Aggregation and solvent electrostriction in a simple dipeptide: a molecular dynamics investigation

Understanding the aggregation of peptides is of both biomedical and technological significance: diseases such as Alzheimer's and Creutzfeldt-Jakob's are believed to occur owing to aggregation of prion peptides, whilst manipulation of the aggregation process offers the possibilities of new biological materials. There is, therefore, a strong motivation to possess, at the molecular level, a detailed description of the mechanisms by which proteins and peptides aggregate. In this work, I will discuss recent work on the simple dipeptide glycyl-l-alanine, which has recently been the subject of neutron diffraction studies (McLain <i>et al</i>, Eur. Biophys. J. 37, 647 (2007), McLain <i>et al</i>, Ang. Chem. Int. Ed. 47, 9059 (2008)). This is a prototypical peptide system that can be simulated using atomistic molecular dynamics, thereby permitting a detailed structural investigation to be undertaken. In particular, I focus upon aggregation and its effect upon the water structure. It is found that the water structure resembles that of high-pressure water, a result with possible implications for the aggregation process.