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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 386] [Impact Index Per Article: 128.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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Xing Y, Nandakumar A, Kakinen A, Sun Y, Davis TP, Ke PC, Ding F. Amyloid Aggregation under the Lens of Liquid-Liquid Phase Separation. J Phys Chem Lett 2021; 12:368-378. [PMID: 33356290 PMCID: PMC7855599 DOI: 10.1021/acs.jpclett.0c02567] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Increasing experiments suggest that amyloid peptides can undergo liquid-liquid phase separation (LLPS) before the formation of amyloid fibrils. However, the exact role of LLPS in amyloid aggregation at the molecular level remains elusive. Here, we investigated the LLPS and amyloid fibrillization of a coarse-grained peptide, capable of capturing fundamental properties of amyloid aggregation over a wide range of concentrations in molecular dynamics simulations. On the basis of the Flory-Huggins theory of polymer solutions, we determined the binodal and spinodal concentrations of LLPS in the low-concentration regime, ϕBL and ϕSL, respectively. Only at concentrations above ϕBL, peptides formed metastable or stable oligomers corresponding to the high-density liquid phase (HDLP) in LLPS, out of which the nucleated conformational conversion to fibril seeds occurred. Below ϕSL, the HDLP was metastable and transient, and the subsequent fibrillization process followed the traditional nucleation and elongation mechanisms. Only above ϕSL, the HDLP became stable, and the initial fibril nucleation and growth were governed by the high local peptide concentrations. The predicted saturation of amyloid aggregation half-times with increasing peptide concentration to a constant, instead of the traditional power-law scaling to zero, was confirmed by simulations and by a thioflavin-T kinetic assay and the transmission electron microscopy of islet amyloid polypeptide (IAPP) aggregation. Our study provides a unified picture of amyloid aggregation for a wide range of concentrations within the framework of LLPS, which may help us better understand the etiology of amyloid diseases, where the amyloid protein concentration can vary by ∼9 orders of magnitude depending on the organ location and facilitate the engineering of novel amyloid-based functional materials.
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Affiliation(s)
- Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
| | - Aparna Nandakumar
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Aleksandr Kakinen
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld 4072, Australia
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Pu Chu Ke, ; Feng Ding,
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA
- Pu Chu Ke, ; Feng Ding,
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Abstract
The aggregation of monomeric amyloid β protein (Aβ) peptide into oligomers and amyloid fibrils in the mammalian brain is associated with Alzheimer's disease. Insight into the thermodynamic stability of the Aβ peptide in different polymeric states is fundamental to defining and predicting the aggregation process. Experimental determination of Aβ thermodynamic behavior is challenging due to the transient nature of Aβ oligomers and the low peptide solubility. Furthermore, quantitative calculation of a thermodynamic phase diagram for a specific peptide requires extremely long computational times. Here, using a coarse-grained protein model, molecular dynamics (MD) simulations are performed to determine an equilibrium concentration and temperature phase diagram for the amyloidogenic peptide fragment Aβ16-22 Our results reveal that the only thermodynamically stable phases are the solution phase and the macroscopic fibrillar phase, and that there also exists a hierarchy of metastable phases. The boundary line between the solution phase and fibril phase is found by calculating the temperature-dependent solubility of a macroscopic Aβ16-22 fibril consisting of an infinite number of β-sheet layers. This in silico determination of an equilibrium (solubility) phase diagram for a real amyloid-forming peptide, Aβ16-22, over the temperature range of 277-330 K agrees well with fibrillation experiments and transmission electron microscopy (TEM) measurements of the fibril morphologies formed. This in silico approach of predicting peptide solubility is also potentially useful for optimizing biopharmaceutical production and manufacturing nanofiber scaffolds for tissue engineering.
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4
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Hung NB, Le DM, Hoang TX. Sequence dependent aggregation of peptides and fibril formation. J Chem Phys 2018; 147:105102. [PMID: 28915764 DOI: 10.1063/1.5001517] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the links between amino acid sequence and amyloid fibril formation is key for understanding protein misfolding diseases. Here we use Monte Carlo simulations to study the aggregation of short peptides in a coarse-grained model with hydrophobic-polar (HP) amino acid sequences and correlated side chain orientations for hydrophobic contacts. A significant heterogeneity is observed in the aggregate structures and in the thermodynamics of aggregation for systems of different HP sequences and different numbers of peptides. Fibril-like ordered aggregates are found for several sequences that contain the common HPH pattern, while other sequences may form helix bundles or disordered aggregates. A wide variation of the aggregation transition temperatures among sequences, even among those of the same hydrophobic fraction, indicates that not all sequences undergo aggregation at a presumable physiological temperature. The transition is found to be the most cooperative for sequences forming fibril-like structures. For a fibril-prone sequence, it is shown that fibril formation follows the nucleation and growth mechanism. Interestingly, a binary mixture of peptides of an aggregation-prone and a non-aggregation-prone sequence shows the association and conversion of the latter to the fibrillar structure. Our study highlights the role of a sequence in selecting fibril-like aggregates and also the impact of a structural template on fibril formation by peptides of unrelated sequences.
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Affiliation(s)
- Nguyen Ba Hung
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam
| | - Duy-Manh Le
- Institute of Research and Development, Duy Tan University, K7/25 Quang Trung, Da Nang, Vietnam
| | - Trinh X Hoang
- Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan, Ba Dinh, Hanoi, Vietnam
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5
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Auer S. Simple Model of the Effect of Solution Conditions on the Nucleation of Amyloid Fibrils. J Phys Chem B 2017; 121:8893-8901. [DOI: 10.1021/acs.jpcb.7b05400] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefan Auer
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
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6
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Carpency TN, Gunton JD, Rickman JM. Phase behavior of patchy spheroidal fluids. J Chem Phys 2016; 145:214904. [DOI: 10.1063/1.4969074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- T. N. Carpency
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - J. D. Gunton
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - J. M. Rickman
- Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA
- Department of Materials Science and Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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7
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Irbäck A, Wessén J. Thermodynamics of amyloid formation and the role of intersheet interactions. J Chem Phys 2016; 143:105104. [PMID: 26374063 DOI: 10.1063/1.4930280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The self-assembly of proteins into β-sheet-rich amyloid fibrils has been observed to occur with sigmoidal kinetics, indicating that the system initially is trapped in a metastable state. Here, we use a minimal lattice-based model to explore the thermodynamic forces driving amyloid formation in a finite canonical (NVT) system. By means of generalized-ensemble Monte Carlo techniques and a semi-analytical method, the thermodynamic properties of this model are investigated for different sets of intersheet interaction parameters. When the interactions support lateral growth into multi-layered fibrillar structures, an evaporation/condensation transition is observed, between a supersaturated solution state and a thermodynamically distinct state where small and large fibril-like species exist in equilibrium. Intermediate-size aggregates are statistically suppressed. These properties do not hold if aggregate growth is one-dimensional.
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Affiliation(s)
- Anders Irbäck
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Jonas Wessén
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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8
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Nucleation of polymorphic amyloid fibrils. Biophys J 2016; 108:1176-86. [PMID: 25762329 DOI: 10.1016/j.bpj.2015.01.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 01/09/2015] [Accepted: 01/13/2015] [Indexed: 11/23/2022] Open
Abstract
One and the same protein can self-assemble into amyloid fibrils with different morphologies. The phenomenon of fibril polymorphism is relevant biologically because different fibril polymorphs can have different toxicity, but there is no tool for predicting which polymorph forms and under what conditions. Here, we consider the nucleation of polymorphic amyloid fibrils occurring by direct polymerization of monomeric proteins into fibrils. We treat this process within the framework of our newly developed nonstandard nucleation theory, which allows prediction of the concentration dependence of the nucleation rate for different fibril polymorphs. The results highlight that the concentration dependence of the nucleation rate is closely linked with the protein solubility and a threshold monomer concentration below which fibril formation becomes biologically irrelevant. The relation between the nucleation rate, the fibril solubility, the threshold concentration, and the binding energies of the fibril building blocks within fibrils might prove a valuable tool for designing new experiments to control the formation of particular fibril polymorphs.
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Emperador A, Sfriso P, Villarreal MA, Gelpí JL, Orozco M. PACSAB: Coarse-Grained Force Field for the Study of Protein–Protein Interactions and Conformational Sampling in Multiprotein Systems. J Chem Theory Comput 2015; 11:5929-38. [DOI: 10.1021/acs.jctc.5b00660] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Agustí Emperador
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri
i Reixac 10, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona 08028, Spain
| | - Pedro Sfriso
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri
i Reixac 10, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona 08028, Spain
| | - Marcos Ariel Villarreal
- Instituto de Investigaciones en Fisicoquímica de Córdoba
- Departamento de Matemática y Física, CONICET-Universidad Nacional de Córdoba, University City, Córdoba 5000, Argentina
| | - Josep Lluis Gelpí
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri
i Reixac 10, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona 08028, Spain
- Barcelona Supercomputing Center, Jordi Girona
29, Barcelona 08034, Spain
- Departament de Bioquímica, Facultat de Biologia, Avgda Diagonal 645, Barcelona 08028, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri
i Reixac 10, Barcelona 08028, Spain
- Joint BSC-IRB Research Program in Computational Biology, IRB Barcelona, Barcelona 08028, Spain
- Barcelona Supercomputing Center, Jordi Girona
29, Barcelona 08034, Spain
- Departament de Bioquímica, Facultat de Biologia, Avgda Diagonal 645, Barcelona 08028, Spain
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Abstract
It is well established that amyloid fibril solubility is protein specific, but how solubility depends on the interactions between the fibril building blocks is not clear. Here we use a simple protein model and perform Monte Carlo simulations to directly measure the solubility of amyloid fibrils as a function of the interaction between the fibril building blocks. Our simulations confirms that the fibril solubility depends on the fibril thickness and that the relationship between the interactions and the solubility can be described by a simple analytical formula. The results presented in this study reveal general rules how side-chain-side-chain interactions, backbone hydrogen bonding, and temperature affect amyloid fibril solubility, which might prove to be a powerful tool to design protein fibrils with desired solubility and aggregation properties in general.
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Affiliation(s)
- L G Rizzi
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - S Auer
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
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Zou Y, Hao W, Li H, Gao Y, Sun Y, Ma G. New insight into amyloid fibril formation of hen egg white lysozyme using a two-step temperature-dependent FTIR approach. J Phys Chem B 2014; 118:9834-43. [PMID: 25080318 DOI: 10.1021/jp504201k] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Hen egg white lysozyme (HEWL) is widely used in the mechanistic study of amyloid fibril formation. Yet, the fibrillation mechanism of HEWL is not well understood. In particular, in situ structural evidence for the on-pathway oligomeric intermediate has never been captured. Such evidence is crucial for confirming nucleated conformational conversion mechanism. Herein, we attempt to use a two-step temperature-dependent Fourier transform infrared (FTIR) approach to capture the in situ evidence for the on-pathway oligomeric intermediate and the oligomer-to-fibril transition during HEWL fibrillation. Key features of this approach include using lower temperature to generate the on-pathway oligomeric intermediate, using elevated temperature to eliminate the interference from the off-pathway oligomer and to facilitate the oligomer-to-fibril transition, and using FTIR difference spectroscopy and atomic force microscopy to tackle structure and morphology. Using such an approach, we reveal that the on-pathway oligomeric intermediate is in parallel β-sheet configuration featuring a frequency at 1622 cm(-1) and the oligomer-to-fibril transition is accompanied by a spectral transition from 1622 to 1618 cm(-1). We also discover the beneficial role of the off-pathway oligomer in the capturing of the transient on-pathway oligomeric intermediate by serving as a monomer-releasing reservoir. This approach should also be useful in other amyloidogenic systems.
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Affiliation(s)
- Ye Zou
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
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12
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Auer S. Amyloid Fibril Nucleation: Effect of Amino Acid Hydrophobicity. J Phys Chem B 2014; 118:5289-99. [DOI: 10.1021/jp411370y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Stefan Auer
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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13
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Kashchiev D, Cabriolu R, Auer S. Confounding the paradigm: peculiarities of amyloid fibril nucleation. J Am Chem Soc 2013; 135:1531-9. [PMID: 23305200 DOI: 10.1021/ja311228d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fibrils of amyloid proteins are currently of great interest because of their involvement in various amyloid-related diseases and nanotechnological products. In a recent kinetic Monte Carlo simulation study (Cabriolu, R.; Kashchiev, D.; Auer, S. J. Chem. Phys.2012, 137, 204903), we found that our simulation data for the rate of amyloid fibril nucleation occurring by direct polymerization of monomeric protein could not be described adequately by nucleation theory. It turned out that the process occurred in a peculiar way, thus confounding the nucleation paradigm and demanding a new theoretical treatment. In the present study, we reconsider the theoretical approach to nucleation of amyloid fibrils and derive new expressions for the stationary rate of the process. As these expressions provide a remarkably good description of the simulation data, by using them we propose a theoretical dependence of the amyloid-β(40) fibril nucleation rate on the concentration of monomeric protein in the solution. This dependence reveals the existence of a threshold concentration below which the fibril nucleation in small enough solution volumes is practically arrested, and above which the process occurs vigorously, because then each monomeric protein in the solution acts as fibril nucleus. The presented expressions for the threshold concentration and for the dependence of the fibril nucleation rate on the concentration of monomeric protein can be a valuable guide in designing new therapeutic and/or technological strategies for prevention or stimulation of amyloid fibril formation.
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Affiliation(s)
- Dimo Kashchiev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, ul. Acad. G. Bonchev 11, Sofia 1113, Bulgaria
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14
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Cabriolu R, Kashchiev D, Auer S. Breakdown of nucleation theory for crystals with strongly anisotropic interactions between molecules. J Chem Phys 2012. [DOI: 10.1063/1.4767531] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Two-step nucleation of amyloid fibrils: omnipresent or not? J Mol Biol 2012; 422:723-730. [PMID: 22721952 DOI: 10.1016/j.jmb.2012.06.022] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/11/2012] [Accepted: 06/13/2012] [Indexed: 11/23/2022]
Abstract
Amyloid protein fibrils feature in various diseases and nanotechnological products. Currently, it is debated whether they nucleate in one step (i.e., directly from the protein solution) or in two steps (step one being the appearance of nonfibrillar oligomers in the solution and step two being the oligomer conversion into fibrils). We employ nucleation theory to gain insight into the idiosyncrasy of two-step fibril nucleation and to determine the conditions under which this process can take place. Presenting an expression for the rate of two-step fibril nucleation, we use it to qualitatively describe experimental data for two-step nucleated amyloid-β fibrils. Our analysis helps in understanding why, in some experiments, oligomers rather than fibrils form and remain structurally unchanged and why, in others, the oligomers convert into fibrils.
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16
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Ricchiuto P, Brukhno AV, Auer S. Protein Aggregation: Kinetics versus Thermodynamics. J Phys Chem B 2012; 116:5384-90. [DOI: 10.1021/jp302797c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Piero Ricchiuto
- Centre for Molecular Nanoscience,
School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andrey V. Brukhno
- Centre for Molecular Nanoscience,
School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Stefan Auer
- Centre for Molecular Nanoscience,
School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom
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