Thermodynamic Selection of Steric Zipper Patterns in the Amyloid Cross-β Spine

Abstract

At the core of amyloid fibrils is the cross-β spine, a long tape of β-sheets formed by the constituent proteins. Recent high-resolution x-ray studies show that the unit of this filamentous structure is a β-sheet bilayer with side chains within the bilayer forming a tightly interdigitating “steric zipper” interface. However, for a given peptide, different bilayer patterns are possible, and no quantitative explanation exists regarding which pattern is selected or under what condition there can be more than one pattern observed, exhibiting molecular polymorphism. We address the structural selection mechanism by performing molecular dynamics simulations to calculate the free energy of incorporating a peptide monomer into a β-sheet bilayer. We test filaments formed by several types of peptides including GNNQQNY, NNQQ, VEALYL, KLVFFAE and STVIIE, and find that the patterns with the lowest binding free energy correspond to available atomistic structures with high accuracy. Molecular polymorphism, as exhibited by NNQQ, is likely because there are more than one most stable structures whose binding free energies differ by less than the thermal energy. Detailed analysis of individual energy terms reveals that these short peptides are not strained nor do they lose much conformational entropy upon incorporating into a β-sheet bilayer. The selection of a bilayer pattern is determined mainly by the van der Waals and hydrophobic forces as a quantitative measure of shape complementarity among side chains between the β-sheets. The requirement for self-complementary steric zipper formation supports that amyloid fibrils form more easily among similar or same sequences, and it also makes parallel β-sheets generally preferred over anti-parallel ones. But the presence of charged side chains appears to kinetically drive anti-parallel β-sheets to form at early stages of assembly, after which the bilayer formation is likely driven by energetics.

Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations

“…29 The promiscuous polymorphism found for amyloid aggregates 17,18,84 may also be explained by the thermodynamic selection of the most stable steric zipper motif in the nucleus. 27,86 The observed initial hydrophobic collapse of the peptides is an early event in the oligomerization and therefore not rate limiting for the nucleation, as deduced from simulations 51 and experiments. 26,27 In line with the present findings, this might suggest a mechanistic continuum for amyloidogenic aggregation with the principal characteristics of a condensation-ordering mechanism.…”

Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers

“…Polymorphs of NNQQ are observed to form in microcrystals and this supports the notion that short amyloid protein segments are prone to kinetically driven aggregation. [41][42][43] In summary, we show that our CME-based formalism -using transition likelihood maximization and TBA assignment -can be coupled with enhanced sampling REMD simulations with explicit water molecules to characterize the kinetics of dimer formation of short NNQQ amyloid-forming peptides. Importantly, the extracted temperature-dependent kinetic mechanism does not rely on any assumption regarding the functional form (e.g., Arrhenius or not) of the transition rates.…”

Yeast Cell Adhesion Molecules Have Functional Amyloid-Forming Sequences

“…These protein aggregates can also occur naturally in adhesive bacterial curli (3), melanosomes (14), condensed peptide hormone arrays (24), as regulatory prions in yeast (2,5), and fungal hydrophobins, which are nonantigenic coats to some fungi (1,33,39). Nevertheless, such natural occurrences are relatively few, considering the negative free energy for amyloid formation (28).…”