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Rotational dynamics of a protein under shear flow studied by the Eckart frame formalism
ID
Papež, Petra
(
Author
),
ID
Merzel, Franci
(
Author
),
ID
Praprotnik, Matej
(
Author
)
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MD5: 3FB36809271751669A1CC37B5E799B62
URL - Source URL, Visit
https://pubs.acs.org/doi/10.1021/acs.jpcb.3c02324
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Abstract
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
Views:
573
Downloads:
34
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Record is a part of a journal
Title:
The journal of physical chemistry. B
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
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