Docking interactions determine early cleavage events in insulin proteolysis by pepsin: Experiment and simulation.

Autor: Koliński M; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland; Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 5 Pawinskiego St., 02-106 Warsaw, Poland. Electronic address: mkolinski@imdik.pan.pl., Kmiecik S; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland., Dec R; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland., Piejko M; Cell Bank, Department of Cell Biology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 7 Gronostajowa St., 30-387 Krakow, Poland; 3rd Department of General Surgery, Jagiellonian University Medical College, 35-37 Pradnicka St., 31-202 Krakow, Poland., Mak P; Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 7 Gronostajowa St., 30-387 Krakow, Poland., Dzwolak W; Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur St., 02-093 Warsaw, Poland. Electronic address: wdzwolak@chem.uw.edu.pl.
Jazyk: angličtina
Zdroj: International journal of biological macromolecules [Int J Biol Macromol] 2020 Apr 15; Vol. 149, pp. 1151-1160. Date of Electronic Publication: 2020 Jan 27.
DOI: 10.1016/j.ijbiomac.2020.01.253
Abstrakt: In silico modelling of cascade enzymatic proteolysis is an exceedingly complex and challenging task. Here, we study partial proteolysis of insulin by pepsin: a process leading to the release of a highly amyloidogenic two chain 'H-fragment'. The H-fragment retains several cleavage sites for pepsin. However, under favorable conditions H-monomers rapidly self-assemble into proteolysis-resistant amyloid fibrils whose composition provides snapshots of early and intermediate stages of the proteolysis. In this work, we report a remarkable agreement of experimentally determined and simulation-predicted cleavage sites on different stages of the proteolysis. Prediction of cleavage sites was based on the comprehensive analysis of the docking interactions from direct simulation of coupled folding and binding of insulin (or its cleaved derivatives) to pepsin. The most frequent interactions were found to be between the pepsin's active site, or its direct vicinity, and the experimentally determined insulin cleavage sites, which suggest that the docking interactions govern the proteolytic process.
Competing Interests: Declaration of competing interest The authors declare no conflict of interests.
(Copyright © 2020 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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