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Characterization of protein interaction surface on fatty acyl selectivity of starter condensation domain in lipopeptide biosynthesis

  • Wenjie Fan
  • Hao Liu
  • Panpan Liu
  • Xi Deng
  • Haifeng Chen
  • Qian LiuEmail author
  • Yan FengEmail author
Biotechnologically relevant enzymes and proteins

Abstract

Lipopeptides are important non-ribosomal peptide synthetases (NRPSs) products with broad therapeutic potential in biotechnology and biopharmaceutical applications. Fatty acyl modifications in N-terminal of lipopeptides have attracted wide interest in the engineering processes of altered fatty acyl selectivity. In this study, we focused on the starter condensation domain of antibiotic A54145 (lptC1) and its indiscriminate selectivity of fatty acyl substrates, which results in multi-component products. Using in silico analysis, five site-directed mutations at protein–protein interface were identified with altered activity and selectivity towards wild type lptC1. The variants Y149W and A330T exhibited changed substrate selectivity to prefer longer branched chain fatty acyl substrate, while T16A and A350D showed improved selectivity for shorter linear chain fatty acyl substrates. Subsequently, molecular dynamics (MD) simulations were performed to analyze the impact of these residues on the changes of catalytic activity and conformation. Through in silico analysis, the altered binding free energy were coincident with the corresponding activity performance of the variants, and surface forces indicated that other factors or processes may influence the activity and selectivity. Moreover, the MD results revealed even altered active center conformations, implying the importance of these interface residues affected on distant active center thus reflected to catalysis activity. Based on the biochemistry and computational results, our work provides detailed insights from molecular and dynamics aspects into the role of C1’s interface residues during complex NRPS biosynthesis machinery, prompting further rational engineering for lipopeptide catalysis.

Keywords

Nonribosomal peptide synthetase Condensation domain Protein–protein interaction Fatty acyl selectivity Lipopeptide biosynthesis Protein engineering 

Notes

Funding information

This work was financially supported by the Ministry of Science and Technology of China (2017YFE0103300), Natural Science Foundation of China (31600637) and National Key R&D Program of China (2018YFA0900400).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical statement

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

253_2019_10251_MOESM1_ESM.pdf (1.5 mb)
ESM 1 (PDF 1.45 mb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiChina

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