Behind the paper - Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms

Discover the story behind our paper, "Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms", which was published in npj Biofilms and Microbiomes

Like Comment

Our article entitled "Designed α-sheet peptides suppress amyloid formation in Staphylococcus aureus biofilms" was published in the journal npj Biofilms and Microbiomes. The Nature Research team had a few questions for us about our article, which me and my colleague Alissa Bleem have answered below.

What was the main aim of your research and why did you decide to investigate this?

Hospital acquired infections (HAI) place a major burden on health care systems, resulting in prolonged hospitalizations, increased complications, and higher costs. The difficulties of these infections are further exacerbated by the fact that the majority of HAI are associated with biofilm formation on some type of implanted medical device. When bacteria dwell in biofilms, they produce an adhesive extracellular matrix (EM) that encases the cells and shields them from antibiotic treatments and the patient’s own immune response. In recent years, a growing body of research has suggested that amyloid fibrils serve as a major protein scaffold in the EM, giving rise to the resistant phenotypes observed in HAI. Our research is concerned with prohibiting the formation of amyloid in Staphyloccocus aureus biofilms by targeting a specific pre-amyloid intermediate containing non-standard secondary structure, which we refer to as “α-sheet”. 

How did you go about designing your study? 

We first observed α-sheet structures in molecular dynamics (MD) simulations of mammalian amyloid proteins. When we simulate the dynamics of these proteins under amyloidogenic conditions, they all converge on a common structural intermediate, regardless of native secondary structure. This intermediate is characterized by the alternation of consecutive residue (f,y) angles in the aL and aR helical conformations, resulting in the alignment of carbonyl oxygens on one side of the sheet and amide protons on the other – hence the name “α-sheet”. References and more information on our initial MD discoveries and our α-sheet hypothesis can be found in the paper. Our subsequent studies demonstrated that peptides designed to bind these intermediates are capable of inhibiting aggregation in three different mammalian amyloid systems (references in the paper), providing support for what could have been a computational artifact. The inhibitory peptides are composed of alternating L/D amino acids to enforce a polar α-sheet structure and promote complementarity with the α-sheet target.

What challenges did you face?

In the case of S. aureus, amyloid fibrils are formed by small peptides called phenol soluble modulins (PSMs). We hypothesized that PSMs undergo structural changes during aggregation, converting from α-helical monomers to α-sheet intermediates and ultimately to β-sheet fibrils. By applying designed peptides in vitro and in situ, we sought to inhibit the fibrillation process and demonstrate a novel biofilm prevention strategy.

What were the key findings from your research?

The study of amyloid formation in biofilms in situ remains a difficult problem. The EM is comprised of a wide variety of macromolecules, many of which bind nonspecifically to the fluorophores and dyes commonly used for amyloid detection in vitro. As such, we had to incorporate other imaging techniques (e.g. transmission electron microscopy) to investigate interactions between designed α-sheet peptides and PSMs. Additionally, the PSM we chose for our biophysical studies, PSMα1, is very hydrophobic and aggregation-prone. As such, special laboratory plastics were used to prevent nonspecific adhesion, and precautions were taken to ensure solubility of the peptide.

What were the key findings from your research?

This study supports our hypothesis that α-sheet is a common structure formed during amyloid fibrillation, regardless of the native protein structure, sequence, or origin. We have shown that the assembly of amyloids in S. aureus biofilms is inhibited by designed α-sheet peptides, and we have demonstrated that PSMα1 adopts α-sheet structure on the pathway to fibril formation. These results provide a framework for next-generation peptide designs to target amyloid in the EM, rendering biofilms less robust.

What next? What further research is needed in this area?

Due to the generality of the α-sheet hypothesis, our design approach could apply to a variety of other amyloid-producing bacteria such as Pseudomonas aeruginosa, Escherichia coli, and Strep mutans. We have preliminary results supporting inhibition by our compounds in these other systems and further testing is on going, but it is encouraging that our compounds preferentially bind the toxic oligomers and inhibit amyloid formation in a variety of mammalian amyloid systems and both gram positive and gram negative bacteria.


Read the article in full

Valerie Daggett

Professor, University of Washington