Method for determining the chirality sign of peptide nanotubes using the dipole moments vectors calculations

  • Vladimir Bystrov Institute of Mathematical Problems of Biology, Keldysh Institute of Applied Mathematics, RAS, 142290 Pushchino, Moscow region, Russia
  • Alla Sidorova Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
  • Aleksei Lutsenko Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
  • Denis Shpigun Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
  • Vsevolod Tverdislov Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia
  • Pavel Zelenovskiy School of Natural Sciences and Mathematics, Ural Federal University, Ekaterinburg 620000, Russia; Department of Physics & CICECO - Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
  • Svitlana Kopyl Department of Physics & CICECO - Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
  • Andrei Kholkin Department of Physics & CICECO - Aveiro Institute of Materials, University of Aveiro, 3810-193 Aveiro, Portugal
DOI: https://doi.org/10.34624/nmse.v3i1.23956
Keywords: proteins, amino acids, dipeptides, peptide nanotubes, helices, dipole moment

Abstract

In this work the method for calculating the index and sign of chirality using the values of the dipole moments of each individual dipeptides forming a helix structure of a peptide nanotube is proposed.

Calculations of the individual dipeptide dipole moments using semi-empirical quantum method PM3 and force field method Amber are preformed in the frame of HyperChem software package.

Results obtained for diphenylalnine (FF) peptide nanotube (PNT) with two different initial chirality L-FF and D-FF shows correct results of the chirality changes on D and L for helical PNT, corresponding to the law of the change in the sign of chirality, when the hierarchical structure of the molecular system becomes more complex. 

The results obtained give us a new opportunity to see the physical basis for the formation of the type and sign of chirality and open up new possibilities for a quantitative study of this phenomenon. This approach can be applied to other similar structures and peptide nanotubes based on other amino acids and dipeptides.

Published
2021-03-17
Issue
Vol 3 No 1 (2021): Nanomaterials Science & Engineering
Section
Articles

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