Domain-wise dissection of thermal stability enhancement in multidomain proteins

Jisung Oh; Prasannavenkatesh Durai; Priyadharshini Kannan; Jaehui Park; Young Joo Yeon; Won-Kyu Lee; Keunwan Park; Moon-Hyeong Seo

doi:10.1016/j.ijbiomac.2023.124141

Domain-wise dissection of thermal stability enhancement in multidomain proteins

Int J Biol Macromol. 2023 May 15:237:124141. doi: 10.1016/j.ijbiomac.2023.124141. Epub 2023 Mar 21.

Authors

Jisung Oh¹, Prasannavenkatesh Durai², Priyadharshini Kannan³, Jaehui Park⁴, Young Joo Yeon⁵, Won-Kyu Lee⁶, Keunwan Park⁷, Moon-Hyeong Seo⁸

Affiliations

¹ Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea.
² Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea.
³ Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea.
⁴ College of Pharmacy, Chungbuk National University, Chungbuk 28160, South Korea.
⁵ Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung 25457, South Korea.
⁶ New Drug Development Center, Osong Medical Innovation Foundation, Chungbuk 28160, South Korea.
⁷ Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju 29493, South Korea. Electronic address: keunwan@kist.re.kr.
⁸ Natural Product Research Center, Korea Institute of Science and Technology, Gangneung 25451, South Korea; Department of Convergence Medicine, Yonsei University Wonju College of Medicine, Wonju 26426, South Korea. Electronic address: mhseo@kist.re.kr.

PMID: 36958447
DOI: 10.1016/j.ijbiomac.2023.124141

Abstract

Stability is critical for the proper functioning of all proteins. Optimization of protein thermostability is a key step in the development of industrial enzymes and biologics. Herein, we demonstrate that multidomain proteins can be stabilized significantly using domain-based engineering followed by the recombination of the optimized domains. Domain-level analysis of designed protein variants with similar structures but different thermal profiles showed that the independent enhancement of the thermostability of a constituent domain improves the overall stability of the whole multidomain protein. The crystal structure and AlphaFold-predicted model of the designed proteins via domain-recombination provided a molecular explanation for domain-based stepwise stabilization. Our study suggests that domain-based modular engineering can minimize the sequence space for calculations in computational design and experimental errors, thereby offering useful guidance for multidomain protein engineering.

Keywords: Glutamine-binding protein; Hydroxyacyl-coenzyme A dehydrogenase; Melting temperature; Protein engineering; Protein thermal stability; Tyrosine-protein kinase SYK.

MeSH terms

Enzyme Stability
Mutant Proteins / chemistry
Proteins* / chemistry

Substances

Proteins
Mutant Proteins