Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers
In this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation w...
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MDPI AG
2020-07-01
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| Series: | Polymers |
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| Online Access: | https://www.mdpi.com/2073-4360/12/8/1657 |
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| author | Sofia E. Mikhtaniuk Valeriy V. Bezrodnyi Oleg V. Shavykin Igor M. Neelov Nadezhda N. Sheveleva Anastasia V. Penkova Denis A. Markelov |
| author_facet | Sofia E. Mikhtaniuk Valeriy V. Bezrodnyi Oleg V. Shavykin Igor M. Neelov Nadezhda N. Sheveleva Anastasia V. Penkova Denis A. Markelov |
| author_sort | Sofia E. Mikhtaniuk |
| collection | DOAJ |
| description | In this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation was performed by molecular dynamics method in a wide range of temperatures. We have shown that the Lys-2Lys dendrimer has a larger size but smaller fluctuations as well as lower internal density in comparison with the Lys-2Gly dendrimer. The Lys-2Lys dendrimer has larger charge but counterions form more ion pairs with its NH<inline-formula> <math display="inline"> <semantics> <msubsup> <mrow></mrow> <mn>3</mn> <mo>+</mo> </msubsup> </semantics> </math> </inline-formula> groups and reduce the bare charge and zeta potential of the first dendrimer more strongly. It was demonstrated that these differences between dendrimers are due to the lower flexibility and the larger charge (+2) of each 2Lys spacers in comparison with 2Gly ones. The terminal CH<sub>2</sub><inline-formula></inline-formula> groups in both dendrimers move faster than the inner CH<sub>2</sub> groups. The calculated temperature dependencies of the spin-lattice relaxation times of these groups for both dendrimers are in a good agreement with the experimental results obtained by NMR. |
| first_indexed | 2024-03-10T18:12:38Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4360 |
| language | English |
| last_indexed | 2024-03-10T18:12:38Z |
| publishDate | 2020-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Polymers |
| spelling | doaj.art-01a8e8f0110046cda161767b47fe90ed2023-11-20T07:57:15ZengMDPI AGPolymers2073-43602020-07-01128165710.3390/polym12081657Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their SpacersSofia E. Mikhtaniuk0Valeriy V. Bezrodnyi1Oleg V. Shavykin2Igor M. Neelov3Nadezhda N. Sheveleva4Anastasia V. Penkova5Denis A. Markelov6St. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 St. Petersburg, RussiaSt. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 St. Petersburg, RussiaSt. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 St. Petersburg, RussiaSt. Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy pr. 49, 197101 St. Petersburg, RussiaSt. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, RussiaSt. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, RussiaSt. Petersburg State University, 7/9 Universitetskaya nab., 199034 St. Petersburg, RussiaIn this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation was performed by molecular dynamics method in a wide range of temperatures. We have shown that the Lys-2Lys dendrimer has a larger size but smaller fluctuations as well as lower internal density in comparison with the Lys-2Gly dendrimer. The Lys-2Lys dendrimer has larger charge but counterions form more ion pairs with its NH<inline-formula> <math display="inline"> <semantics> <msubsup> <mrow></mrow> <mn>3</mn> <mo>+</mo> </msubsup> </semantics> </math> </inline-formula> groups and reduce the bare charge and zeta potential of the first dendrimer more strongly. It was demonstrated that these differences between dendrimers are due to the lower flexibility and the larger charge (+2) of each 2Lys spacers in comparison with 2Gly ones. The terminal CH<sub>2</sub><inline-formula></inline-formula> groups in both dendrimers move faster than the inner CH<sub>2</sub> groups. The calculated temperature dependencies of the spin-lattice relaxation times of these groups for both dendrimers are in a good agreement with the experimental results obtained by NMR.https://www.mdpi.com/2073-4360/12/8/1657peptide dendrimercomputer simulationmolecular dynamicsNMRspin-lattice relaxation timecharged macroion |
| spellingShingle | Sofia E. Mikhtaniuk Valeriy V. Bezrodnyi Oleg V. Shavykin Igor M. Neelov Nadezhda N. Sheveleva Anastasia V. Penkova Denis A. Markelov Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers Polymers peptide dendrimer computer simulation molecular dynamics NMR spin-lattice relaxation time charged macroion |
| title | Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers |
| title_full | Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers |
| title_fullStr | Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers |
| title_full_unstemmed | Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers |
| title_short | Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers |
| title_sort | comparison of structure and local dynamics of two peptide dendrimers with the same backbone but with different side groups in their spacers |
| topic | peptide dendrimer computer simulation molecular dynamics NMR spin-lattice relaxation time charged macroion |
| url | https://www.mdpi.com/2073-4360/12/8/1657 |
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