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Biomolecules 2017, 7(3), 58; doi:10.3390/biom7030058

Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry

1
Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
2
Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editor: Sarah Perrett
Received: 13 July 2017 / Revised: 30 July 2017 / Accepted: 31 July 2017 / Published: 4 August 2017
(This article belongs to the Special Issue Functional Amyloids)
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Abstract

Functional amyloids are important structural and functional components of many biofilms, yet our knowledge of these fascinating polymers is limited to a few examples for which the native amyloids have been isolated in pure form. Isolation of the functional amyloids from other cell components represents a major bottleneck in the search for new functional amyloid systems. Here we present a label-free quantitative mass spectrometry method that allows identification of amyloid proteins directly in cell lysates. The method takes advantage of the extreme structural stability and polymeric nature of functional amyloids and the ability of concentrated formic acid to depolymerize the amyloids. An automated data processing pipeline that provides a short list of amyloid protein candidates was developed based on an amyloid-specific sigmoidal abundance signature in samples treated with increasing concentrations of formic acid. The method was evaluated using the Escherichia coli curli and the Pseudomonas Fap system. It confidently identified the major amyloid subunit for both systems, as well as the minor subunit for the curli system. A few non-amyloid proteins also displayed the sigmoidal abundance signature. However, only one of these contained a sec-dependent signal peptide, which characterizes most of all secreted proteins, including all currently known functional bacterial amyloids. View Full-Text
Keywords: functional amyloids; biofilm; nanomaterials; mass spectrometry functional amyloids; biofilm; nanomaterials; mass spectrometry
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Danielsen, H.N.; Hansen, S.H.; Herbst, F.-A.; Kjeldal, H.; Stensballe, A.; Nielsen, P.H.; Dueholm, M.S. Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry. Biomolecules 2017, 7, 58.

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