Short cell-penetrating peptides: a model of interactions with gene promoter sites

Bull Exp Biol Med. 2013 Jan;154(3):403-10. doi: 10.1007/s10517-013-1961-3.

Abstract

Analysis of the main parameters of molecular mechanics (number of hydrogen bonds, hydrophobic and electrostatic interactions, DNA-peptide complex minimization energy) provided the data to validate the previously proposed qualitative models of peptide-DNA interactions and to evaluate their quantitative characteristics. Based on these estimations, a three-dimensional model of Lys-Glu and Ala-Glu-Asp-Gly peptide interactions with DNA sites (GCAG and ATTTC) located in the promoter zones of genes encoding CD5, IL-2, MMP2, and Tram1 signal molecules.

MeSH terms

  • Base Sequence
  • Binding Sites
  • CD5 Antigens / genetics
  • Cell-Penetrating Peptides / metabolism
  • DNA / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins / analysis
  • Dipeptides / chemistry*
  • Dipeptides / metabolism
  • Interleukin-2 / genetics
  • Matrix Metalloproteinase 2 / genetics*
  • Membrane Glycoproteins / genetics*
  • Membrane Transport Proteins / genetics*
  • Molecular Sequence Data
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Peptide Fragments
  • Promoter Regions, Genetic*
  • Static Electricity

Substances

  • CD5 Antigens
  • Cell-Penetrating Peptides
  • DNA-Binding Proteins
  • Dipeptides
  • Interleukin-2
  • Membrane Glycoproteins
  • Membrane Transport Proteins
  • Oligopeptides
  • Peptide Fragments
  • TRAM1 protein, human
  • DNA
  • MMP2 protein, human
  • Matrix Metalloproteinase 2
  • lysylglutamic acid
  • alanyl-glutamyl-aspartyl-glycine