Understanding cellular house-keeping of proteins by extrapolation of the reaction mechanism displayed by manganese-dependent enzymes on protein biosynthetic machineries

SNIC 2019/3-10


SNIC Medium Compute

Principal Investigator:

Per-Olof Syrén


Kungliga Tekniska högskolan

Start Date:


End Date:


Primary Classification:

10602: Biochemistry and Molecular Biology

Secondary Classification:

10407: Theoretical Chemistry

Tertiary Classification:

10604: Cell Biology



This project is funded by VR, SSF and FORMAS through a 2017 Future Research Leader grant. Published papers using PDC SNIC 2018/3-59: 2 (2 journal covers, one publication in impact factor ~ 5). Manuscripts under preparation: 1 This present investigation is centered on deciphering the fundamental biochemical reaction mechanisms that underpin cellular house-keeping of proteins. Enhancing our uncomplete understanding of protein turnover is a highly relevant research area, as protein synthesis and degradation are indispensable for life. The proposed project utilizes quantum mechanical calculations to explore the chemistry that governs protein synthesis and proteases/amidases. The crucial importance of proteases for homeostasis is illustrated by the fact that many genetic diseases are closely associated with proteolytic activity. Moreover cascades of proteases are key factors for cancer and tumor progression and Alzeimer’s disease. Tertiary amide bonds are of significant interest, as these functional units are introduced in proteins and peptides throughout all kingdoms of life to mediate protein stability and bioactivity. Many drugs and natural products containing prolines - or other tertiary reacting nitrogen atoms – display potent bioactivities and are key players in cell signaling. One important example is the blood-pressure-controlling peptide bradykinin. The assembly of the HIV-virus requires the hydrolysis of a tertiary amide bond. Hence, a detailed understanding of the reaction mechanism by which these peptides are metabolized and assembled would be of high interest in medicine as well as in industrial biotechnology. Great progress was made in 2018/3-59, as we unraveled how tertiary amide bonds are hydrolyzed in the cell by prolidase enzymes. It was shown for the first time, how these bi-metal proteases dissect tertiary amide bonds by a unique anti nucleophilic attack and protonation. The prevalence of our suggested reaction mechanism in nature, and its importance during protein synthesis remain unknown. To overcome this hurdle, this project uses state of the art quantum mechanical calculations to elucidate how biosynthetic machineries assemble tertiary amide bonds. Cells use the incorporation of proline amino acids as a general strategy to protect peptides from degradation by proteolytic enzymes. Hence, the tertiary amide bond is crucial for the housekeeping of cellular proteins, which is of high importance in cancer and other diseases. We have previously shown that proteases display two distinct catalytic strategies to facilitate proteolysis (e.g. see the PDC-supported work J. Org. Chem. 2018, 83, 13543−13548). Our work has furthermore received a positive response from the scientific community. It is envisaged that the present investigation centered on biosynthesis of tertiary amide bonds will reveal additional catalytic strategies. The results generated will moreover be of high value in industrial biotechnology, where tertiary amide bonds are key motifs in biopharmaceuticals and in novel bio-based nanomaterials. Motivation to Beskow: Per-Olof Syrén (PI) has several funded projects from VR, FORMAS and SSF whose success are entirely dependent on running US-GAMESS on Beskow. Calculations are based on very large models of complex biocatalysts containing metals.