Sub-THz acoustic excitation of protein motion

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

The application of terahertz radiation has been shown to affect both protein structure and cellular function. As the key to such structural changes lies in the dynamic response of a protein, we focus on the susceptibility of the protein’s internal dynamics to mechanical stress induced by acoustic pressure waves. We use the open-boundary molecular dynamics method, which allows us to simulate the protein exposed to acoustic waves. By analyzing the dynamic fluctuations of the protein subunits, we demonstrate that the protein is highly susceptible to acoustic waves with frequencies corresponding to those of the internal protein vibrations. This is confirmed by changes in the compactness of the protein structure. As the amplitude of the pressure wave increases, even larger deviations from average positions and larger changes in protein compactness are observed. Furthermore, performing the mode-projection analysis, we show that the breathing-like character of collective modes is enhanced at frequencies corresponding to those used to excite the protein.

• Language: English
• Keywords: molecular dynamics, acoustical properties, acoustic wave propagation, mechanical stress, terahertz radiation, proteins
• 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: 8 str.
• Numbering: Vol. 159, iss. 13, art. 135101
• PID: 20.500.12556/RUL-164665
• UDC: 577
• ISSN on article: 1089-7690
• DOI: 10.1063/5.0163801
• COBISS.SI-ID: 170525187
• Publication date in RUL: 06.11.2024

Record is a part of a journal

• Title: Journal of chemical physics
• Shortened title: J. chem. phys. online
• Publisher: AIP Publishing
• ISSN: 1089-7690
• COBISS.SI-ID: 18985767

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, proteini, beljakovine, simulacije, akustika, frekvence