Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.
Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA.
J Biol Chem. 2021 Jan-Jun;296:100686. doi: 10.1016/j.jbc.2021.100686. Epub 2021 Apr 21.
Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2K. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2K recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2K-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C-H-2K interface. We propose a model whereby different peptides alter the flexibility of H-2K, which in turn changes the strength of electrostatic interactions across the protein-protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.
自然杀伤 (NK) 细胞通过消除下调 I 类主要组织相容性复合体 (MHC) 蛋白的细胞来预防疾病，例如在细胞转化或病毒感染时。抑制性小鼠 NK 受体 Ly49C 特异性识别 I 类 MHC 蛋白 H-2K。与其他 NK 受体不同，Ly49C 表现出对 H-2K 识别的肽依赖性敏感性，尽管进行了详细的结构研究，但仍未解释这种敏感性。为了更深入地了解 Ly49C 肽敏感性，我们通过生化和动态变构的角度来研究 Ly49C 的识别。我们发现，Ly49C 的肽敏感性源于 H-2K 结合亲和力的微小差异。尽管分子动力学模拟支持肽依赖性蛋白动力学在产生这些结合亲和力差异方面的作用，但量热测量表明这是一个焓驱动而不是熵驱动的过程。定量连锁分析表明，这是由于肽依赖性动态调节 Ly49C-H-2K 界面上的静电相互作用。我们提出了一个模型，即不同的肽改变 H-2K 的灵活性，进而改变蛋白质-蛋白质界面上静电相互作用的强度。我们的研究结果提供了对肽如何改变 Ly49C 结合亲和力的定量评估，提出了潜在的机制，并证明了肽驱动的变构作用在 I 类 MHC 蛋白中发挥作用。最后，我们的模型提供了解决方案，说明动态变构如何影响某些但不是所有 I 类 MHC 配体的结合，具体取决于界面的结构和化学组成。
