Design of cyborg proteins by loop region replacement with oligo(ethylene glycol): exploring suitable mutations for cyborg protein construction using machine learning

被引：3

作者：

Yospanya, Wijak ^{[1
]}

Matsumura, Akari ^{[2
]}

Imasato, Yukihiro ^{[1
]}

Itou, Tomoyuki ^{[3
]}

Aoki, Yusuke ^{[1
]}

Nakazawa, Hikaru ^{[3
]}

Matsui, Takashi ^{[2
]}

Yokoyama, Takeshi ^{[2
]}

Ui, Mihoko ^{[4
]}

Umetsu, Mitsuo ^{[3
]}

Nagatoishi, Satoru ^{[5
,6
]}

Tsumoto, Kouhei ^{[5
,6
,7
]}

Tanaka, Yoshikazu ^{[2
]}

Kinbara, Kazushi ^{[1
,8
]}

机构：

[1] Tokyo Inst Technol, Sch Life Sci & Technol, 4259 B58 Nagatsuta Cho,Midori Ku, Yokohama 2268501, Japan

[2] Tohoku Univ, Grad Sch Life Sci, 2-1-1 Katahira,Aoba Ku, Sendai, Miyagi 9808577, Japan

[3] Tohoku Univ, Grad Sch Engn, Dept Biomol Engn, Aoba Ku, Sendai 9808579, Japan

[4] Tohoku Univ, Inst Multidisciplinary Res Adv Mat, 2-1-1 Katahira,Aoba Ku, Sendai, Miyagi 9808577, Japan

[5] Univ Tokyo, Med Device Dev & Regulat Res Ctr, Sch Engn, 7-3-1 Hongo,Bunkyo Ku, Tokyo 1138654, Japan

[6] Univ Tokyo, Sch Engn, Dept Bioengn, 7-3-1 Hongo,Bunkyo Ku, Tokyo 1138654, Japan

[7] Univ Tokyo, Sch Engn, Dept Chem & Biotechnol, 7-3-1 Hongo,Bunkyo Ku, Tokyo 1138654, Japan

[8] Tokyo Inst Technol, Inst Innovat Res, Res Ctr Autonomous Syst Mat ASMat, 4259 Nagatsuta Cho,Midori Ku, Yokohama, Kanagawa 2268501, Japan

来源：

BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN | 2024年 / 97卷 / 09期

关键词：

machine learning; oligo(ethylene glycol); peptide backbone engineering; SITE-SPECIFIC INCORPORATION; AMINO-ACID; DIRECTED EVOLUTION; PEPTIDE; DESCRIPTORS; INFORMATION; CHEMISTRY; SELECTION; LENGTH; SCALE;

D O I：

10.1093/bulcsj/uoae090

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We synthesized a "cyborg protein," wherein a synthetic molecule partially substitutes the main peptide chain by linking 2 protein domains with a synthetic oligomer. Green fluorescent protein (GFP) served as the model for constructing the cyborg proteins. We prepared circularly permuted GFP (cpGFP) with new termini between beta 10 and beta 11, where the original N- and C-termini were linked by a cleavable peptide loop. The cyborg GFP was constructed from cpGFP by linking the beta 10 and beta 11 with oligo(ethylene glycol) (OEG) using maleimide-cysteine couplings, followed by the enzymatic cleavage of the N- and C-termini linking loop by thrombin. With the help of machine learning, we were able to obtain the cpGFP mutants that significantly alter the fluorescence intensity (53% increase) by thrombin treatment, which splits cpGFP into 2 fragments (fragmented GFP), and by heat shock. When the cyborg GFP was constructed using this mutant, the fluorescence intensity increased by 13% after heat treatment, similar to cpGFP (33% increase), and the behavior was significantly different from that of the fragmented GFP. This result suggests the possibility that the OEG chain in the cyborg protein plays a similar role to the peptide in the main chain of the protein. Graphical Abstract We synthesized a "cyborg protein" by replacing peptide at the loop region of GFP with oligo(ethylene glycol). The suitable cpGFP was obtained by machine learning, and the cyborg GFP was synthesized. The cyborg GFP has similar fluorescence characteristics as cpGFP, indicating the possibility of constructing cyborg proteins having oligo(ethylene glycol) resembling the functions of a peptide loop.

引用

页数：8