Testing the transferability of a coarse-grained model to intrinsically disordered proteins

The intermediate-resolution coarse-grained protein model PLUM [T. Bereau and M. Deserno, J. Chem. Phys., 2009, 130, 235106] is used to simulate small systems of intrinsically disordered proteins involved in biomineralisation. With minor adjustments to reduce bias toward stable secondary structure, the model generates conformational ensembles conforming to structural predictions from atomistic simulation. Without additional structural information as input, the model distinguishes regions of the chain by predicted degree of disorder, manifestation of structure, and involvement in chain dimerisation. The model is also able to distinguish dimerisation behaviour between one intrinsically disordered peptide and a closely related mutant. We contrast this against the poor ability of PLUM to model the S1 quartz-binding peptide.

Learning from nature: polymorph-selective binding of the nacre peptide n16N

In this thesis the results of large scale molecular simulations of interfacial peptide systems are presented, elucidating the interactions responsible for polymorph selective adsorption behaviour of many peptides. This insight provides a first step to understanding the biomineralisation of nacre(mother of pearl), and the production of bio-inspired composites.