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Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism

[Image: see text] Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced the...

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Autores principales: Papež, Petra, Merzel, Franci, Praprotnik, Matej
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10461304/
https://www.ncbi.nlm.nih.gov/pubmed/37556834
http://dx.doi.org/10.1021/acs.jpcb.3c02324
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author Papež, Petra
Merzel, Franci
Praprotnik, Matej
author_facet Papež, Petra
Merzel, Franci
Praprotnik, Matej
author_sort Papež, Petra
collection PubMed
description [Image: see text] Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule.
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spelling pubmed-104613042023-08-29 Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism Papež, Petra Merzel, Franci Praprotnik, Matej J Phys Chem B [Image: see text] Proteins are natural polymers that play an essential role in both living organisms and biotechnological applications. During certain bioprocessing steps, they can be exposed to significant mechanical stress induced by, for example, shear flow or sonication, resulting in reduced therapeutic efficacy, aggregation, or even a loss of activity. For this reason, there is a need to understand and determine the susceptibility of the protein activity to the experienced mechanical stress. To acquire this knowledge, it is necessary to study the rotational dynamics of the protein. Commonly, the rotational dynamics of soft molecules is interpreted based on a theoretical analysis performed in an inertial laboratory frame. However, the obtained angular velocity mixes pure rotations and vibrations with angular momentum, consequently lacking a clear dynamical interpretation. On the other hand, the use of the noninertial internal Eckart frame allows the determination of pure angular velocity as it minimizes the coupling between the rotational and vibrational degrees of freedom. In the present work, by conducting open-boundary molecular dynamics simulations and exploiting the Eckart frame formalism, we study the rotational dynamics of a small protein under the shear flow of various strengths. Our results show that the angular velocity increases nonlinearly with increasing shear rate. Furthermore, the protein gains vibrational angular momentum at higher shear rates, which is reflected in the higher angular velocity computed by employing the Eckart frame formalism and confirmed by analysis of the contributions to the total kinetic energy of the biomolecule. American Chemical Society 2023-08-09 /pmc/articles/PMC10461304/ /pubmed/37556834 http://dx.doi.org/10.1021/acs.jpcb.3c02324 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Papež, Petra
Merzel, Franci
Praprotnik, Matej
Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title_full Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title_fullStr Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title_full_unstemmed Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title_short Rotational Dynamics of a Protein under Shear Flow Studied by the Eckart Frame Formalism
title_sort rotational dynamics of a protein under shear flow studied by the eckart frame formalism
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10461304/
https://www.ncbi.nlm.nih.gov/pubmed/37556834
http://dx.doi.org/10.1021/acs.jpcb.3c02324
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