Allosteric activation mechanism of bovine chymosin revealed by bias-exchange metadynamics and molecular dynamics simulations

Research output: Contribution to journalArticle

The aspartic protease, bovine chymosin, catalyses the proteolysis of κ-casein proteins in milk. The bovine chymosin–κ-casein complex is of industrial interest as the enzyme is widely employed in the manufacturing of processed dairy products. The apo form of the enzyme adopts a self-inhibited conformation in which the side chain of Tyr77 occludes the binding site. On the basis of kinetic, mutagenesis and crystallographic data, it has been widely reported that a HPHPH sequence in the P8-P4 residues of the natural substrate κ-casein acts as the allosteric activator, but the mechanism by which this occurs has not previously been elucidated due to the challenges associated with studying this process by experimental methods. Here we have employed two computational techniques, molecular dynamics and bias exchange metadynamics simulations, to study the mechanism of allosteric activation and to compute the free energy surface for the process. The simulations reveal that allosteric activation is initiated by interactions between the HPHPH sequence of κ-casein and a small α-helical region of chymosin (residues 112-116). A small conformational change in the α-helix causes the side chain of Phe114 to vacate a pocket that may then be occupied by the side chain of Tyr77. The free energy surface for the self-inhibited to open transition is significantly altered by the presence of the HPHPH sequence of κ-casein.
Original languageEnglish
Pages (from-to)10453-10462
Number of pages10
JournalJournal of Physical Chemistry B
Volume120
Issue number40
Early online date14 Sep 2016
DOIs
StateE-pub ahead of print - 14 Sep 2016

    Research areas

  • chymosin, molecular dynamics, bias-exchange metadynamics, cheese production, computational chemistry, aspartic protease, enzyme, proteolysis, k-casein, milk, casein micelles

Bibliographical note

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Physical Chemistry B, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/acs.jpcb.6b07491

Equipment

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  1. ARCHIE-WeSt (UOSHPC)

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