Conformational Heterogeneity of a Protein in Proline Solutions

Abstract

The use of amino acids as osmolytes or excipients in protein formulation is well known. The nature of amino acids regulates protein conformations. [1] In recent work, we have explored the effects of basic and aromatic amino acids on the conformational stability of proteins. [2, 3] In the amino acids library, proline is the only proteinogenic secondary amino acid, which is a secondary amine. Proline is known to inhibit protein aggregation [4]; however, its effects on proteins’ conformation are not known. In this work, we performed a series of atomistic molecular dynamics simulations of a small globular protein in proline solutions of different concentrations and temperatures to explore the conformational stability of the protein and the sensitivity of proline concentrations toward the protein’s structure preservation. [5] Our study suggests that being unfolded in pure water and 2 M proline, a significant amount of initial native contacts of the protein were broken with retaining minimal % helicity. From the thorough cluster analysis using a k-mean algorithm and constructing a free energy landscape using root-mean-square deviations and the remaining fraction of native contact as reaction coordinates, we have identified the transition metastable structures during the unfolding process in pure water and at 2M proline concentration. However, above this concentration, proline is found to act as an osmolyte. The details of the results will be shown and discussed.