon amyloid fibrils, marking, to the best of our knowledge, the first-principles mechanistic investigation of fibrils using QM/MM methods. Therefore, our findings offer fruitful insights for future research into the mechanisms of related amyloid catalysis.
摘要：
胰高血糖素是一种关键的肽激素，有助于控制血糖水平和脂质代谢。虽然胰高血糖素淀粉样纤维的形成已被证明，它们的生物学功能仍然是神秘的。最近,我们实验证明，胰高血糖素淀粉样纤维可以作为催化剂在几个生物反应，包括酯化，脂质水解，和去磷酸化。在这里，我们提出了多尺度量子力学/分子力学（QM/MM）模拟的酰化步骤在对硝基苯基乙酸酯（p-NPA）的酯解，由天然胰高血糖素淀粉样纤维催化，作为一个模型系统来阐明它们的催化功能。这一步骤需要一个协调一致的机制，涉及从丝氨酸到组氨酸的质子转移，然后是丝氨酸氧阴离子对p-NPA羰基碳的亲核攻击。我们在线性响应近似（LRA）框架（PDLD/S-LRA-2000）和经验价键（EVB）方法中使用蛋白质-偶极Langevin-偶极（PDLD）计算了该反应的结合能和自由能曲线。这包括在水性环境和原纤维中的反应模拟，使我们能够估计原纤维的催化作用。与21.9kcalmol-1的实验值相比，我们的EVB计算获得了酶催化反应的23.4kcalmol-1的屏障（与观察到的4.7kcalmol-1相比，计算出的催化效果为3.2kcalmol-1）。从参考溶液反应过渡到淀粉样原纤维时，这种紧密的一致性以及屏障的减少为胰高血糖素淀粉样原纤维的催化作用提供了支持证据。此外，采用PDLD/S-LRA-2000方法进一步加强了酶的催化作用。这项研究的结果对我们理解胰高血糖素淀粉样纤维的催化作用有重要意义。标记,据我们所知,使用QM/MM方法对原纤维进行第一性原理机理研究。因此,我们的发现为相关淀粉样蛋白催化机制的未来研究提供了丰富的见解。
