Dynamics of locking of peptides onto growing amyloid fibrils

Abstract

Sequence-dependent variations in the growth mechanism and stability of amyloid fibrils, which are implicated in a number of neurodegenerative diseases, are poorly understood. We have carried out extensive all-atom molecular dynamics simulations to monitor the structural changes that occur upon addition of random coil (RC) monomer fragments from the yeast prion Sup35 and A␤-peptide onto a preformed fibril. Using the atomic resolution structures of the microcrystals as the starting points, we show that the RC 3 ␤-strand transition for the Sup35 fragment occurs abruptly over a very narrow time interval, whereas the acquisition of strand content is less dramatic for the hydrophobic-rich A␤-peptide. Expulsion of water, resulting in the formation of a dry interface between 2 adjacent sheets of the Sup35 fibril, occurs in 2 stages. Ejection of a small number of discrete water molecules in the second stage follows a rapid decrease in the number of water molecules in the first stage. Stability of the Sup35 fibril is increased by a network of hydrogen bonds involving both backbone and side chains, whereas the marginal stability of the A␤-fibrils is largely due to the formation of weak dispersion interaction between the hydrophobic side chains. The importance of the network of hydrogen bonds is further illustrated by mutational studies, which show that substitution of the Asn and Gln residues to Ala compromises the Sup35 fibril stability. Despite the similarity in the architecture of the amyloid fibrils, the growth mechanism and stability of the fibrils depend dramatically on the sequence.all-atom simulations ͉ amyloid growth dynamics ͉ growth mechanism of fibrils ͉ sequence-dependent addition process ͉ Sup35 and A␤-peptide A number of neurodegenerative diseases, such as Alzheimer's and Parkinson's diseases and transmissible prion disorders are associated with the formation of amyloid protein fibrils with a characteristic ␤-structure. In addition to proteins directly implicated in diseases, others that are unrelated by sequence or structure also form fibrils rich in ␤-sheet structure (1). These observations make it urgent to understand the molecular basis of amyloid fibril formation (1-3). The structures of the amyloid fibrils share a characteristic cross-␤ motif (4-7) with the peptides (or the proteins) forming extended ␤-strands that span the length of the fibril. Depending on the sequence, the strands in a given sheet are arranged in a parallel or antiparallel manner (8, 9) and lie perpendicular to the fibril axis. The near-universal morphology of the fibrils (without consideration of strains) suggests that the global mechanism that drives their formation from monomers may be similar (3). Indeed, several variations of the nucleated polymerization mechanism (NPM) have been used to account for amyloid fibril formation (10-12). According to the NPM, fluctuations (induced by denaturation stress, for example) lead to monomer conformations that can associate with other monomers to form fluid-like oligomers. If the size of the...

Kinetic theory of amyloid fibril templating

“…This is in agreement with simulations showing a very fast locking step when the register between the fibril and incoming molecule is correct. 47 On the other hand, it is also possible to envision a model that does allow a direct conversion from the docked state to the locked state. This would require a polypeptide to bind to the fibril end at multiple positions along its length separated by unbound coil regions.…”

Stepwise Organization of the β-Structure Identifies Key Regions Essential for the Propagation and Cytotoxicity of Insulin Amyloid Fibrils

“…The growing ends of seed fibrils are generally considered to behave like a template in the template-dependent self-propagation mechanism of amyloid fibrils, onto which precursor proteins attach and successively change their conformation to replicate the same template structure, referred to as the dock-lock model (43,44). Previous pre-steady state kinetic studies performed with Trp fluorescence (45) and H/D exchange com- bined with NMR analysis (46), and R 2 relaxation dispersion and transferred cross-saturation NMR experiments (47) have suggested the presence of short amino acid regions involving the formation of a transient monomer-seed complex within precursor proteins.…”

Replica exchange molecular dynamics of the thermodynamics of fibril growth of Alzheimer's Aβ42 peptide

“…21 The growth process has also been probed by various computational studies that study how monomers of Aβ-fragments add to preformed oligomers. [22][23][24][25][26][27] For instance, Buchete and Hummer 28 proposed from all-atom molecular dynamics simulations of Aβ 40 a three-step process, where strong hydrophobic interactions align the C-terminal segments of the incoming peptide with such in the fibril encoura) Electronic mail: minghan2000@gmail.com. b) Electronic mail: hansmann@mtu.edu.…”