Expanding the universe of functional metalloproteins through AI-assisted computational design

金属蛋白是一类含量丰富的蛋白质。它们以高效率执行地球上一些最困难和最具生命力的反应。它们作为绿色生物催化剂在能源生产和生物修复方面具有潜在的应用前景。为这些蛋白质添加新的功能或产生全新的金属蛋白是具有挑战性的。计算方法将被用于设计新的功能金属蛋白。该项目还将向高中生和本科生介绍蛋白质工程。该项目的目标是扩大功能金属蛋白的宇宙。为了解决天然蛋白质的局限性和目前传统设计方法面临的挑战，将利用机器学习的最新进展与蛋白质设计软件相结合，产生：(A)具有不同形状的功能电子转移蛋白质库，其中包含著名的2His-1Cys铜结合基序(T1Cu位)；(B)具有3His锌结合基序(水解酶活性位点)的功能催化蛋白质库；以及(C)利用非规范的BPY-Ala氨基酸进行金属配位的新平台。希望所获得的结果将对蛋白质形状对金属中心性质的调节作用以及设计新的金属蛋白质的规则提供新的见解。本文提出的方法可推广到其他金属蛋白的设计(双核、血红素结合等)。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Metalloproteins are an abundant class of proteins. They perform some of the most difficult and life-sustaining reactions on earth with high efficiency. They have potential as green biocatalysts for applications in energy production and bioremediation. Adding new functions to these proteins or generating completely novel metalloproteins is challenging. Computational methods will be used to design new functional metalloproteins. The project will also introduce high school students and undergraduates to protein engineering.The goal of this project is to expand the universe of functional metalloproteins. To address the limitations of native proteins and the current challenges facing traditional design approaches, latest advances in machine learning in combination with protein design software will be applied to generate: (a) a library of functional electron transfer proteins with diverse shapes that contain a well-known 2His-1Cys copper binding motif (T1Cu site), (b) a library of functional catalytic proteins with 3His zinc binding motifs (hydrolase active site), and (c) a new platform for metal coordination using the non-canonical bpy-ala amino acid. It is hoped that the results obtained will provide new insight into the role of protein shape on tuning properties of the metal center and the rules for designing new metalloproteins. Methods developed in this proposal can be generalized to the design of other metalloproteins (dinuclear, heme binding, etc.) and small molecule-binding proteins, largely expanding the current scope of functional protein design.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.