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Issue 20, 2013
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Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α → β transition in full protein context

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Abstract

An α → β transition underlies the first step of disease causing amyloidogenesis in many proteins. In view of this, many studies have been carried out using peptide models to characterize these secondary structural transitions. In this paper we show that an insertion/duplication mutant ‘L20’ of bacteriophage T4 lysozyme (M. Sagermann, W. A. Baase and B. W. Matthews, Proc. Natl. Acad. Sci. U.S.A., 1999, 96, 6078) displays an α → β transition. We performed molecular dynamics (MD) simulation of L20, using the GROMACS package of programs and united atom GROMOS 53a6 force field for a time period of 600 ns at 300 K, in explicit water. Our MD simulation demonstrated that the transition occurs in a duplicated α-helical region inserted tandemly at the N-terminus of the ‘parent’ helix. We show that a C-terminal β-sheet anchors the parent helix while the loosely held N-terminal loop in the duplicate region is vulnerable to solvent attack and thus undergoes an α → β transition. Main chain–solvent interactions were seen to stabilize the observed β-structure. Thus L20 serves as a good protein model for characterization of α → β transition in a full length protein.

Graphical abstract: Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α → β transition in full protein context

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Publication details

The article was received on 03 Dec 2012, accepted on 19 Mar 2013 and first published on 21 Mar 2013


Article type: Paper
DOI: 10.1039/C3CP44327B
Citation: Phys. Chem. Chem. Phys., 2013,15, 7819-7830
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    Molecular dynamics study of an insertion/duplication mutant of bacteriophage T4 lysozyme reveals the nature of α → β transition in full protein context

    H. Kaur and Y. U. Sasidhar, Phys. Chem. Chem. Phys., 2013, 15, 7819
    DOI: 10.1039/C3CP44327B

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