Rotational dynamics of a protein under shear flow studied by the Eckart frame formalism

Papež, Petra (author), Merzel, Franci (author), Praprotnik, Matej (author)

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.

• Language: English
• Keywords: energy, kinetics, molecules, protein structure, rotational dynamics
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FMF - Faculty of Mathematics and Physics
• Publication status: Published
• Publication version: Version of Record
• Year: 2023
• Number of pages: Str. 7231-7243
• Numbering: Vol. 127, iss. 33
• PID: 20.500.12556/RUL-152675
• UDC: 577
• ISSN on article: 1520-5207
• DOI: 10.1021/acs.jpcb.3c02324
• COBISS.SI-ID: 163312899
• Publication date in RUL: 04.12.2023

PAPEŽ, Petra, MERZEL, Franci and PRAPROTNIK, Matej, 2023, Rotational dynamics of a protein under shear flow studied by the Eckart frame formalism. The journal of physical chemistry [online]. 2023. Vol. 127, no. 33, p. 7231–7243. [Accessed 8 April 2025]. DOI 10.1021/acs.jpcb.3c02324. Retrieved from: https://repozitorij.uni-lj.si/IzpisGradiva.php?lang=eng&id=152675

Record is a part of a journal

• Title: The journal of physical chemistry
• Shortened title: J. phys. chem., B (Online)
• Publisher: American Chemical Society
• ISSN: 1520-5207
• COBISS.SI-ID: 18984743

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.

Secondary language

• Language: Slovenian
• Keywords: biokemija, beljakovine, proteini, mehanske obremenitve, dinamika molekul, vibracije, analize

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: P1-0002
• Name: Večskalno modeliranje in simulacija mehke in biološke snovi v in izven ravnovesja

• Funder: ARRS - Slovenian Research Agency
• Project number: J1-3027
• Name: Večskalne simulacije tekočinskih tokov v nanomaterialih