Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
Department of Medicine and Surgery, University of Perugia, Perugia, Italy.
Protein Sci. 2022 May;31(5):e4303. doi: 10.1002/pro.4303.
The conformational landscape of a protein is constantly expanded by genetic variations that have a minimal impact on the function(s) while causing subtle effects on protein structure. The wider the conformational space sampled by these variants, the higher the probabilities to adapt to changes in environmental conditions. However, the probability that a single mutation may result in a pathogenic phenotype also increases. Here we present a paradigmatic example of how protein evolution balances structural stability and dynamics to maximize protein adaptability and preserve protein fitness. We took advantage of known genetic variations of human alanine:glyoxylate aminotransferase (AGT1), which is present as a common major allelic form (AGT-Ma) and a minor polymorphic form (AGT-Mi) expressed in 20% of Caucasian population. By integrating crystallographic studies and molecular dynamics simulations, we show that AGT-Ma is endowed with structurally unstable (frustrated) regions, which become disordered in AGT-Mi. An in-depth biochemical characterization of variants from an anticonsensus library, encompassing the frustrated regions, correlates this plasticity to a fitness window defined by AGT-Ma and AGT-Mi. Finally, co-immunoprecipitation analysis suggests that structural frustration in AGT1 could favor additional functions related to protein-protein interactions. These results expand our understanding of protein structural evolution by establishing that naturally occurring genetic variations tip the balance between stability and frustration to maximize the ensemble of conformations falling within a well-defined fitness window, thus expanding the adaptability potential of the protein.
蛋白质的构象景观不断通过遗传变异而扩展，这些变异对功能的影响极小，而对蛋白质结构产生微妙的影响。这些变体所采样的构象空间越宽，适应环境变化的概率就越高。然而，单一突变导致致病性表型的概率也会增加。在这里，我们展示了一个典型的例子，说明蛋白质进化如何平衡结构稳定性和动力学，以最大限度地提高蛋白质的适应性并保持蛋白质的适应性。我们利用已知的人类丙氨酸：乙醛酸氨基转移酶 (AGT1) 的遗传变异，它存在于常见的主要等位形式 (AGT-Ma) 和在 20%的白种人群中表达的次要多态形式 (AGT-Mi)。通过整合晶体学研究和分子动力学模拟，我们表明 AGT-Ma 具有结构不稳定（受阻）的区域，这些区域在 AGT-Mi 中变得无序。对包含受阻区域的反共识文库变体进行深入的生化特征分析，将这种可塑性与由 AGT-Ma 和 AGT-Mi 定义的适应性窗口相关联。最后，共免疫沉淀分析表明，AGT1 中的结构受阻可能有利于与蛋白质-蛋白质相互作用相关的其他功能。这些结果通过确定自然发生的遗传变异在稳定性和受阻之间取得平衡，以最大限度地提高落在明确定义的适应性窗口内的构象组合的适应性潜力，从而扩展了蛋白质的适应性潜力，从而扩展了我们对蛋白质结构进化的理解。
