Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.
Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States.
J Chem Inf Model. 2024 Jul 22;64(14):5657-5670. doi: 10.1021/acs.jcim.4c00662. Epub 2024 Jul 4.
Insulin is a clinical insulin variant where a conserved valine at the third residue on insulin's A chain (Val) is replaced with a leucine (Leu), weakening insulin receptor (IR) binding by 140-500-fold. This severe impact on binding from a subtle modification has posed an intriguing problem for decades. Although experimental investigations of natural and unnatural A3 mutations have highlighted the sensitivity of insulin-IR binding at this site, atomistic explanations of these binding trends have remained elusive. We investigate this problem computationally using λ-dynamics free energy calculations to model structural changes in response to perturbations of the Val side chain and to calculate associated relative changes in binding free energy (ΔΔ). The Leu mutation and seven other A3 substitutions were studied in this work. The calculated ΔΔ results showed high agreement compared to experimental binding potencies with a Pearson correlation of 0.88 and a mean unsigned error of 0.68 kcal/mol. Extensive structural analyses of λ-dynamics trajectories revealed that critical interactions were disrupted between insulin and the insulin receptor as a result of the A3 mutations. This investigation also quantifies the effect that adding an A3 C atom or losing an A3 C atom has on insulin's binding affinity to the IR. Thus, λ-dynamics was able to successfully model the effects of mutations to insulin's A3 side chain on its protein-protein interactions with the IR and shed new light on a decades-old mystery: the exquisite sensitivity of hormone-receptor binding to a subtle modification of an invariant insulin residue.
胰岛素是一种临床胰岛素变体,其 A 链第 3 位保守的缬氨酸(Val)被亮氨酸(Leu)取代,从而使胰岛素受体(IR)的结合力减弱 140-500 倍。这种微妙修饰对结合的严重影响几十年来一直是一个令人着迷的问题。尽管对天然和非天然 A3 突变的实验研究强调了该位点胰岛素-IR 结合的敏感性,但对这些结合趋势的原子解释仍然难以捉摸。我们使用 λ-动力学自由能计算来计算该问题,以模拟结构变化以响应对 Val 侧链的扰动,并计算相关的结合自由能变化(ΔΔ)。在这项工作中研究了 Leu 突变和其他七个 A3 取代。与实验结合势相比,计算出的ΔΔ结果具有较高的一致性,Pearson 相关系数为 0.88,平均未签名误差为 0.68 kcal/mol。对 λ-动力学轨迹的广泛结构分析表明,由于 A3 突变,胰岛素与胰岛素受体之间的关键相互作用被破坏。该研究还量化了在 A3 侧链添加一个 C 原子或失去一个 A3 C 原子对胰岛素与 IR 结合亲和力的影响。因此,λ-动力学能够成功地模拟胰岛素 A3 侧链突变对其与 IR 的蛋白质-蛋白质相互作用的影响,并为一个几十年来的谜团提供了新的线索:激素受体结合对胰岛素不变残基的微妙修饰的极高敏感性。