Exploring the Structural Properties of Positively Charged Peptide Dendrimers.

We report a combined experimental and computational approach to study the structural behavior of positively charged peptide dendrimers. Third-generation dendrimers containing combinations of positive/neutral amino acid residues in the different dendrimer generations were synthesized and their overall size evaluated using diffusion NMR. Molecular dynamics simulations were performed to obtain a comprehensive description of the molecular-level phenomena substantiating the structural differences observed.

Structuring Peptide Dendrimers through pH Modulation and Substrate Binding.

Dendrimers are a family of ramified synthetic molecules. pH effects and electrostatic interactions are known to be crucial players to explain the conformational and functional behaviors observed in these systems. Nonetheless, to date, no computational study involving these systems has explicitly addressed the protonation equilibrium taking place at different pH values for dendrimers containing multiple ionizable sites.

Unfolding the conformational behavior of peptide dendrimers: insights from molecular dynamics simulations.

We present here the first comprehensive structural characterization of peptide dendrimers using molecular simulation methods. Multiple long molecular dynamics simulations are used to extensively sample the conformational preferences of five third-generation peptide dendrimers, including some known to bind aquacobalamine. We start by analyzing the compactness of the conformations thus sampled using their radius of gyration profiles.