Simulation of protein diffusion: a sensitive probe of protein–solvent interactions
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes ( L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity an...
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ftdatacite:10.6084/m9.figshare.6154604.v2 2023-05-15T13:50:25+02:00 Simulation of protein diffusion: a sensitive probe of protein–solvent interactions Ferrario, Valerio Pleiss, Jürgen 2018 https://dx.doi.org/10.6084/m9.figshare.6154604.v2 https://tandf.figshare.com/articles/Simulation_of_protein_diffusion_a_sensitive_probe_of_protein-solvent_interactions/6154604/2 unknown Taylor & Francis https://dx.doi.org/10.1080/07391102.2018.1461689 https://dx.doi.org/10.6084/m9.figshare.6154604 Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Biophysics Biochemistry 29999 Physical Sciences not elsewhere classified FOS Physical sciences Biotechnology 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences Ecology FOS Biological sciences Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Cancer Inorganic Chemistry Plant Biology Text article-journal Journal contribution ScholarlyArticle 2018 ftdatacite https://doi.org/10.6084/m9.figshare.6154604.v2 https://doi.org/10.1080/07391102.2018.1461689 https://doi.org/10.6084/m9.figshare.6154604 2021-11-05T12:55:41Z Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes ( L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius ( R S ), which was derived from the diffusion coefficient and the viscosity. R S was compared to the geometric radius ( R G ) of CALB, which was derived from the protein density. R S and R G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient. Text Antarc* Antarctica DataCite Metadata Store (German National Library of Science and Technology) |
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Biophysics Biochemistry 29999 Physical Sciences not elsewhere classified FOS Physical sciences Biotechnology 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences Ecology FOS Biological sciences Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Cancer Inorganic Chemistry Plant Biology |
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Biophysics Biochemistry 29999 Physical Sciences not elsewhere classified FOS Physical sciences Biotechnology 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences Ecology FOS Biological sciences Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Cancer Inorganic Chemistry Plant Biology Ferrario, Valerio Pleiss, Jürgen Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
topic_facet |
Biophysics Biochemistry 29999 Physical Sciences not elsewhere classified FOS Physical sciences Biotechnology 39999 Chemical Sciences not elsewhere classified FOS Chemical sciences Ecology FOS Biological sciences Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Cancer Inorganic Chemistry Plant Biology |
description |
Aqueous solutions of Candida antarctica lipase B (CALB) were simulated considering three different water models (SPC/E, TIP3P, TIP4P) by a series of molecular dynamics (MD) simulations of three different box sizes ( L = 9, 14, and 19 nm) to determine the diffusion coefficient, the water viscosity and the protein density. The protein–water systems were equilibrated for 500 ns, followed by 100 ns production runs which were analysed. The diffusional properties of CALB were characterized by the Stokes radius ( R S ), which was derived from the diffusion coefficient and the viscosity. R S was compared to the geometric radius ( R G ) of CALB, which was derived from the protein density. R S and R G differed by 0.27 nm for SPC/E and by 0.40 and 0.39 nm for TIP3P and TIP4P, respectively, which characterizes the thickness of the diffusive hydration layer on the protein surface. The simulated hydration layer of CALB resulted in agreement with those experimentally determined for other seven different proteins of comparable size. By avoiding the most common pitfalls, protein diffusion can be reliably simulated: simulating different box sizes to account for the finite size effect, equilibrating the protein–water system sufficiently, and using the complete production run for the determination of the diffusion coefficient. |
format |
Text |
author |
Ferrario, Valerio Pleiss, Jürgen |
author_facet |
Ferrario, Valerio Pleiss, Jürgen |
author_sort |
Ferrario, Valerio |
title |
Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
title_short |
Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
title_full |
Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
title_fullStr |
Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
title_full_unstemmed |
Simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
title_sort |
simulation of protein diffusion: a sensitive probe of protein–solvent interactions |
publisher |
Taylor & Francis |
publishDate |
2018 |
url |
https://dx.doi.org/10.6084/m9.figshare.6154604.v2 https://tandf.figshare.com/articles/Simulation_of_protein_diffusion_a_sensitive_probe_of_protein-solvent_interactions/6154604/2 |
genre |
Antarc* Antarctica |
genre_facet |
Antarc* Antarctica |
op_relation |
https://dx.doi.org/10.1080/07391102.2018.1461689 https://dx.doi.org/10.6084/m9.figshare.6154604 |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.6154604.v2 https://doi.org/10.1080/07391102.2018.1461689 https://doi.org/10.6084/m9.figshare.6154604 |
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