Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction.
Thermodynamic analysis of an entropically driven, high-affinity nanobody-HIV p24 interaction.
复制标题
DOI：
10.1016/j.bpj.2022.12.019
复制
发表时间：
2023-01-17
影响因子：
3.4
通讯作者：
McKendry, Rachel A.
中科院分区：
文献类型：
--
作者：
Brookes, Jennifer C.;Gray, Eleanor R.;Loynachan, Colleen N.;Gut, Michelle J.;Miller, Benjamin S.;Brogan, Alex P. S.;McKendry, Rachel A.
蛋白质-蛋白质相互作用是生命过程的基础。对这些相互作用的补充计算、结构和生物物理研究使人们能够理解它们的特异性和强度背后的力量。单链抗体等抗体片段具有完整抗体的特异性和亲和力，但其大小仅为其一小部分，可加快整个分子研究和远端效应，而不会超出建模系统的计算能力。我们之前报道了与 HIV-1 衣壳蛋白 p24 结合的高亲和力纳米抗体 59H10 的晶体结构，并使用全原子分子动力学模拟推导出了关键的相互作用。我们研究了密切相关的中亲和力 (37E7) 和低亲和力纳米抗体 (48G11) 的特性，以了解三个 (37E7) 或一个 (48G11) 氨基酸的变化如何影响这些相互作用；然而，焓和熵的贡献并未量化。在这里，我们报告使用定性和定量实验以及计算机方法来分离熵和熵的贡献。我们使用互补圆二色光谱和分子动力学模拟来定性描述分离的纳米抗体和与 p24 复合的纳米抗体之间的变化。使用等温滴定量热法等定量技术以及 WaterMap 和自由能扰动方案，我们发现高 (59H10) 和中 (37E7) 亲和力纳米抗体与 HIV-1 p24 结合的差异是熵驱动的，这是由 59H10 疏水表面释放不稳定的水造成的。我们的结果提供了并行体外和计算机研究实用性的范例，并强调氨基酸和水分子之间熵相互作用的差异足以驱动亲和力的数量级差异。
Protein-protein interactions are fundamental to life processes. Complementary computational, structural, and biophysical studies of these interactions enable the forces behind their specificity and strength to be understood. Antibody fragments such as single-chain antibodies have the specificity and affinity of full antibodies but a fraction of their size, expediting whole molecule studies and distal effects without exceeding the computational capacity of modeling systems. We previously reported the crystal structure of a high-affinity nanobody 59H10 bound to HIV-1 capsid protein p24 and deduced key interactions using all-atom molecular dynamics simulations. We studied the properties of closely related medium (37E7) and low (48G11) affinity nanobodies, to understand how changes of three (37E7) or one (48G11) amino acids impacted these interactions; however, the contributions of enthalpy and entropy were not quantified. Here, we report the use of qualitative and quantitative experimental and in silico approaches to separate the contributions of enthalpy and entropy. We used complementary circular dichroism spectroscopy and molecular dynamics simulations to qualitatively delineate changes between nanobodies in isolation and complexed with p24. Using quantitative techniques such as isothermal titration calorimetry alongside WaterMap and Free Energy Perturbation protocols, we found the difference between high (59H10) and medium (37E7) affinity nanobodies on binding to HIV-1 p24 is entropically driven, accounted for by the release of unstable waters from the hydrophobic surface of 59H10. Our results provide an exemplar of the utility of parallel in vitro and in silico studies and highlight that differences in entropic interactions between amino acids and water molecules are sufficient to drive orders of magnitude differences in affinity.
登录
查看更多内容
影响因子：
15
作者：
Abel, Robert;Young, Tom;Friesner, Richard A.
通讯作者：
Friesner, Richard A.
影响因子：
5.3
作者：
Gray, Eleanor R.;Brookes, Jennifer C.;McKendry, Rachel A.
通讯作者：
McKendry, Rachel A.
影响因子：
2.8
作者：
Berisio R;Vitagliano L
通讯作者：
Vitagliano L
影响因子：
1.5
作者：
Gorlani, Andrea;Brouwers, Joachim;Verrips, Theo
通讯作者：
Verrips, Theo
DOI：
10.1016/j.str.2021.01.005
发表时间：
2021-06-03
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Guest JD;Vreven T;Zhou J;Moal I;Jeliazkov JR;Gray JJ;Weng Z;Pierce BG
通讯作者：
Pierce BG