Amyloid fibril nucleation

Jarrett JT, Lansbury PT Jr. Amyloid fibril formation requires a chemically discriminating nucleation event studies of an amyloidogenic sequence from the bacterial protein OsmB. Biochemistry 1992 31 12345-12352. 

The model of amyloid fibril formation is a nucleation step followed by growth, where the nucleation mechanism dictates the concentration and time dependence of the aggregation (Harper and Lansbury, 1997 ... 

Paul van der Schoot, Nucleation and Co-Operativity in Supramolecular Polymers Michael J. McPherson, Kier James, Stuart Kyle, Stephen Parsons, and Jessica Riley, Recombinant Production of Self-Assembling Peptides Boxun Leng, Lei Huang, and Zhengzhong Shao, Inspiration from Natural Silks and Their Proteins Sally L. Gras, Surface- and Solution-Based Assembly of Amyloid Fibrils for Biomedical and Nanotechnology Applications... 

Our study shows that UV exposure of prion protein, P2-microglobulin and a-synuclein leads to loss of ability of these proteins to form amyloid fibrils de novo. However, they retained the ability to elongate the fibrils when provided with preformed fibrils as seeds. Thus, UV exposure selectively compromises the ability to nucleate fibril growth. 

Two basic models have been proposed for amyloid fibril formation from the intermediates.In the nucleation model, the intermediates cluster to form nuclei. Fibril is formed from the nucleus after the nucleus has reached a critical size. Such fibrils add on to its ends to form aggregates. In the polymerization model, intermediate peptide-PF complexes are formed and associate end to end or laterally to form fibrils. 

Fig. 11.20 The concept of switch-peptides [207,208] in situ induction of conformational changes by enzyme-triggered acyl migration results in the nucleation of a helix (left) or a c/s-amide bond-induced kink conformation (right) for the breaking of/i-sheet templates (e.g. amyloid fibrils).

Kinetic analyses in the absence of denaturants provided evidence that the conversion process can be separated into two stages, first the binding of PrP-sen to PrP and then a slower conversion of the bound PrP-sen to PrP-res (Bessen et al, 1997 DebBurman et al, 1997 Horiuchi et al, 1999). These observations, and the formation of amyloid fibril polymers by PrP-res, are consistent with an autocatalytic or templated nucleated polymerization mechanism. However, the fact that PrP-res usually induces the conversion of only substoichiometric quantities of PrP-sen in current cell-free reactions makes the reaction less continuous than typical nucleated polymerizations of proteins or peptides. This may be a technical problem rather than a fundamental limitation of the reaction mechanism. On the other hand, since PrP-res forms continuously for long periods of time in vivo, there may be important elements of the mechanism, such as cofactors or microenvironments, that remain to be elucidated (DebBurman et al, 1997 Saborio etal, 1999). 

Lomakin A, Chung DS, Benedek GB, Kirschner DA, Teplow DB. On the nucleation and growth of amyloid beta protein fibrils detection of nuclei... 

They have many of the morphological and ultrastructural characteristics of disease filaments [11, 12] (Fig. 45-5). Assembly is a nucleation-dependent process that occurs through its amino-terminal repeats. The carboxy-terminal region, in contrast, is inhibitory. Assembly is accompanied by the transition from random coil to a [3-pleated sheet. By electron diffraction, a-synuclein filaments show a conformation characteristic of amyloid fibers. Under the conditions of these experiments, P- and y-synucleins failed to assemble, consistent with their absence from the filamentous lesions of the human diseases. When incubated with a-synuclein, P- and y-synucleins inhibit the fibrillation of a-synuclein, suggesting that they may indirectly influence the pathogenesis of Lewy body diseases and multiple system atrophy. 

Lomakin, A., Chung, D. S., Benedek, G. B., Kirschner, D. A., and Teplow, D. B. (1996). On the nucleation and growth of amyloid beta-protein fibrils Detection of nuclei and quantitation of rate constants. Proc. Natl. Acad. Sci. USA 93, 1125-1129. 

Jiang, Y., Li, H., Zhu, L., Zhou, J. M., and Perrett, S. (2004). Amyloid nucleation and hierarchical assembly of Ure2p fibrils. Role of asparagine/glutamine repeat and nonrepeat regions of the prion domains./. Biol. Chem. 279, 3361-3369. 

The threshold concentration of monomer that must be exceeded for any observable polymer formation in a self-assembling system. In the context of Oosawa s condensation-equilibrium model for protein polymerization, the cooperativity of nucleation and the intrinsic thermodynamic instability of nuclei contribute to the sudden onset of polymer formation as the monomer concentration reaches and exceeds the critical concentration. Condensation-equilibrium processes that exhibit critical concentration behavior in vitro include F-actin formation from G-actin, microtubule self-assembly from tubulin, and fibril formation from amyloid P protein. Critical concentration behavior will also occur in indefinite isodesmic polymerization reactions that involve a stable template. One example is the elongation of microtubules from centrosomes, basal bodies, or axonemes. 

Lansbury and his group have shown that amyloid formation is a nucleation-dependent process and that the nucleation step can be evaded by using seeds of preformed fibrils. The nucleation process is a rate-limiting step in amy-loidogenesis. ft is characterized by a lag phase. During the time required for nucleus formation, the protein appears to be soluble. Nucleus formation requires a series of association steps that are thermodynamically unfavorable because the resultant intermolecular interactions do not outweigh the entropic cost of association [60]. Once the nucleus has formed, further addition of monomers becomes thermodynamically favorable. The nucleation is concentration dependent [61] and shows the presence of hydrophobic cooperativity in the process [62]. 

The actual mechanism of self-association of monomeric protein into amyloid is complex and three mechanisms of stmcture conversion have been proposed (32) In templated assembly, a monomeric native state peptide binds to an existing nucleus. Upon binding, there is a change in the secondary stmcture of the monomer as it is added to the growing chain. Monomer directed conversion involves the presence of a misfolded monomer that templates the stmcture conversion of a native monomer, followed by disassociation and chain formation. The third model is nucleated polymerization, which is the most widely accepted model for the fibril growth. 

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