Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations
Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in w...
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| Format: | Article |
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MDPI AG
2023-05-01
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| Series: | Molecules |
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| Online Access: | https://www.mdpi.com/1420-3049/28/10/4070 |
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| author | Elena Ermakova Olga Makshakova Rauf Kurbanov Ilya Ibraev Yuriy Zuev Igor Sedov |
| author_facet | Elena Ermakova Olga Makshakova Rauf Kurbanov Ilya Ibraev Yuriy Zuev Igor Sedov |
| author_sort | Elena Ermakova |
| collection | DOAJ |
| description | Uperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation. |
| first_indexed | 2024-03-11T03:27:23Z |
| format | Article |
| id | doaj.art-659174bedfae42b399696549cd9c06b2 |
| institution | Directory Open Access Journal |
| issn | 1420-3049 |
| language | English |
| last_indexed | 2024-03-11T03:27:23Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Molecules |
| spelling | doaj.art-659174bedfae42b399696549cd9c06b22023-11-18T02:38:49ZengMDPI AGMolecules1420-30492023-05-012810407010.3390/molecules28104070Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics SimulationsElena Ermakova0Olga Makshakova1Rauf Kurbanov2Ilya Ibraev3Yuriy Zuev4Igor Sedov5Kazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, RussiaKazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, RussiaKazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, RussiaChemical Institute, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, RussiaKazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, RussiaKazan Institute of Biochemistry and Biophysics, FRC Kazan Scientific Center of RAS, Lobachevsky Str., 2/31, Kazan 420111, RussiaUperin 3.5 is a remarkable natural peptide obtained from the skin of toadlets comprised of 17 amino acids which exhibits both antimicrobial and amyloidogenic properties. Molecular dynamics simulations were performed to study the β-aggregation process of uperin 3.5 as well as two of its mutants, in which the positively charged residues Arg7 and Lys8 have been replaced by alanine. All three peptides rapidly underwent spontaneous aggregation and conformational transition from random coils to beta-rich structures. The simulations reveal that the initial and essential step of the aggregation process involves peptide dimerization and the formation of small beta-sheets. A decrease in positive charge and an increase in the number of hydrophobic residues in the mutant peptides lead to an increase in the rate of their aggregation.https://www.mdpi.com/1420-3049/28/10/4070uperinmolecular dynamics simulationsamyloid peptidesaggregation |
| spellingShingle | Elena Ermakova Olga Makshakova Rauf Kurbanov Ilya Ibraev Yuriy Zuev Igor Sedov Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations Molecules uperin molecular dynamics simulations amyloid peptides aggregation |
| title | Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations |
| title_full | Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations |
| title_fullStr | Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations |
| title_full_unstemmed | Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations |
| title_short | Aggregation of Amyloidogenic Peptide Uperin—Molecular Dynamics Simulations |
| title_sort | aggregation of amyloidogenic peptide uperin molecular dynamics simulations |
| topic | uperin molecular dynamics simulations amyloid peptides aggregation |
| url | https://www.mdpi.com/1420-3049/28/10/4070 |
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