Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record
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Conformational analysis and water dynamics : a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record. / Fonseca, Beatriz; Freeman, Colin L.; Collins, Matthew J.
In: Chemical Physics, Vol. 561, 111602, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Conformational analysis and water dynamics
T2 - a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record
AU - Fonseca, Beatriz
AU - Freeman, Colin L.
AU - Collins, Matthew J.
N1 - Publisher Copyright: © 2022 The Authors
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - Protein hydrolysis
KW - Protein survival
KW - Water dynamics
KW - β-lactoglobulin
U2 - 10.1016/j.chemphys.2022.111602
DO - 10.1016/j.chemphys.2022.111602
M3 - Journal article
AN - SCOPUS:85131699108
VL - 561
JO - Chemical Physics
JF - Chemical Physics
SN - 0301-0104
M1 - 111602
ER -
ID: 316743977