Elsevier

Chemical Physics

Volume 535, 1 July 2020, 110777
Chemical Physics

Computational studies of fibrillation induced selective cytotoxicity of cross-α amyloid – Phenol Soluble Modulin α3

https://doi.org/10.1016/j.chemphys.2020.110777Get rights and content

Abstract

Phenol soluble modulin (PSM) α3, the most toxic member of α-toxin in Staphylococcus aureus bacteria, forms cross-α amyloid fibrils and is selectively toxic to the mammalian cell membranes. In this work, it has been discovered that hydrophobic interactions play a major role in fibril formation of PSM-α3 strands, with stabilization energy of 28.7 kCal mol−1. We considered two model bilayers mimicking mammalian and bacterial cell membranes, and found that single α-helix strand penetration is energetically unfavorable in both of them. Hence, we propose a simple model using energetics to understand the reason for selective toxicity of the peptide to the mammalian cell membrane. This study, besides enhancing the understanding of PSM-α3, can also act as a stepping stone in future drug development against S. aureus.

Introduction

Amyloids are infamous in the scientific community today because of various life threatening diseases including Alzheimer’s and Parkinson’s diseases. The general structure of amyloids consist of repeating units of peptides, mostly cross-β sheets with each peptide running perpendicular to the fibril axis [1], [2]. However, in 2017, the dictionary of amyloids had a major amendment with cross-α structures, which had all attributes of conventional amyloid structure but was formed using repeating α-helices [3]. The structure was observed in Phenol Soluble Modulin (PSM) α3, one of the toxic proteins secreted by Staphylococcus aureus [4]. Proteins which fold as cross-α amyloids have also been designed experimentally, implying that the cross-α structure of PSM-α3 is not an exception in the amyloid chemistry [5].

The bacteria that secretes PSM-α3 does not carry a good fame either. Staphylococcus aureus has been known to cause various diseases like impetigo, folliculitis, osteomyelitis, septic arthritis, endocarditis and pneumonia, just to name a few [6], [7]. The phenol soluble modulins are collectively responsible for various notorious activities which includes cytolysis and biofilm formation [8]. The latter takes place through two of the other members of PSM family, PSM-α1 and PSM-α4, which are predicted to form cross-β amyloids, unlike PSM-α3 [9].

The crystal structure of fibrils formed by PSM-α3 were found to contain two layers of α-helices, where the helix runs perpendicular to the fibril axis, similar to conventional cross-β amyloid. The distance between two adjacent helices in each layer was experimentally determined to be 1.05 nm, with the layers lying at a distance of 1.13 nm. The distances are found to be large compared to that of the conventional cross-β fibrils, which are in the range of 0.4–0.6 nm [3]. The peptide was also found to exhibit an overall charge of  +2e. The individual α-helix strand of PSM-α3 was found to be harmless to both mammalian and bacterial cell membranes [4]. However, the fibrils were experimentally observed to specifically penetrate the mammalian cell membrane, but lie on the surface of the bacterial cell membrane. The fibrillation process was found to occur faster in the presence of cell membranes. In another experimental study, point mutations at various locations of the peptide with alanine, points out to the possibility of salt bridge between Asp13 and Lys17 to be the major factor for the stability of the fibrils [10].

The structural uniqueness of PSM-α3, its selective cytotoxicity for mammalian cell membranes and the need for a cure motivated us to take up the challenge and explore the system computationally. In this work, we have studied the stability of the fibrils and the possible interactions responsible for it, the interaction of single strand PSM-α3 with model mammalian and bacterial bilayers and the changes induced in both the peptide and the bilayer in presence of each other [4]. At the end, we propose a model using the data obtained in order to understand the necessity for fibrillation while interacting with the bilayer and specifically penetrating the mammalian one.

Section snippets

Computational details

All the simulations have been performed using all atom classical molecular dynamics (MD). Structural information of the peptide bio-assembly has been obtained from the RCSB database. The systems consisting of solvated protein and bilayers have been prepared using CHARMM-GUI [11], [12], [13], [14], [15], [16]. Charmm-36 m force field [17], [18] has been used to obtain the parameters for the peptide and the bilayer molecules whereas water has been modeled using TIP3P [19], [20]. Na+ and Cl− ions

Stability of PSM-α3 Fibrils

The crystal structure of amyloid fibril of PSM-α3 consists of two layers, with the helices in each layer running perpendicular to the fibril axis (Fig. 1a). Each layer can be subdivided into two sections, such that the α-helices of two sections in a layer lie end to end. For an individual α-helix strand, two distinct surfaces were observed – which were dominated by hydrophobic and hydrophilic amino acids. In the fibril, it was found that the hydrophobic surfaces of the individual strands faced

Conclusions

From this work, we can conclude that the PSM-α3 forms cross-α amyloid fibrils spontaneously, with a stabilization energy of 28.7 kCal mol−1 for monomer addition. One of the possible reason that the system remains as cross-α fibrils, which has been considered as an intermediate for formation of cross-β structure, is the high energy requirement for degeneration of the protein from the cross-α structure. A single peptide, when placed near the bilayer, has been found to move to the surface of both

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Acknowledgements

The authors gratefully acknowledge NISER – Bhubaneswar for providing computational facilities.

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