AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants,Journal of Chemical Information and Modeling

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AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2024-09-03 , DOI: 10.1021/acs.jcim.4c01388
Reyes Núñez-Franco ₁ , M Milagros Muriel-Olaya ₁ , Gonzalo Jiménez-Osés _{1,

2} , Francesca Peccati _{1,

2}

Affiliation

Artificial intelligence-based protein structure prediction methods such as AlphaFold2 have emerged as powerful tools for characterizing proteins sequence-structure relationship offering unprecedented opportunities for the molecular interpretation of biological and biochemical phenomena. While initially confined to providing a static representation of proteins through their global free-energy minimum, AlphaFold2 has demonstrated the ability to partially sample conformational landscapes, providing insights into protein dynamics, which is fundamental for interpreting and potentially tuning the function of natural and artificial proteins. In this study, we show that targeted column masking of AlphaFold2’s multiple sequence alignment enables the characterization and estimation of the population ratio of the two main conformations of engineered green fluorescent proteins with alternative β-strands. The possibility of quickly estimating relative populations through AlphaFold2 predictions is expected to speed-up the computational design of related systems for sensing applications.

中文翻译：

AlphaFold2 预测绿色荧光蛋白变体中的替代构象群

基于人工智能的蛋白质结构预测方法（例如 AlphaFold2）已成为表征蛋白质序列结构关系的强大工具，为生物和生化现象的分子解释提供了前所未有的机会。虽然最初仅限于通过其全局自由能最小值提供蛋白质的静态表示，但 AlphaFold2 已经证明了对构象景观进行部分采样的能力，提供了对蛋白质动力学的见解，这对于解释和潜在调整天然和人造蛋白质的功能至关重要。在这项研究中，我们表明，AlphaFold2 的多序列比对的目标列掩蔽能够表征和估计具有替代 β 链的工程绿色荧光蛋白的两种主要构象的群体比率。通过 AlphaFold2 预测快速估计相对种群的可能性有望加快传感应用相关系统的计算设计。

更新日期：2024-09-03

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