Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics
ReviewProtein aggregation kinetics, mechanism, and curve-fitting: A review of the literature
Introduction
The aggregation1 of proteins such as amyloid-β, polyglutamine, α-synuclein, and prions has been suggested to be intimately associated with neurodegenerative disorders such as Alzheimer's [1], Huntington's [2], Parkinson's [3], and prion [4] diseases, respectively. Aggregation is also a nuisance in industrial applications where it can interfere with the production and characterization of therapeutic polypeptides [5]. Naturally occurring, productive protein aggregation is also important in nature in cases such as the protein fibrillation reaction of n(G-actin) → (F-actin)n, where G-actin is the globular, and F-actin the fibrillar form, of the protein actin.
For the purposes of this review, we will categorize protein aggregation into three classes: (i) naturally occurring, productive aggregation as in the n(G-actin) → (F-actin)n example mentioned. This reaction occurs throughout the human body, as well as in other organisms, and is necessary in controlling the mobility and shape of the cells [6]. Another example of naturally occurring protein aggregation includes the enzyme glutamate dehydrogenase [7], [8], [9], [10]. Both actin and glutamate dehydrogenase function with aggregation of a protein in its native state. A second class of aggregation phenomenon can be classified as (ii) unwanted aggregation in biology. This class includes α-synuclein, amyloid β, polyglutamine, and prions as common examples of proteins that aggregate and are suspected to play a key role in the neurodegenerative diseases Parkinson's [3], Alzheimer's [1], Huntington's [2], and prion [4] diseases, respectively. This type of aggregation is generally believed to involve aggregation of the protein in a non-native state (vide infra). The final class of aggregation phenomenon is (iii) unwanted aggregation in an industrial setting. This class of aggregation usually produces amorphous aggregates and its control and understanding is important to the biotechnology industry for keeping proteins in a non-aggregated, bottleable, long-shelf-life form [11].
Because of its importance, the kinetics and mechanism of protein aggregation have been of interest for approximately fifty years [12]. Protein aggregation is, therefore, a topic that has been the subject of numerous other recent reviews, although from perspectives different than herein [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25], [26]. Of particular interest is the excellent and critical review on the detailed steps of protein aggregation recently published by C. J. Roberts [14], as well as a review on entropy-driven polymerization of proteins by M. A. Lauffer [26]. However, still missing in our opinion among the available reviews of the expansive protein aggregation literature is an analysis and review focusing on models that can fit kinetic data, give useful, quantitative rate constants, and ideally provide mechanistic insight. Key questions to be answered herein include: (i) How many distinct mechanisms actually exist in the literature for protein aggregation? (ii) What is the essence of each mechanism? (iii) Which mechanisms or models have been used to curve-fit kinetic data? (iv) Do any of these mechanisms have similarities to each other? Also, (v) which of the terms used in the sometimes confusing nomenclature2 in the protein aggregation literature have the same meaning? These are some of the key questions we hope to answer herein. In short, a main goal of the present contribution is to analyze and report the primary (in our opinion) literature contributions to protein aggregation kinetics, mechanism, and curve-fitting.
In what follows we have tried to identify key papers in terms of the 5 main classes (vide infra) of mechanistic models in the literature, and to trace each (class of) mechanism back to its earliest origins. Our goal is to distill the literature to its essential components, again in our view. We apologize in advance to the authors of literature we were not able to cover in the space available or have somehow inadvertently missed.
We begin with a brief survey of the physical methods used to measure protein aggregation noting whether the methods are direct or indirect, in-situ or ex-situ, and whether the method is able to measure kinetics. Next, we discuss what is known about the starting proteins, products, and intermediates of protein aggregation—since knowing one's products and intermediates is key to rigorous mechanistic science. Third, we tabulate and discuss the main thermodynamic and kinetic based studies we have found that support what turns out to be the 5 main classes of suggested mechanisms of protein aggregation, all in a somewhat historical order. We also briefly discuss empirical approaches that have been used to fit protein aggregation kinetic data. We end with a discussion of what seems to be some of the common pitfalls in attacking the highly complex problem of the mechanism(s) of protein aggregation. We also list some of the important unsolved problems and hence needed future research directions, and then conclude with a Summary and Conclusions section of the highlights of this review.
Section snippets
Advantages and disadvantages of the physical methods used to monitor protein aggregation
The kinetics and products of protein aggregation have been measured using at least 18 different analytical techniques, each having its own intrinsic advantages and disadvantages. Each technique is summarized in Table 1 and discussed in more detail in the Supporting information. The interested reader is also referred to the recent, excellent review by S. E. Bondos that compares the various methods used to detect protein aggregation, with an emphasis on the concentration and volume ranges for
Starting proteins, products, and detectable intermediates of protein aggregation
It has long been known that “know your product(s)” is the first rule of rigorous mechanistic science, since the steps in any proposed mechanism must add up to those observed products. We review, therefore, what is generally known vs. not known about the starting proteins, products, and any detectable intermediates of protein aggregation when fibrils are formed, as this category involves many important studies of (native and non-native) protein aggregation. While a main goal of this review is to
Thermochemistry of protein aggregation
The aggregation of many biologically important proteins including, but not limited to, tobacco mosaic virus, tubulin, sickle cell hemoglobin, collagen, actin, myosin, flagellin, glutamate dehydrogenase, and α-chymotrypsin have been shown to exhibit a positive enthalpy and entropy [26], [74]. We refer the readers to the scholarly work contained in references [26] and [74] for the quantitative ΔH° and ΔS° values. The positive enthalpy (i.e., endothermic nature) has been verified by calorimetry
Approaches to determine the kinetics and mechanism of protein aggregation
As Scheme 2 illustrates, many approaches exist in the literature for determining the kinetics and mechanism of protein aggregation. Kinetic, thermodynamic, empirical, or other approaches can provide useful information depending upon what one is trying to obtain from the analysis. Herein, we are most interested in being able to curve-fit kinetic data and extract useful information from that data—kinetics being a required part of reliable mechanistic studies. Therefore, the majority of what
Three problem areas in the protein aggregation kinetic and mechanistic literature
One must ask, why has such an important question, as ‘what are the mechanism(s) of protein aggregation?’, yet to be unequivocally answered despite the numerous contributions cited herein? The simple answer is that protein aggregation is a highly complex problem with complicated molecular level and kinetic details, along with associated complex mathematics. In hopes of moving this area forward, we list a few possible problem areas of importance, in our opinion, for future studies in protein
Summary and conclusions
Despite the importance of the problem and the nearly 50 years of research aimed at determining the mechanism(s) and rate constant(s) for protein aggregation, many questions still remain. Frieden concisely summarizes the state of affairs in his recent review: “In spite of the extensive literature, however, the mechanism of [protein] aggregation is poorly understood” [16]. The focus of the present review has been to examine the protein aggregation literature from the perspective of trying to fit
Acknowledgements
We thank Mr. Steve Hays for his graphic design of the schematic fibril pictured in Scheme 1. We also thank Professors Eric D. Ross and Jeffrey N. Agar for providing their insightful comments on the manuscript. Finally, we gratefully acknowledge NSF grant #0611588 for partial support of this project.
References (163)
- et al.
Alzheimer's disease
Lancet
(2006) - et al.
Parkinson's disease: mechanisms and models
Neuron
(2003) Mechanism of bovine liver glutamate dehydrogenase self-assembly: II. Simulation of relaxation spectra for an open linear polymerization proceeding via a sequential addition of monomer units
J. Mol. Biol.
(1975)- et al.
Mechanism of bovine liver glutamate dehydrogenase self-association I. Kinetic evidence for a random association of polymer chains
J. Mol. Biol.
(1975) - et al.
Mechanism of bovine liver glutamate dehydrogenase self-assembly III. Characterization of the association–dissociation stoichiometry with quasi-elastic light scattering
J. Mol. Biol.
(1976) - et al.
Self-assembly and aggregation of proteins
Curr. Opin. Colloid Interface Sci.
(2007) Kinetics of amyloid formation and membrane interaction with amyloidogenic proteins
Biochim. Biophys. Acta
(2007)For protein misassembly, it's the “I” decade
Cell
(1996)- et al.
Evidence for a partially folded intermediate in α-synuclein fibril formation
J. Biol. Chem.
(2001) - et al.
Conformational constraints for amyloid fibrillation: the importance of being unfolded
Biochim. Biophys. Acta
(2004)
Common core structure of amyloid fibrils by synchrotron X-ray diffraction
J. Mol. Biol.
Biophys. J.
Three-dimensional reconstruction of the 14-filament fibers of hemoglobin S
J. Mol. Biol.
The high resolution crystal structure of deoxyhemoglobin S
J. Mol. Biol.
Hierarchical structures of fibrillar collagens
Micron
Competing pathways determine fibril morphology in the self-assembly of beta(2)-microglobulin into amyloid
J. Mol. Biol.
Mechanism of protein fibril formation: nucleated polymerization with competing off-pathway aggregation
Biophys. J.
α-Synuclein, especially the Parkinson's disease-associated mutants, forms pore-like annular and tubular protofibrils
J. Mol. Biol.
Characterization of oligomeric intermediates in α-synuclein fibrillation: FRET studies of Y125W/Y133F/Y136F α-synuclein
J. Mol. Biol.
Annular oligomeric amyloid intermediates observed by in situ atomic force microscopy
J. Biol. Chem.
A general model for amyloid fibril assembly based on morphological studies using atomic force microscopy
Biophys. J.
Kinetics and mechanism of amyloid formation by the prion protein H1 peptide as determined by time-dependent ESR
Chem. Biol.
Formation of critical oligomers is a key event during conformational transition of recombinant Syrian hamster prion protein
J. Biol. Chem.
Time-resolved infrared spectroscopy of pH-induced aggregation of the Alzheimer Aβ1–28 peptide
J. Mol. Biol.
The cooperative nature of G–F transformation of actin
Biochim. Biophys. Acta
A theory of linear and helical aggregations of macromolecules
J. Mol. Biol.
Size distribution of protein polymers
J. Theor. Biol.
A simple model of the reaction between polyadenylic acid and polyuridylic acid
Biochem. Biophys. Res. Commun.
Kinetics of the cooperative association of actin to actin filaments
Biophys. Chem.
The kinetics of actin nucleation and polymerization
J. Biol. Chem.
On one-dimensional nucleation and growth of “living” polymers II. Growth at constant monomer concentration
J. Theor. Biol.
Cooperative polymerization reactions: analytical approximations, numerical examples, and experimental strategy
Biophys. J.
Prionics or the kinetic basis of prion diseases
Biophys. Chem.
The polyglutamine diseases
Molecular biology of prion diseases
Science
A false paradise — mixed blessings in the protein universe: the amyloid as a new challenge in drug development
Curr. Med. Chem.
Actin is a polar, self-assembling, dynamic polymer
Glutamate dehydrogenase: anatomy of a regulatory enzyme
Acc. Chem. Res.
Kinetics of irreversible protein aggregation: analysis of extended Lumry–Eyring models and implications for predicting protein shelf life
J. Phys. Chem. B
G–F transformation of actin as a fibrous condensation
J. Polym. Sci.
Aβ oligomers. A decade of discovery
J. Neurochem.
Non-native protein aggregation kinetics
Biotechnol. Bioeng.
Protein misfolding and aggregation
Biotechnol. Prog.
Protein aggregation processes: in search of the mechanism
Protein Sci.
Theoretical approaches to protein aggregation
Protein Pept. Lett.
Amyloid fibrils from the viewpoint of protein folding
Cell. Mol. Life Sci.
Soluble protein oligomers as emerging toxins in Alzheimer's and other amyloid diseases
Life
Prevention of amyloid-like aggregation as a driving force of protein evolution
EMBO Rep.
Neurodegenerative aspects of protein aggregation
Acta Neurobiol. Exp.
Insights into the amyloid folding problem from solid-state NMR
Biochemistry
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