TY - JOUR

T1 - Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers

AU - Mikhtaniuk, Sofia E.

AU - Bezrodnyi, Valeriy V.

AU - Shavykin , Oleg V.

AU - Neelov, Igor M.

AU - Sheveleva , Nadezhda N.

AU - Penkova , Anastasia V.

AU - Markelov, Denis A.

N1 - Publisher Copyright: © 2020 by the authors.

PY - 2020/8

Y1 - 2020/8

N2 - 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 +3 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 2 groups in both dendrimers move faster than the inner CH 2 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.

AB - 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 +3 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 2 groups in both dendrimers move faster than the inner CH 2 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.

KW - peptide dendrimer

KW - computer simulation

KW - molecular dynamics

KW - NMR

KW - spin-lattice relaxation time

KW - charged macroion

KW - Zeta Potential

KW - Computer simulation

KW - Charged macroion

KW - Molecular dynamics

KW - Zeta potential

KW - Spin-lattice relaxation time

KW - Peptide dendrimer

KW - LATTICE NMR RELAXATION

KW - MOLECULAR-DYNAMICS

KW - BEAD-ROD MODEL

KW - zeta potential

KW - BROWNIAN DYNAMICS

KW - IN-VITRO

KW - POLY-L-LYSINE

KW - COMPUTER-SIMULATION

KW - ANTICANCER SIRNA COCKTAILS

KW - BIOLOGICAL-PROPERTIES

KW - ELONGATIONAL FLOW

UR - http://www.scopus.com/inward/record.url?scp=85089467908&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/da050eea-438f-3f1f-a36a-3fe55629c673/

U2 - https://doi.org/10.3390/polym12081657

DO - https://doi.org/10.3390/polym12081657

M3 - Article

VL - 12

JO - Polymers

JF - Polymers

SN - 2073-4360

IS - 8

M1 - 1657

ER -