Aggregation-Induced Asymmetric Charge States of Amino Acids in Supramolecular Nanofibers

Abstract

Electrostatic interactions contribute critically to the kinetic pathways and thermodynamic outcomes of peptide selfassembly involving one or more than one charged amino acids. While it is well understood in protein folding that those amino acids with acidic/basic side chains could shift their pK a s when placed in a hydrophobic microenvironment, to what extent aggregation of monomeric peptide units from the bulk solution could alter their charged status and how this change in pK a values would reciprocally impact their assembly outcomes. Here, we design and analyze two solution systems containing peptide amphiphiles with hydrocarbon chains of different lengths to determine the factor of deprotonation on assembly. Our results suggest that models of supramolecular nanofibers with uniformly distributed, fully charged amino acids are oversimplified. We demonstrate, with molecular dynamics simulations, and validate with experimental results that asymmetric, different protonation states of the peptides lead to distinct nanostructures after self-assembly. The results give estimates on the electrostatic interactions in peptide amphiphiles required for their self-assembly and shed light on modeling molecular assembly systems containing charged amino acids.

Microscopically segregated ligand distribution in co-assembled peptide-amphiphile nanofibers

“…C 12 is the hydrocarbon hydrophobic core, V (valine) provides hydrogen bonds, hydrophobicity and E (glutamic acid) is negatively charged and hydrophilic. Our previous study shows that only the outer E of the PA is deprotonated or carries −1 e charge 32 in a self-assembled fiber. Keeping this in mind, we also model the inner glutamic acid as protonated.…”

“…GROMACS 2021.5 42 and MARTINI3 force field 33,43 are combined in the coarse-grained simulations. We used similar definitions of MARTINI3 beads for C12 as defined in our previous work 32 and mapped bond, angle parameters with all-atom simulation (see ESI†). Our previous work showed that Martini 3 would provide a similar fiber structure to CHARRM36 force-field.…”

Tips and Tricks in the Modeling of Supramolecular Peptide Assemblies

“…However, the highly condensed structures of SPAs involves additional challenges, such as the local p K a , which might differ from that in the bulk solution, leading to variations in the ionization of the amino acids . For instance, glutamic acids were found to be only partially charged at the surface of SPA nanofibers . Addressing these ionization variations requires constant-pH simulations, implemented in GROMACS, , NAMD, and AMBER .…”

“… 95 For instance, glutamic acids were found to be only partially charged at the surface of SPA nanofibers. 96 Addressing these ionization variations requires constant-pH simulations, implemented in GROMACS, 97 , 98 NAMD, 99 and AMBER. 100 However, given their high computational demand, large systems, such as SPA structures, are still challenging for constant-pH simulations.…”

Glucose‐Triggered Gelation of Supramolecular Peptide Nanocoils with Glucose‐Binding Motifs

“…It is also important to note that the expected pK a of amino acids and prosthetic motifs used to construct all of the MDPs here could shift as a result of their position on the peptide and/or due to aggregation-induced pK a shifts. [30,31] Efforts to quantify pK a values for the various ionizable groups in these peptides via titration did not yield precise measurements and instead suggested a range of charged states, likely due to a broadened charge distribution resulting from peptide assembly.…”