Text

theses

A computational design of collagen mimetic peptides (CMPs) that self-assemble orthogonally (mutually exclusively), in the presence of other pre-existing collagen trimer mixtures, in vitro, has been proposed. The orthogonality in self-assembly was brought about by orthogonal patterning of ionic salt bridges and residues, along the collagen trimers’ axial length. Through the aid of circular dichroism spectroscopy alone, a novel experimental protocol was set-up to rapidly assess the level of cross-talk that may arise in such designed ‘heterogeneous monomer to trimer folding’ mixture environments. It is shown that the designed collagen mimetic peptides are stable and hetero-specific within their composite 3 chain peptide ecosystem. We experimentally demonstrate the extent to which loss in specificity could possibly occur, upon moving to a higher order ‘more than 3 monomers in solution’ peptide ensemble. Although the desired level of multi-state orthogonality was not achieved in the current design, the experimental results obtained were used to estimate the stability and specificity barrier threshold that one might run into, if one were to instead design orthogonal systems where-in specificity is incorporated during the computational design stage itself a priori. A Pareto frontier plot indicating the specificity versus stability trade-off is plotted. We conclude that a bottom-up design approach, incorporating design of specificity during the sequence design stage, would be a better way forward for achieving self-assembling orthogonality. In contrast to the complex chaperone assisted protein folding systems existing in nature, our method is a simplistic first step towards the complementary approach of modular synthetic collagen molecule design.

ETD_7848

Ph.D.

Includes bibliographical references

by Sandeep Vishwanath Belure

doi:10.7282/T3DJ5J2R

ETD doctoral

The author owns the copyright to this work.