Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides
Abstract

The presence of surfaces influences the fibril formation kinetics of peptides and proteins. We present a systematic study of the aggregation kinetics of amyloidogenic peptides caused by different surfaces using molecular simulations of model peptides and thioflavin T fluorescence experiments. Increasing the monomer–surface attraction affects the nucleation and growth of small oligomers in a nonlinear manner: Weakly attractive surfaces lead to retardation; strongly attractive surfaces lead to acceleration. Further, the same type of surface either accelerates or retards growth, depending on the bulk propensity of the peptide to form fibrils: An attractive surface retards fibril formation of peptides with a high tendency for fibril formation, while the same surface accelerates fibril formation of peptides with a low propensity for fibril formation. The surface effect is thus determined by the relative association propensity of peptides for the surface compared to bulk and by the surface area to protein concentration ratio. This rationalization is in agreement with the measured fibrillar growth of α-synuclein from Parkinson and amyloid β peptide from Alzheimer disease in the presence of surface area introduced in a controlled way in the form of nanoparticles. These findings offer molecular insight into amyloid formation kinetics in complex environments and may be used to tune fibrillation properties in diverse systems.
Introduction
Methods
Dynamic Monte Carlo Simulation
Figure 1

Figure 1. (Left) Two-state peptide model used in dynamic Monte Carlo simulations in the presence of planar surfaces (green). Kinetic and thermodynamic properties are described by the parameters (i) → (iv), discussed in the section “Surface Effect for Peptide Mutants”, as well as through a surface attraction strength, K (Table 1). (Right) Representative snapshot from our simulation where orange/gray are particles in the fibril state, while blue/red particles are in the random coil state.

Figure 2

Figure 2. Interaction energy between a weakly attractive surface (WA) and the α state of the peptide. The left figure depicts the distance dependence of the interaction when PSC is parallel to the wall oriented with its patch toward the wall. The right figure displays the orientation dependence of the interaction when PSC is parallel to the wall in distance close to the interaction minimum.
Kinetic Experiments
Materials
Preparation of Samples for Experiments
Kinetic Assays
Results and Discussion
Effect of Wall Binding Strength
surface type | K/μM–1 | |
---|---|---|
repulsive | R | ∼0 |
weakly attractive | WA | 0.0017 |
attractive | A | 0.075 |
highly attractive | HA | 0.16 |
Figure 3

Figure 3. (Top) Oligomer growth profiles in the presence of planar surfaces with increasing binding strengths (see Table 1) and monomer concentration (colored lines). Each profile represents an average from at least three independent simulations. (Bottom) Corresponding snapshots at an initial monomer concentration of 5.3 mM.
Figure 4

Figure 4. (Left) Half times, τhalf, of the fibril formation in systems with varying monomer affinities for the surface. (Right) τhalf for systems with increasing bulk/surface ratio as a function of surface binding strength. Increased bulk volume is depicted by black circles (1.25 × 105 nm3), red diamonds (3.75 × 105 nm3), and blue squares (7.5 × 105 nm3). The half times represent the time where 50% of the monomers have formed fibrils averaged over three independent simulation runs, and the error bars display the standard deviation.
Effect of Surface/Bulk Ratio
Surface Effect for Peptide Mutants
(i) | monomer–monomer interaction strength corresponding to additional hydrogen bonds, salt bridges, coulomb interaction, etc. within the same monomer–monomer attractive area; | ||||
(ii) | patch size corresponding to added hydrophobic residues or other interactions that result in the same interaction density, but larger attractive area on PSC; | ||||
(iii) | the free energy of the fibrillar conformation corresponding to mutations that affect the free energy difference between solution and the fibrillar state (refolding free energy difference); and | ||||
(iv) | probability of attempts to switch from solution to the fibrillar state corresponding to modified refolding kinetics (internal friction to refold). |
Figure 5

Figure 5. Half times of fibrillar growth of peptide mutants at the repulsive (R) and at the weakly attractive (WA) surfaces. The mutation types are peptide–peptide attraction (top left), width of attractive patch (top, right), α → β transition barrier (bottom, left), and folding probability/friction (bottom, right).
Experiment: Effect of Nanoparticles on α-Synuclein Aggregation
Figure 6

Figure 6. Aggregation kinetics for 20 μM α-synuclein in 10 mM MES/NaOH pH 5.5 in the absence and presence of 23 nm polystyrene nanoparticles. (A) ThT fluorescence as a function of time with no (black), 0.06 g/L (blue), 0.12 g/L (green), or 0.25 g/L (red) nanoparticles. The first 110 h are shown. (B) Half time (average and standard deviation) for fibrillar growth as a function of nanoparticle concentration. The triangles indicate that no aggregation is observed over 215 h in samples with 0.03 g/L or less nanoparticles.
Experiment: Effect of Nanoparticles on Aβ42 Aggregation
Figure 7

Figure 7. Aggregation kinetics for 6 μM Aβ42 in 20 mM sodium phosphate, 0.2 mM EDTA, pH 8.0 in the absence and presence of nanoparticles. (A and C) ThT fluorescence as a function of time with no (black), 0.002 (blue), 0.0044 (light blue), 0.01 (green), 0.022 (yellow), 0.05 (orange), or 0.11 (red) g/L polystyrene nanoparticles of 26 nm diameter with COOH-groups (A) or of 57 nm with NH2-groups (C). The first 2 and 1.2 h are shown, respectively. (B and D) Half times of fibrillar growth as a function of the concentration of nanoparticles (B: anionic, D: cationic) at low, 50, and 300 mM NaCl.
Rationalization of Existing Studies
Conclusion
Supporting Information
This information contains all experimental and simulation growth profiles (Figures S1–S3). This material is available free of charge via the Internet at http://pubs.acs.org.
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgment
This work was supported by the Swedish Research Council and its Linneaus Centre OMM (organizing molecular matter); the Swedish Foundation for Strategic Research; eSSENCE, nanometer structure consortium, and LUNARC at Lund University; the Czech Science Foundation (Grant 14-12598S); the EU seventh Framework (Contract No. 286154 - SYLICA); the European Regional Development Fund (CZ.1.05/1.1.00/02.0068 CEITEC); and MetaCentrum LM2010005.
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Abstract
Figure 1
Figure 1. (Left) Two-state peptide model used in dynamic Monte Carlo simulations in the presence of planar surfaces (green). Kinetic and thermodynamic properties are described by the parameters (i) → (iv), discussed in the section “Surface Effect for Peptide Mutants”, as well as through a surface attraction strength, K (Table 1). (Right) Representative snapshot from our simulation where orange/gray are particles in the fibril state, while blue/red particles are in the random coil state.
Figure 2
Figure 2. Interaction energy between a weakly attractive surface (WA) and the α state of the peptide. The left figure depicts the distance dependence of the interaction when PSC is parallel to the wall oriented with its patch toward the wall. The right figure displays the orientation dependence of the interaction when PSC is parallel to the wall in distance close to the interaction minimum.
Figure 3
Figure 3. (Top) Oligomer growth profiles in the presence of planar surfaces with increasing binding strengths (see Table 1) and monomer concentration (colored lines). Each profile represents an average from at least three independent simulations. (Bottom) Corresponding snapshots at an initial monomer concentration of 5.3 mM.
Figure 4
Figure 4. (Left) Half times, τhalf, of the fibril formation in systems with varying monomer affinities for the surface. (Right) τhalf for systems with increasing bulk/surface ratio as a function of surface binding strength. Increased bulk volume is depicted by black circles (1.25 × 105 nm3), red diamonds (3.75 × 105 nm3), and blue squares (7.5 × 105 nm3). The half times represent the time where 50% of the monomers have formed fibrils averaged over three independent simulation runs, and the error bars display the standard deviation.
Figure 5
Figure 5. Half times of fibrillar growth of peptide mutants at the repulsive (R) and at the weakly attractive (WA) surfaces. The mutation types are peptide–peptide attraction (top left), width of attractive patch (top, right), α → β transition barrier (bottom, left), and folding probability/friction (bottom, right).
Figure 6
Figure 6. Aggregation kinetics for 20 μM α-synuclein in 10 mM MES/NaOH pH 5.5 in the absence and presence of 23 nm polystyrene nanoparticles. (A) ThT fluorescence as a function of time with no (black), 0.06 g/L (blue), 0.12 g/L (green), or 0.25 g/L (red) nanoparticles. The first 110 h are shown. (B) Half time (average and standard deviation) for fibrillar growth as a function of nanoparticle concentration. The triangles indicate that no aggregation is observed over 215 h in samples with 0.03 g/L or less nanoparticles.
Figure 7
Figure 7. Aggregation kinetics for 6 μM Aβ42 in 20 mM sodium phosphate, 0.2 mM EDTA, pH 8.0 in the absence and presence of nanoparticles. (A and C) ThT fluorescence as a function of time with no (black), 0.002 (blue), 0.0044 (light blue), 0.01 (green), 0.022 (yellow), 0.05 (orange), or 0.11 (red) g/L polystyrene nanoparticles of 26 nm diameter with COOH-groups (A) or of 57 nm with NH2-groups (C). The first 2 and 1.2 h are shown, respectively. (B and D) Half times of fibrillar growth as a function of the concentration of nanoparticles (B: anionic, D: cationic) at low, 50, and 300 mM NaCl.
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- 19Cabaleiro-Lago, C.; Quinlan-Pluck, F.; Lynch, I.; Dawson, K. A.; Linse, S. ACS Chem. Neurosci. 2010, 1, 279– 87Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtFansLk%253D&md5=be3eed5653259673092ad02159d5919aDual Effect of Amino Modified Polystyrene Nanoparticles on Amyloid β Protein FibrillationCabaleiro-Lago, Celia; Quinlan-Pluck, Fiona; Lynch, Iseult; Dawson, Kenneth A.; Linse, SaraACS Chemical Neuroscience (2010), 1 (4), 279-287CODEN: ACNCDM; ISSN:1948-7193. (American Chemical Society)The fibrillation kinetics of the amyloid β peptide is analyzed in the presence of cationic polystyrene nanoparticles of different size. The results highlight the importance of the ratio between the peptide and particle concn. Depending on the specific ratio, the kinetic effects vary from acceleration of the fibrillation process by reducing the lag phase at low particle surface area in soln. to inhibition of the fibrillation process at high particle surface area. The kinetic behavior can be explained if we assume a balance between two different pathways: first fibrillation of free monomer in soln. and second nucleation and fibrillation promoted at the particle surface. The overall rate of fibrillation will depend on the interplay between these two pathways, and the predominance of one mechanism over the other will be detd. by the relative equil. and rate consts.
- 20Cabaleiro-Lago, C.; Szczepankiewicz, O.; Linse, S. Langmuir 2012, 28, 1852– 1857Google ScholarThere is no corresponding record for this reference.
- 21Cabaleiro-Lago, C.; Quinlan-Pluck, F.; Lynch, I.; Lindman, S.; Minogue, A. M.; Thulin, E.; Walsh, D. M.; Dawson, K. A.; Linse, S. J. Am. Chem. Soc. 2008, 130, 15437– 43Google ScholarThere is no corresponding record for this reference.
- 22Cabaleiro-Lago, C.; Lynch, I.; Dawson, K. A.; Linse, S. Langmuir 2010, 26, 3453– 61Google ScholarThere is no corresponding record for this reference.
- 23Hellstrand, E.; Sparr, E.; Linse, S. Biophys. J. 2010, 98, 2206– 14Google ScholarThere is no corresponding record for this reference.
- 24Booth, D. R.; Sunde, M.; Bellotti, V.; Robinson, C. V.; Hutchinson, W. L.; Fraser, P. E.; Hawkins, P. N.; Dobson, C. M.; Radford, S. E.; Blake, C. C.; Pepys, M. B. Nature 1997, 385, 787– 93Google ScholarThere is no corresponding record for this reference.
- 25Szczepankiewicz, O.; Cabaleiro-Lago, C.; Tartaglia, G. G.; Vendruscolo, M.; Hunter, T.; Hunter, G. J.; Nilsson, H.; Thulin, E.; Linse, S. Mol. BioSyst. 2011, 7, 521– 32Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXmslGnug%253D%253D&md5=fe76cc0f8633fd6230ebace0ba8a1c4fInteractions in the native state of monellin, which play a protective role against aggregationSzczepankiewicz, Olga; Cabaleiro-Lago, Celia; Tartaglia, Gian Gaetano; Vendruscolo, Michele; Hunter, Therese; Hunter, Gary J.; Nilsson, Hanna; Thulin, Eva; Linse, SaraMolecular BioSystems (2011), 7 (2), 521-532CODEN: MBOIBW; ISSN:1742-206X. (Royal Society of Chemistry)A series of recent studies have provided initial evidence about the role of specific intra-mol. interactions in maintaining proteins in their sol. state and in protecting them from aggregation. Here we show that the amino acid sequence of the protein monellin contains two aggregation-prone regions that are prevented from initiating aggregation by multiple non-covalent interactions that favor their burial within the folded state of the protein. By investigating the behavior of single-chain monellin and a series of five of its mutational variants using a variety of biochem., biophys. and computational techniques, we found that weakening of the non-covalent interaction that stabilizes the native state of the protein leads to an enhanced aggregation propensity. The lag time for fibrillation was found to correlate with the apparent midpoint of thermal denaturation for the series of mutational variants, thus showing that a reduced thermal stability is assocd. with an increased aggregation tendency. We rationalize these findings by showing that the increase in the aggregation propensity upon mutation can be predicted in a quant. manner through the increase in the exposure to solvent of the amyloidogenic regions of the sequence caused by the destabilization of the native state. Our findings, which are further discussed in terms of the structure of monellin and the perturbation by the amino acid substitutions of the contact surface between the two subdomains that compose the folded state of monellin, provide a detailed description of the specific intra-mol. interactions that prevent aggregation by stabilizing the native state of a protein.
- 26Vácha, R.; Frenkel, D. Biophys. J. 2011, 101, 1432– 1439Google ScholarThere is no corresponding record for this reference.
- 27Linse, B.; Linse, S. Mol. BioSyst. 2011, 7, 2296– 2303Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXnsFOiu7k%253D&md5=6cad8566ecfb331a432475cb87740964Monte Carlo simulations of protein amyloid formation reveal origin of sigmoidal aggregation kineticsLinse, Bjoern; Linse, SaraMolecular BioSystems (2011), 7 (7), 2296-2303CODEN: MBOIBW; ISSN:1742-206X. (Royal Society of Chemistry)Severe conditions and lack of a cure for many amyloid diseases make it highly desirable to understand the underlying principles of formation of fibrillar aggregates (amyloid). Here, amyloid formation from peptides was studied using Monte Carlo simulations. Systems of 20, 50, 100, 200, or 500 hexapeptides were simulated. Assocn. kinetics were modeled equal for fibrillar and other (inter- and intra-peptide) contacts and assumed to be faster the lower the effective contact order, which represents the distance in space. Attempts to form contacts were thus accepted with higher probability the lower the effective contact order, whereby formation of new contacts next to pre-existing ones was favored by shorter phys. sepn. Kinetic discrimination was invoked by using 2 different life-times for formed contacts. Contacts within amyloid fibrils were assumed to have on av. longer life-times than other contacts. It was found that the model produced fibrillation kinetics with a distinct lag phase, and that the fibrillar contacts needed to dissoc. on av. 5-20-fold slower than all other contacts for the fibrillar structure to dominate at equil. Anal. of the species distribution along the aggregation process showed that no other intermediate was ever more populated than the dimer. Instead of a single nucleation event, there was a concomitant increase in av. aggregate size over the whole system, and the occurrence of multiple parallel processes made the process more reproducible the larger the simulated system. The sigmoidal shape of the aggregation curves arose from cooperativity among multiple interactions within each pair of peptides in a fibril. A governing factor was the increasing probability as the aggregation process proceeded of neighboring reinforcing contacts. The results explained the very strong bias toward cross β-sheet fibrils in which the possibilities for cooperativity among interactions involving neighboring residues and the repetitive use of optimal side-chain interactions were explored at max.
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- 34Berthelot, D.; Van der Waals; Leduc, A. Comptes Rendus Hebdomadaires des Seances de l’Academie des Sciences 1898, 1703– 1706Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaD28XltFCqtQ%253D%253D&md5=04821df437d446d4c3db51db927ef254On mixtures of gasesBerthelot, D.Comptes Rendus Hebdomadaires des Seances de l'Academie des Sciences (1898), 126 (), 1703CODEN: COREAF ISSN:.The author proposes a formula of the van der Waals type for a mixture of two gases and shows how the constants A and B for the mixture can be calculated from the corresponding constants for the single gases.
- 35Walsh, D. M.; Thulin, E.; Minogue, A. M.; Gustavsson, N.; Pang, E.; Teplow, D. B.; Linse, S. FEBS J. 2009, 276, 1266– 81Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1MXivFensbo%253D&md5=f644980c816e4b65d8920ed8aee05d0aA facile method for expression and purification of the Alzheimer's disease-associated amyloid β-peptideWalsh, Dominic M.; Thulin, Eva; Minogue, Aedin M.; Gustavsson, Niklas; Pang, Eric; Teplow, David B.; Linse, SaraFEBS Journal (2009), 276 (5), 1266-1281CODEN: FJEOAC; ISSN:1742-464X. (Wiley-Blackwell)The authors report the development of a high-level bacterial expression system for the Alzheimer's disease-assocd. amyloid β-peptide (Aβ), together with a scalable and inexpensive purifn. procedure. Aβ(1-40) and Aβ(1-42) coding sequences together with added ATG codons were cloned directly into a Pet vector to facilitate prodn. of Met-Aβ(1-40) and Met-Aβ(1-42), referred to as Aβ(M1-40) and Aβ(M1-42), resp. The expression sequences were designed using codons preferred by Escherichia coli, and the two peptides were expressed in this host in inclusion bodies. Peptides were purified from inclusion bodies using a combination of anion-exchange chromatog. and centrifugal filtration. The method described requires little specialized equipment and provides a facile and inexpensive procedure for prodn. of large amts. of very pure Aβ peptides. Recombinant peptides generated using this protocol produced amyloid fibrils that were indistinguishable from those formed by chem. synthesized Aβ1-40 and Aβ1-42. Formation of fibrils by all peptides was concn.-dependent, and exhibited kinetics typical of a nucleation-dependent polymn. reaction. Recombinant and synthetic peptides exhibited a similar toxic effect on hippocampal neurons, with acute treatment causing inhibition of MTT redn., and chronic treatment resulting in neuritic degeneration and cell loss.
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