Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies
The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary s...
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MDPI AG
2021-12-01
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| Series: | Polymers |
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| Online Access: | https://www.mdpi.com/2073-4360/14/1/123 |
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| author | Qun Zhang Dongqing Shao Peng Xu Zhouting Jiang |
| author_facet | Qun Zhang Dongqing Shao Peng Xu Zhouting Jiang |
| author_sort | Qun Zhang |
| collection | DOAJ |
| description | The effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications. |
| first_indexed | 2024-03-10T03:25:27Z |
| format | Article |
| id | doaj.art-d440403074114e0a9bef42f8df6df043 |
| institution | Directory Open Access Journal |
| issn | 2073-4360 |
| language | English |
| last_indexed | 2024-03-10T03:25:27Z |
| publishDate | 2021-12-01 |
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| series | Polymers |
| spelling | doaj.art-d440403074114e0a9bef42f8df6df0432023-11-23T12:10:12ZengMDPI AGPolymers2073-43602021-12-0114112310.3390/polym14010123Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different FrequenciesQun Zhang0Dongqing Shao1Peng Xu2Zhouting Jiang3Department of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, ChinaDepartment of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, ChinaDepartment of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, ChinaDepartment of Applied Physics, China Jiliang University, No. 258 Xueyuan Street, Xiasha Higher Education Zone, Hangzhou 310018, ChinaThe effect of pulsed and oscillating electric fields with different frequencies on the conformational properties of all-α proteins was investigated by molecular dynamics simulations. The root mean square deviation, the root mean square fluctuation, the dipole moment distribution, and the secondary structure analysis were used to assess the protein samples’ structural characteristics. In the simulation, we found that the higher frequency of the electric field influences the rapid response to the secondary structural transitions. However, the conformational changes measured by RMSD are diminished by applying the electrical field with a higher frequency. During the dipole moment analysis, we found that the magnitude and frequency of the dipole moment was directly related to the strength and frequency of the external electric field. In terms of the type of electric fields, we found that the average values of RMSD and RMSF of whole molecular protein are larger when the protein is exposed in the pulsed electric field. Concerning the typical sample 1BBL, the secondary structure analysis showed that two alpha-helix segments both transit to turns or random coils almost simultaneously when it is exposed in a pulsed electric field. Meanwhile, two segments present the different characteristic times when the transition occurs in the condition of an oscillating electric field. This study also demonstrated that the protein with fewer charged residues or more residues in forming α-helical structures display the higher conformational stability. These conclusions, achieved using MD simulations, provide a theoretical understanding of the effect of the frequency and expression form of external electric fields on the conformational changes of the all-α proteins with charged residues and the guidance for anticipative applications.https://www.mdpi.com/2073-4360/14/1/123molecular dynamics simulationelectric fieldconformational transition |
| spellingShingle | Qun Zhang Dongqing Shao Peng Xu Zhouting Jiang Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies Polymers molecular dynamics simulation electric field conformational transition |
| title | Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies |
| title_full | Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies |
| title_fullStr | Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies |
| title_full_unstemmed | Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies |
| title_short | Effects of an Electric Field on the Conformational Transition of the Protein: Pulsed and Oscillating Electric Fields with Different Frequencies |
| title_sort | effects of an electric field on the conformational transition of the protein pulsed and oscillating electric fields with different frequencies |
| topic | molecular dynamics simulation electric field conformational transition |
| url | https://www.mdpi.com/2073-4360/14/1/123 |
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