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J Comput Aided Mol Des. 2016 Feb;30(2):153-64. doi: 10.1007/s10822-015-9892-x. Epub 2016 Jan 11.

A β-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils.

Author information

1
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece.
2
Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, 157 01, Athens, Greece. veconom@biol.uoa.gr.

Abstract

Pmel17 is a multidomain protein involved in biosynthesis of melanin. This process is facilitated by the formation of Pmel17 amyloid fibrils that serve as a scaffold, important for pigment deposition in melanosomes. A specific luminal domain of human Pmel17, containing 10 tandem imperfect repeats, designated as repeat domain (RPT), forms amyloid fibrils in a pH-controlled mechanism in vitro and has been proposed to be essential for the formation of the fibrillar matrix. Currently, no three-dimensional structure has been resolved for the RPT domain of Pmel17. Here, we examine the structure of the RPT domain by performing sequence threading. The resulting model was subjected to energy minimization and validated through extensive molecular dynamics simulations. Structural analysis indicated that the RPT model exhibits several distinct properties of β-solenoid structures, which have been proposed to be polymerizing components of amyloid fibrils. The derived model is stabilized by an extensive network of hydrogen bonds generated by stacking of highly conserved polar residues of the RPT domain. Furthermore, the key role of invariant glutamate residues is proposed, supporting a pH-dependent mechanism for RPT domain assembly. Conclusively, our work attempts to provide structural insights into the RPT domain structure and to elucidate its contribution to Pmel17 amyloid fibril formation.

KEYWORDS:

Amyloid fibrils; Functional amyloid; Homology modelling; Molecular dynamics; β-Helix

PMID:
26754844
DOI:
10.1007/s10822-015-9892-x
[Indexed for MEDLINE]

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