Two-Step Mechanism of Homogeneous Nucleation of Sickle Cell Hemoglobin Polymers

Galkin, Oleg; Pan, Weichun; Filobelo, Luis; Hirsch, Rhoda Elison; Nagel, Ronald L.; Vekilov, Peter G.

doi:10.1529/biophysj.106.103705

Cited by 107 publications

(131 citation statements)

References 76 publications

(104 reference statements)

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“…We stress that, although the oligomers that form because of attractive nonspecific interactions are rare (and therefore, hard to observe directly), their formation is a crucial onpathway step in the amyloid formation process for peptides with a β-competent state that is not particularly stable. Similar 2SN processes involving amorphous precursors have been identified in very different physical phenomena, such as protein crystal nucleation (67), nucleation of sickle cell hemoglobin polymers (68), and biomineralization (69). The surprising finding of this work is that, at realistic (i.e., low) peptide concentrations, fibril formation must proceed through an intermediate amorphous oligomer and that this pathway leads to highly nontrivial predictions for the dependence of the critical nucleus size and nucleation barrier on monomer concentration and interpeptide interaction.…”

Section: Discussionmentioning

confidence: 57%

Crucial role of nonspecific interactions in amyloid nucleation

Šarić

Chebaro

Knowles

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

172

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Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical onestep nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet-rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.amyloid | protein aggregation | protein oligomers | neurodegeneration | coarse-grained simulations D uring the process of amyloid formation, normally soluble proteins assemble into fibrils that are enriched in β-sheet content and have diameters of a few nanometers and lengths up to several micrometers. This phenomenon has been implicated in a variety of pathogenic processes, including Alzheimer's and Parkinson's diseases, type 2 diabetes, and systemic amyloidoses (1-3). The association with human diseases has largely motivated a long-standing effort to probe the assembly process, and numerous studies have aimed at elucidating the mechanism of amyloid aggregation (4). The basic nature of the aggregation reaction has emerged as a nucleation and growth process (5, 6), where the aggregates are created through a not well-understood primary nucleation event and can grow by recruiting additional peptides or proteins to their ends (7,8). In this paper, we focus on the nature of this primary step in amyloid nucleation and the fundamental initial events that underlie amyloid formation.Amyloidogenic peptides and proteins, when in their nonpathological cellular form, can range in the structures from mainly α-helical to β-sheet and even random coil, whereas the amyloid forms of proteins possess a generic cross-β-structure ...

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Section: Discussionmentioning

confidence: 57%

Crucial role of nonspecific interactions in amyloid nucleation

Šarić

Chebaro

Knowles

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

172

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“…The procedure for determination of the fiber growth rate, R, from sequences of images of the evolution of HbS polymerization and other experimental details are discussed in Ref. 13. In the same article, it was shown that due to the slow diffusive supply of HbS molecules from the solution to the growing end of a fiber, the average growth rate of the HbS fibers is reduced, 14 in comparison to the case of oversupply of material, by a factor κ ≈ 3.…”

Section: Kinetic Model Of Hbs Polymer Fiber Growthmentioning

confidence: 99%

Determination of the Transition-State Entropy for Aggregation Suggests How the Growth of Sickle Cell Hemoglobin Polymers can be Slowed

Vekilov

Pettitt

Choudhury

et al. 2008

Journal of Molecular Biology

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Sickle cell anemia is associated with the mutant hemoglobin HbS, which forms polymers in red blood cells of patients. The growth rate of the polymers is several micrometers per second, ensuring that a polymer fiber reaches the walls of an erythrocyte (which has a 7-μm diameter) within a few seconds after its nucleation. To understand the factors that determine this unusually fast rate, we analyze data on the growth rate of the polymer fibers. We show that the fiber growth follows a first-order Kramerstype kinetics model. The entropy of the transition state for incorporation into a fiber is 95 J mol −1 K −1 , very close to the known entropy of polymerization. This agrees with a recent theoretical estimate for the hydrophobic interaction and suggests that the gain of entropy in the transition state is due to the release of the last layer of water molecules structured around contact sites on the surface of the HbS molecules. As a result of this entropy gain, the free-energy barrier for incorporation of HbS molecules into a fiber is negligible and fiber growth is unprecedentedly fast. This finding suggests that fiber growth can be slowed by components of the red cell cytosol, native or intentionally introduced, which restructure the hydration layer around the HbS molecules and thus lower the transition state entropy for incorporation of an incoming molecule into the growing fiber.

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“…Contrary to the "nucleation theory", these phases are assumed to be stable and already exhibit the final crystal structure. After additional aggregation "postcritical nuclei" are built which form the basis for further crystal growth (Galkin et al 2007;Vekilov 2010b). Under normal gravity, the necessary transport of the building units (ions or molecules) occurs via diffusion and convection.…”

Section: Introductionmentioning

confidence: 99%

Early Hydration of Portland Cement Admixed with Polycarboxylates Studied Under Terrestric and Microgravity Conditions

Lei

Meier

Rinkenburger

et al. 2016

ACT

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The crystallization of ettringite at very early cement hydration (hydration period ~ 10 s) was studied under normal and zero gravity condition utilizing SEM microscopy. Furthermore, the impact of two polycarboxylate superplasticizers (one methacrylate ester-, one methallyl ether -based) on ettringite crystallization was investigated. It was found that under microgravity attained on parabolic flights, generally smaller, but a larger amount of ettringite crystals is formed resulting from the absence of convection and ion diffusion limited crystal growth. Furthermore, the PCE polymers were found to act as morphological catalysts for ettringite even under zero gravity condition.

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Two-Step Mechanism of Homogeneous Nucleation of Sickle Cell Hemoglobin Polymers

Cited by 107 publications

References 76 publications

Crucial role of nonspecific interactions in amyloid nucleation

Crucial role of nonspecific interactions in amyloid nucleation

Determination of the Transition-State Entropy for Aggregation Suggests How the Growth of Sickle Cell Hemoglobin Polymers can be Slowed

Early Hydration of Portland Cement Admixed with Polycarboxylates Studied Under Terrestric and Microgravity Conditions

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