Nucleation fibril

A surface or interface can influence the assembly of fibrils by altering both the process and kinetics of fibril nucleation or elongation. This behavior is not surprising as surface properties are known to influence the absorption, confirmation, and destabilization of globular proteins or smaller peptides (Rocha et al., 2005). Surface properties influence fibril assembly in a similar way by altering the absorption, unfolding, and aggregation of monomers. 

There is certainly evidence that protein properties, including the propensity for fibril formation, influence fibril nucleation and growth on a surface. For example, the peptides Apl-40, Apl-42, and Apt-28 behave differently reflecting their different propensities to form fibrils (Losic et al., 2006). Apt-42 forms fibrils most readily, and Apl-42 fibrils are observed on both mica and HOPG (Kowalewski and Holtzman, 1999 Losic et al., 2006). In contrast, Apl-40 forms fibrils on HPOG but not mica, and Apl-28, the least prone to aggregation, forms fibrils on neither surface (Losic et al., 2006). 

Ultrahigh molecular weight polyethylene/liquid parafiin/dibenzylidene sorbitol ter-naiy blends were studied. Dibenzylidene sorbitol fibrils nucleated UHMWPE and induced the lamellae alignment perpendicular to the flow direction by which the pore size and water permeability and mechanical properties of membrane were enhanced. ... 

A (3 fibril formation an identifiable nucleating species has yet be isolated. Direct observation has been made difficult by the small size of the (3 peptide, which has an effective hydrodynamic radius of 4 nm [98-100], and by the apparent low abundance of nucleating species due to the low probability of their formation. Such species would be formally akin to an enzyme transition state that is usually kinetically inferred or sometimes trapped with certain kinds of inhibitor. In disaggregated, ultrafiltered (20 nm pore size) preparations, less than 1% of the molar peptide concentration is inferred to be present as seeds or nuclei determined by the kinetics of fibril formation [101]. 

Figure 4 Inhibition of nucleated fibril extension by Congo Red fibril... 

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. 

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

Figure 22 Schematic representation of proposed models for the fibril formation in the cases of pH 3.3 and 7.5. (A) hCT monomers in solution (B) a homogeneous association to form the a-helical bundle (micelle) (C) a homogeneous nucleation process to form the P-sheet and heterogeneous association process (D) a heterogeneous fibrillation process to grow a large fibril, a-helix, antiparallel p-sheet, and parallel p-sheet forms are shown by a box, drawn by dark grey and grey, respectively. From Ref. 163 with permission.

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. 

Critically, another important aspect of having heterogeneities is the formation of superstructures such as fibrils. Fibrils or any other structures based on silk crystallization will need heterogeneity to nucleate and grow. 

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 ... 

A comparable folding mechanism was found in silks. A seminal study by Li et al. (2001) found that in vitro formation of silk fibrils is conformation dependent and occurred via a nucleation mechanism. Although now established as amyloidogenic (Kenney et al., 2002), the nature of the silk fibril assembly remains unclear. Noteworthy is the evidence for a cross-nucleation ability of silk proteins, supporting the amyloidogenicity of silk (Lundmark et al., 2005). 

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. 

Blaschke, U. K., Eikenberry, E. F., Hulmes, D. J. S., Galla, H. J., and Bruckner, P. (2000). Collagen XI nucleates self-assembly and limits lateral growth of cartilage fibrils./. Biol. Chem. 275, 10370-10378. 

Fig. 11 Craze in commercial polystyrene showing the characteristic steps nucleation through void formation in a pre-craze zone, growth of the fibrillar structure of the widening craze by drawing-in of new matrix material in the process zone, and final breakdown of the fibrillar matter transforming a craze into a crack (the crack front is more advanced in the center of the specimen, shielded by a curtain of unbroken fibrils marked by the arrow). The fibril thickness depends—of course—on the molecular variables, the strain rate-stress-temperature regime of the crazing sample and on its treatment (preparation, annealing) and geometry (solid, thin film) for PS typical values of between 2.5 and 30 nm are found [1,60,61]...

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