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

[Image: see text] 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 addi...

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Autores principales: Arsiccio, Andrea, Ganguly, Pritam, La Cortiglia, Lorenzo, Shea, Joan-Emma, Pisano, Roberto
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2020
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901642/
https://www.ncbi.nlm.nih.gov/pubmed/32790371
http://dx.doi.org/10.1021/acs.jpcb.0c05345
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author Arsiccio, Andrea
Ganguly, Pritam
La Cortiglia, Lorenzo
Shea, Joan-Emma
Pisano, Roberto
author_facet Arsiccio, Andrea
Ganguly, Pritam
La Cortiglia, Lorenzo
Shea, Joan-Emma
Pisano, Roberto
author_sort Arsiccio, Andrea
collection PubMed
description [Image: see text] 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.
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spelling pubmed-79016422021-02-24 ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction Arsiccio, Andrea Ganguly, Pritam La Cortiglia, Lorenzo Shea, Joan-Emma Pisano, Roberto J Phys Chem B [Image: see text] 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. American Chemical Society 2020-08-11 2020-09-10 /pmc/articles/PMC7901642/ /pubmed/32790371 http://dx.doi.org/10.1021/acs.jpcb.0c05345 Text en Made available through a Creative Commons CC-BY License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html)
spellingShingle Arsiccio, Andrea
Ganguly, Pritam
La Cortiglia, Lorenzo
Shea, Joan-Emma
Pisano, Roberto
ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title_full ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title_fullStr ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title_full_unstemmed ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title_short ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein–Osmolyte Interaction
title_sort add force field for sugars and polyols: predicting the additivity of protein–osmolyte interaction
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901642/
https://www.ncbi.nlm.nih.gov/pubmed/32790371
http://dx.doi.org/10.1021/acs.jpcb.0c05345
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