Repository logo
 

Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record

Published version
Peer-reviewed

Type

Article

Change log

Authors

Fonseca, B 
Freeman, CL 
Collins, MJ 

Abstract

One of the greatest successes of the application of Palaeoproteomics to Archaeology is its use by a number of authors to track evidence of dairying practice, both in terms of its origin and the selection of animal species. To this end, the whey protein β-lactoglobulin entrapped in pottery and dental calculus is widely studied because it is so frequently recovered but why is it differentially preserved? Hydrolysis plays a big part in the breakdown of proteins. Therefore, it is essential to explore the role of water in degradation to uncover some of the patterns linked to protein survival. One approach to understand the hydrolytic process is to examine the molecular behaviour of this protein and in particular of the peptide most commonly recovered: T125PEVDXEALEK135. In this study, we use Molecular Dynamics, with the Amber14SB forcefield and the SPC/E water model in Gromacs 2020, to first explore the dynamics of this peptide in bulk water. Despite the difficulties in describing reactive processes with classical methods, we were able to identify geometric arrangements between water and protein residues which are similar to the ones described in the literature for protein hydrolysis. These arrangements helped to identify potential sites for hydrolysis along the bovine β-lactoglobulin T125PEVDDEALEK135 amino acid chain.

Description

Keywords

Protein hydrolysis, beta-lactoglobulin, Water dynamics, Protein survival

Journal Title

Chemical Physics

Conference Name

Journal ISSN

0301-0104
1873-4421

Volume Title

561

Publisher

Elsevier BV
Sponsorship
European Research Council (787282)