研究提出 keep-score 框架：谷氨酰胺可在蛋白组尺度被替换而保持折叠
Folding without glutamine: Proteome-scale removal of a canonical amino acid
作者提出 keep-score 计算框架，用 ProteinMPNN 结构概率与多序列比对保守性两种独立方法评估氨基酸的结构可替换性，结果两种方法都指向谷氨酰胺得分最低，脯氨酸和甘氨酸最高。研究将 4,148 个蛋白中的全部谷氨酰胺替换为 ProteinMPNN 给出的最优替代，并用 AlphaFold2 建模，85.5% 的模型 TMscore 超过 0.8，与重建天然序列 85.9% 的基线相当；ESMFold 预测、Rosetta 能量计算和构象系综比较也未发现系统性错误折叠。
来源：PLOS Computational Biology · journals.plos.org
by Alejandro Garciarrubio, Blanca Ramos-Cerrillo, Enrique Morett, Lorenzo Segovia
All known life uses a canonical alphabet of 20 amino acids, yet which residues are structurally essential remains untested at proteome scale. Isoleucine was recently eliminated from ribosomal proteins in Escherichia coli, establishing that amino acid alphabet reduction is feasible. Here we ask whether an entire amino acid can be eliminated from a proteome, and develop a computational framework to identify the best target. Using two independent approaches — ProteinMPNN structure-based probabilities and multiple sequence alignment conservation — we define “keep-score” as the fraction of positions where the native residue is optimal. Both methods converge on an unexpected candidate: glutamine has the lowest keep-score, with proline and glycine the highest — counter to substitution-matrix intuition. Glutamine’s low keep-score is not explained by a single obvious substitute; glutamate is preferred in only 14% of replacements. Removing this target proteome-wide, we replaced every glutamine across 4,148 proteins with ProteinMPNN-optimal alternatives and modeled the resulting sequences with AlphaFold2. The recoded proteome maintained native-like structures: 85.5% of models exceeded a TMscore of 0.8, indistinguishable from the 85.9% baseline for rebuilt native sequences. Orthogonal validation — ESMFold predictions, Rosetta energy calculations, and conformational ensemble comparisons — revealed no evidence of systematic misfolding attributable to glutamine removal. As a consistency check, a glutamine-free TEM-1 β-lactamase designed with ProteinMPNN conferred ampicillin resistance in E. coli, indicating fold preservation can extend to biological function. Evolutionary evidence further supports these findings: 24% of E. coli proteins have glutamine-free orthologs in prokaryotic genomes, and glutamine ranks lowest in keep-score in Saccharomyces cerevisiae. These results show that an entire amino acid can be removed from a proteome with folds broadly preserved, establishing keep-score as a general framework and glutamine as the primary candidate for recoding. Crucially, this reflects a computational analysis of structural replaceability, not a demonstration of biological dispensability.