Features collected from each amino acid.

Polyhydroxyalkanoate (PHA) synthases are a group of complex, dimeric enzymes which catalyze polymerization of R-hydroxyacids into PHAs. PHA properties depend on their monomer composition but enzymes found in nature have limited specificities to certain R-hydroxyacids only. In this study, a conditional variational autoencoder was used for the first time to design novel PHA synthases. The model was trained with native protein sequences obtained from Uniprot and was used for the creation of approximately 10 000 new PHA synthase enzymes. Out of these, 16 sequences were selected for in vivo validation. The selection criteria included the presence of conserved residues such as catalytic amino acids and amino acids in the dimer interface and structural features like the number of -helices in the N-terminal part of the enzyme. Two of the 16 novel PHA synthases that had substantial numbers of amino acid substitutions (87 and 98) with respect to the most similar native enzymes were confirmed active and produced poly(hydroxybutyrate) (PHB) when expressed in yeast S. cerevisiae. The results show the power of AI based methods to create active variants of highly complex dimer enzymes.聚羟基脂肪酸酯（Polyhydroxyalkanoate, PHA）合酶是一类复杂的二聚体酶，能够催化R-羟基酸聚合生成PHA。PHA的性能取决于其单体组成，但天然存在的该类酶仅对特定的R-羟基酸具有有限的底物特异性。本研究首次采用条件变分自编码器（conditional variational autoencoder）设计新型PHA合酶：该模型以从UniProt获取的天然蛋白质序列进行训练，用于生成约10000条新型PHA合酶序列。从中筛选出16条序列开展体内验证，筛选标准包括保守残基的存在（如催化氨基酸、二聚体界面处的氨基酸）以及酶N端区域的α-螺旋数量等结构特征。16条新型PHA合酶中，有2条与最相似的天然酶相比存在大量氨基酸替换（替换位点分别为87和98个），经验证具有催化活性，在酿酒酵母（S. cerevisiae）中表达时可生成聚羟基丁酸酯（poly(hydroxybutyrate), PHB）。本研究结果彰显了基于人工智能的方法用于构建高度复杂二聚体酶活性变体的潜力。