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The Journal of Physical Chemistry B
Article . 2020 . Peer-reviewed
License: CC BY
Data sources: Crossref
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The Journal of Physical Chemistry B
Article
License: CC BY
Data sources: UnpayWall
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PubMed Central
Other literature type . 2020
Data sources: PubMed Central
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ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction

Authors: Andrea Arsiccio; Pritam Ganguly; Lorenzo La Cortiglia; Joan-Emma Shea; Roberto Pisano;

ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction

Abstract

The protein-osmolyte interaction has been shown experimentally to follow an additive construct, where the individual osmolyte-backbone and osmolyte-side-chain interactions contribute to the overall conformational stability of proteins. Here, we computationally reconstruct this additive relation using molecular dynamics simulations, focusing on sugars and polyols, including sucrose and sorbitol, as model osmolytes. A new set of parameters (ADD) is developed for this purpose, using the individual Kirkwood-Buff integrals for sugar-backbone and sugar-side-chain interactions as target experimental data. We show that the ADD parameters can reproduce the additivity of protein-sugar interactions and correctly predict sucrose and sorbitol self-association and their interaction with water. The accurate description of the separate osmolyte-backbone and osmolyte-side-chain contributions also automatically translates into a good prediction of preferential exclusion from the surface of ribonuclease A and α-chymotrypsinogen A. The description of sugar polarity is improved compared to previous force fields, resulting in closer agreement with the experimental data and better compatibility with charged groups, such as the guanidinium moiety. The ADD parameters are developed in combination with the CHARMM36m force field for proteins, but good compatibility is also observed with the AMBER 99SB-ILDN and the OPLS-AA force fields. Overall, exploiting the additivity of protein-osmolyte interactions is a promising approach for the development of new force fields.

Keywords

molecular dynamics; force field; polyols; sugars; proteins, Polymers, Proteins, Water, Molecular Dynamics Simulation, Sugars

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
18
Top 10%
Average
Top 10%
Green
hybrid