Eur. Phys. J. E 34, 5 (2011)
https://doi.org/10.1140/epje/i2011-11005-0

Computer simulations of the growth of synthetic peptide fibres

¹ H.H. Wills Physics Laboratory, University of Bristol, Tyndall Avenue, BS8 1TL, Bristol, UK
² Unilever Research Colworth, Colworth Park, Sharnbrook, MK44 1LQ, Bedfordshire, UK
³ The School of Chemistry, University of Bristol, BS8 1TS, Bristol, UK
⁴ Department of Biochemistry, University of Bristol, University Walk, BS8 1TD, Bristol, UK

s.hanna@bristol.ac.uk

Received: 2 April 2010
Accepted: 29 November 2010
Published online: 10 January 2011

Abstract

We present a coarse-grained computer model designed to study the growth of fibres in a synthetic self-assembling peptide system. The system consists of two 28 residue -helical sequences, denoted AB and CD, in which the interactions between the half peptides, A, B, C and D, may be tuned individually to promote different types of growth behaviour. In the model, AB and CD are represented by double ended rods, with interaction sites distributed along their lengths. Monte Carlo simulations are performed to follow fibre growth. It is found that lateral and longitudinal growth of the fibre are governed by different mechanisms --the former is diffusion limited with a very small activation energy for the addition of units, whereas the latter occurs via a process of secondary nucleation at the fibre ends. As a result, longitudinal growth generally proceeds more slowly than lateral growth. Furthermore, it is shown that the aspect ratio of the growing fibre may be controlled by adjusting the temperature and the relative strengths of the interactions. The predictions of the model are discussed in the context of published data from real peptide systems.