Effect of Arginine-Rich Peptide Length on the Structureand Binding Strength of siRNA–Peptide Complexes.

Heparindecomplexation experiments, as well as all-atom (AA) andcoarse-grained (CG) molecular dynamics (MD) simulations, were performedto determine the effect of the size of arginine(Arg)-rich peptideson the structure and binding strength of the siRNA–peptidecomplex. At a fixed peptide/siRNA mole ratio of 5:1 or 10:1, the siRNAcomplexes with peptides longer than nine Arg residues are more easilydecomplexed by heparin than are those with nine Arg residues. At thesemole ratios, peptides longer than nine Arg residues have cationic/anioniccharge ratios in excess of unity, and produce more weakly bound complexesthan nine Arg residue ones do. AA simulations of mixtures of peptideswith a single siRNA show formation of an electrostatically inducedcomplex, and the longer peptides produce a larger complex, but withno significant increase in the number of Arg residues bound to thesiRNA. Larger-scale CG-MD simulations show that multiple siRNAs canbe linked together by peptides into a large complex, as observed inthe experiments. The peptides longer than nine residues, which atmole ratio 5:1 yield a peptide/siRNA charge ratio in excess of unity,include many noninteracting Arg residues, which repel each other electrostatically.This leads to a less dense complex than for 9-residue peptides, whichcan explain why these longer complexes are more easily decomplexedby heparin molecules, as observed in the experiments. The key roleof the charge ratio is supported by simulations that show that, ata mole ratio of 2.5 peptides per siRNA, the longer 18-residue peptidehas a charge ratio of roughly unity and also shows a tight complex,just as the 9-residue peptide does at a 5:1 mole ratio, where itscharge ratio is also unity. [ABSTRACT FROM AUTHOR]