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

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Ansari, Samiul M. and Coletta, Andrea and Kirkeby Skeby, Katrine and Sørensen, Jesper and Schiøtt, Birgit and Palmer, David S. (2016) Allosteric activation mechanism of bovine chymosin revealed by bias-exchange metadynamics and molecular dynamics simulations. Journal of Physical Chemistry B, 120 (40). pp. 10453-10462. ISSN 1520-6106 (https://doi.org/10.1021/acs.jpcb.6b07491)

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Abstract

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.

ORCID iDs

Ansari, Samiul M. ORCID logoORCID: https://orcid.org/0000-0003-1066-1112, Coletta, Andrea, Kirkeby Skeby, Katrine, Sørensen, Jesper, Schiøtt, Birgit and Palmer, David S. ORCID logoORCID: https://orcid.org/0000-0003-4356-9144;
  • Item type:Article
    ID code:57778
    Dates:
    Date
    Event
    14 September 2016
    Published
    14 September 2016
    Published Online
    12 September 2016
    Accepted
    Notes: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
    Subjects:Science > Chemistry
    Department:Faculty of Science > Pure and Applied Chemistry
    Depositing user: Pure Administrator
    Date deposited:13 Sep 2016 11:24
    Last modified:11 Nov 2024 11:30
    Related URLs:
    URI:https://strathprints.strath.ac.uk/id/eprint/57778
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