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

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

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.

• Jezik: Angleški jezik
• Ključne besede: energy, kinetics, molecules, protein structure, rotational dynamics
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: FMF - Fakulteta za matematiko in fiziko
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2023
• Št. strani: Str. 7231-7243
• Številčenje: Vol. 127, iss. 33
• PID: 20.500.12556/RUL-152675
• UDK: 577
• ISSN pri članku: 1520-5207
• DOI: 10.1021/acs.jpcb.3c02324
• COBISS.SI-ID: 163312899
• Datum objave v RUL: 04.12.2023

Gradivo je del revije

• Naslov: The journal of physical chemistry. B
• Skrajšan naslov: J. phys. chem., B (Online)
• Založnik: American Chemical Society
• ISSN: 1520-5207
• COBISS.SI-ID: 18984743

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: biokemija, beljakovine, proteini, mehanske obremenitve, dinamika molekul, vibracije, analize

Projekti

• Financer: ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
• Številka projekta: P1-0002
• Naslov: Večskalno modeliranje in simulacija mehke in biološke snovi v in izven ravnovesja

• Financer: ARRS - Agencija za raziskovalno dejavnost Republike Slovenije
• Številka projekta: J1-3027
• Naslov: Večskalne simulacije tekočinskih tokov v nanomaterialih