Charge effects on the fibril-forming peptide KTVIIE: a two-dimensional replica exchange simulation study

Abstract

The assembly of peptides into ordered nanostructures is increasingly recognized as both a bioengineering tool for generating new materials and a critical aspect of aggregation processes that underlie neurological diseases such as Alzheimer's disease, Parkinson's disease, and Huntington's disease. There is a major problem in understanding how extremely subtle sequence changes can lead to profound and often unexpected differences in self-assembly behavior. To better delineate the complex interplay of different microscopic driving forces in such cases, we develop a methodology to quantify and compare the propensity of different peptide sequences to form small oligomers during early self-assembly stages. This umbrella-sampling replica exchange molecular dynamics method performs a replica exchange molecular dynamics simulation along peptide association reaction coordinates using umbrella restraints. With this method, we study a set of sequence-similar peptides that differ in net charge: K(+)TVIIE(-), K(+)TVIIE, and (+)K(+)TVIIE. Interestingly, experiments show that only the monovalent peptide, K(+)TVIIE, forms fibrils, whereas the others do not. We examine dimer, trimer, and tetramer formation processes of these peptides, and compute high-accuracy potential of mean force association curves. The potential of mean forces recapitulate a higher stability and equilibrium constant of the fibril-forming peptide, similar to experiment, but reveal that entropic contributions to association free energies can play a surprisingly significant role. The simulations also show behavior reminiscent of experimental aggregate polymorphism, revealed in multiple stable conformational states and association pathways. Our results suggest that sequence changes can have significant effects on self-assembly through not only direct peptide-peptide interactions but conformational entropies and degeneracies as well.

Figure 1

Normalized PMF (top), average energy (middle), and entropy (bottom) curves for dimerization (left), trimerization (middle), and tetramerization (left) processes. p indicates associations involving one or two performed parallel dimers, whereas a that of antiparallel dimers. All curves are computed using the WHAM technique applied to the REMD simulation data and shifted to zero at a great distance. Block-average statistical errors of each curve around the binding regime are <0.5 kcal/mole, 1.2 kcal/mole, and 2.4 kcal/mole for normalized PMF, average energy, and entropy, respectively (error bars not shown to maintain clarity). The bumps in the PMF curves are reproducible, and are actually due to discreet shifts in hydrogen bond alignment and breaking as peptides associate or are pulled apart.

Figure 2

Direct and solvation electrostatic energies with respect to distance (shifted to zero at complete dissociation). The panels correspond to dimerization (top), trimerization from an antiparallel dimer and monomer (middle), and trimerization from a parallel dimer and monomer (bottom).

Figure 3

2D contour plots of PMFs with respect to the interchain distance (between chain centroids) and interchain orientation (cosine angle between vectors connecting the end residues of each chain). Normalized PMFs are used and shifted to zero at far distances. The top row is for the zwitterionic peptides, and the bottom row is for the monovalent ones. Colors indicate free energy values in kcal/mol. The arrows on the right point toward the parallel (P) and antiparallel (A) orientations.

Figure 4

Hierarchy of oligomerization of the (A) zwitterionic and (B) monovalent peptide. Blue arrows are peptides and the percentages show the relative frequency of alignment motifs for the given mechanism. Only simulated reaction paths have the clustered percentages written above the lines, which are calculated using 2D PMF contour plots. Black dotted lines indicate the addition of monomer, green dotted lines indicate the addition of an antiparallel dimer, and orange dotted lines indicate the addition of a parallel dimer.