1
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Xia P, Cao Y, Zhao Q, Li H. Energy gap of conformational transition related with temperature for the NACore of α-synuclein. Phys Chem Chem Phys 2024; 26:23062-23072. [PMID: 39175373 DOI: 10.1039/d4cp02131b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
Abstract
Pathological aggregation of α-synuclein (α-syn) into amyloid fibrils is a major feature of Parkinson's disease (PD). The self-assembly of α-syn is mainly governed by a non-amyloid-β component core (NACore). However, the effects of concentrations and temperatures on their conformational transition remain unclear. To answer this question, we investigated the aggregation kinetics of NACore oligomers in silico by performing several independent all-atom molecular dynamics simulations. The simulation results show that tetramers are more prone to form β-sheets at 300 K than dimers and octamers. We also found that the NACore oligomers had higher β-sheet and β-barrel contents at 310 K. The inter-chain hydrophobic interactions, the backbone hydrogen bonding, the residue-residue interactions between V70-V77 as well as V77-V77 play important roles in the aggregation tendency of NACore octamers at 310 K. Interestingly, the energy gap analysis revealed that the conformational transition of NACore oligomers from intermediate states (β-barrel conformation) to stable structures (β-sheet layers) was dependent on the temperatures. In short, our study provides insight into the kinetic and thermodynamic mechanisms of the conformational transition of NACore at different concentrations and temperatures, contributing to a better understanding of the aggregation process of α-syn in Parkinson's disease.
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Affiliation(s)
- Pengxuan Xia
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yuanming Cao
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Qingjie Zhao
- The Research Center of Chiral Drugs, Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
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2
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Liang L, Zhang Y, Zhu Y, Bai J, Ni Y, Wan J, Yue H, Zhao Q, Li H. Structures and Dynamics of β-Rich Oligomers of ATTR (105-115) Assembly. ACS Chem Neurosci 2024; 15:1356-1365. [PMID: 38483181 DOI: 10.1021/acschemneuro.3c00574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Transthyretin (TTR) is a tetrameric homologous protein that can dissociate into monomers. Misfolding and aggregation of TTR can lead to amyloid transthyretin amyloidosis (ATTR), which can cause many diseases (e.g., senile systemic amyloidosis, familial amyloid cardiomyopathy, and familial amyloid polyneuropathy). Despite growing evidence indicating that small oligomers play a critical role in regulating cytotoxicity, the structures of these oligomeric intermediates and their conformational transformations are still unclear, impeding our understanding of neurodegenerative mechanisms and the development of therapeutics targeting early aggregation species. The TTR monomer protein consists of various fragments prone to self-aggregation, including the residue 105-115 sequence. Therefore, our study investigated the assembly progress of ATTR (105-115) peptides using all-atom molecular dynamics simulations. The findings indicate that the probability of β-sheet content increases with increasing numbers of peptides. Additionally, interactions between hydrophobic residues L110 and L111 are crucial for the formation of a β-rich oligomer formation. These β-rich oligomers may adopt β-barrel conformations, potentially toxic oligomer species. Free-energy analysis reveals that β-barrel conformations serve as intermediates for these β-rich oligomers. Our insights into the structural ensemble dynamics of ATTR (105-115) contribute to understanding the physical mechanisms underlying the β-barrel oligomers of ATTR. These findings may shed light on the pathological role of ATTR in neurodegenerative diseases and offer potential therapeutic targets.
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Affiliation(s)
- Liqun Liang
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yuqi Zhang
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yanyan Zhu
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Juxia Bai
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Yangyang Ni
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Junfeng Wan
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
| | - Haiyan Yue
- Naval Medical Center of PLA, Department of Gastroenterology, Naval Medical University, Shanghai 200433, China
| | - Qingjie Zhao
- Shanghai Frontiers Science Center for TCM Chemical Biology, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China
| | - Huiyu Li
- College of Mathematics and Physics, Shanghai University of Electric Power, Shanghai 200090, China
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3
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John T, Rampioni A, Poger D, Mark AE. Molecular Insights into the Dynamics of Amyloid Fibril Growth: Elongation and Lateral Assembly of GNNQQNY Protofibrils. ACS Chem Neurosci 2024; 15:716-723. [PMID: 38235697 DOI: 10.1021/acschemneuro.3c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Abstract
The self-assembly of peptides and proteins into β-sheet rich amyloid fibrils is linked to both functional and pathological states. In this study, the growth of fibrillar structures of the short peptide GNNQQNY, a fragment from the yeast prion Sup35 protein, was examined. Molecular dynamics simulations were used to study alternative mechanisms of fibril growth, including elongation through binding of monomers as well as fibril self-assembly into larger, more mature structures. It was found that after binding, monomers diffused along preformed fibrils toward the ends, supporting the mechanism of fibril growth via elongation. Lateral assembly of protofibrils was found to occur readily, suggesting that this could be the key to transitioning from isolated fibrils to mature multilayer structures. Overall, the work provides mechanistic insights into the competitive pathways that govern amyloid fibril growth.
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Affiliation(s)
- Torsten John
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Aldo Rampioni
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia
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4
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Pretti E, Shell MS. Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6. Proc Natl Acad Sci U S A 2023; 120:e2309995120. [PMID: 37983502 PMCID: PMC10691331 DOI: 10.1073/pnas.2309995120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023] Open
Abstract
The PHF6 (Val-Gln-Ile-Val-Tyr-Lys) motif, found in all isoforms of the microtubule-associated protein tau, forms an integral part of ordered cores of amyloid fibrils formed in tauopathies and is thought to play a fundamental role in tau aggregation. Because PHF6 as an isolated hexapeptide assembles into ordered fibrils on its own, it is investigated as a minimal model for insight into the initial stages of aggregation of larger tau fragments. Even for this small peptide, however, the large length and time scales associated with fibrillization pose challenges for simulation studies of its dynamic assembly, equilibrium configurational landscape, and phase behavior. Here, we develop an accurate, bottom-up coarse-grained model of PHF6 for large-scale simulations of its aggregation, which we use to uncover molecular interactions and thermodynamic driving forces governing its assembly. The model, not trained on any explicit information about fibrillar structure, predicts coexistence of formed fibrils with monomers in solution, and we calculate a putative equilibrium phase diagram in concentration-temperature space. We also characterize the configurational and free energetic landscape of PHF6 oligomers. Importantly, we demonstrate with a model of heparin that this widely studied cofactor enhances the aggregation propensity of PHF6 by ordering monomers during nucleation and remaining associated with growing fibrils, consistent with experimentally characterized heparin-tau interactions. Overall, this effort provides detailed molecular insight into PHF6 aggregation thermodynamics and pathways and, furthermore, demonstrates the potential of modern multiscale modeling techniques to produce predictive models of amyloidogenic peptides simultaneously capturing sequence-specific effects and emergent aggregate structures.
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Affiliation(s)
- Evan Pretti
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106-5080
| | - M. Scott Shell
- Department of Chemical Engineering, University of California, Santa Barbara, CA93106-5080
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5
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Nguyen PH, Derreumaux P. Multistep molecular mechanisms of Aβ16-22 fibril formation revealed by lattice Monte Carlo simulations. J Chem Phys 2023; 158:235101. [PMID: 37318171 DOI: 10.1063/5.0149419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
As a model of self-assembly from disordered monomers to fibrils, the amyloid-β fragment Aβ16-22 was subject to past numerous experimental and computational studies. Because dynamics information between milliseconds and seconds cannot be assessed by both studies, we lack a full understanding of its oligomerization. Lattice simulations are particularly well suited to capture pathways to fibrils. In this study, we explored the aggregation of 10 Aβ16-22 peptides using 65 lattice Monte Carlo simulations, each simulation consisting of 3 × 109 steps. Based on a total of 24 and 41 simulations that converge and do not converge to the fibril state, respectively, we are able to reveal the diversity of the pathways leading to fibril structure and the conformational traps slowing down the fibril formation.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 Rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France (IUF), 75005 Paris, France
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6
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Iorio A, Timr Š, Chiodo L, Derreumaux P, Sterpone F. Evolution of large Aβ16-22 aggregates at atomic details and potential of mean force associated to peptide unbinding and fragmentation events. Proteins 2023. [PMID: 37139594 DOI: 10.1002/prot.26500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 05/05/2023]
Abstract
Atomic characterization of large nonfibrillar aggregates of amyloid polypeptides cannot be determined by experimental means. Starting from β-rich aggregates of Y and elongated topologies predicted by coarse-grained simulations and consisting of more than 100 Aβ16-22 peptides, we performed atomistic molecular dynamics (MD), replica exchange with solute scaling (REST2), and umbrella sampling simulations using the CHARMM36m force field in explicit solvent. Here, we explored the dynamics within 3 μs, the free energy landscape, and the potential of mean force associated with either the unbinding of one single peptide in different configurations within the aggregate or fragmentation events of a large number of peptides. Within the time scale of MD and REST2, we find that the aggregates experience slow global conformational plasticity, and remain essentially random coil though we observe slow beta-strand structuring with a dominance of antiparallel beta-sheets over parallel beta-sheets. Enhanced REST2 simulation is able to capture fragmentation events, and the free energy of fragmentation of a large block of peptides is found to be similar to the free energy associated with fibril depolymerization by one chain for longer Aβ sequences.
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Affiliation(s)
- Antonio Iorio
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
| | - Štěpán Timr
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Letizia Chiodo
- Research Unit in Non Linear Physics and Mathematical Modeling Engineering Department of Campus Bio-Medico, University of Rome, Rome, Italy
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
- Institut Universitaire de France, Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique (UPR 9080), CNRS, Université Paris Cité, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Paris, France
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7
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Tan Y, Chen Y, Liu X, Tang Y, Lao Z, Wei G. Dissecting how ALS-associated D290V mutation enhances pathogenic aggregation of hnRNPA2 286-291 peptides: Dynamics and conformational ensembles. Int J Biol Macromol 2023; 241:124659. [PMID: 37119915 DOI: 10.1016/j.ijbiomac.2023.124659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
The aggregation of RNA binding proteins, including hnRNPA1/2, TDP-43 and FUS, is heavily implicated in causing or increasing disease risk for a series of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). A recent experimental study demonstrated that an ALS-related D290V mutation in the low complexity domain (LCD) of hnRNPA2 can enhance the aggregation propensity of wild type (WT) hnRNPA2286-291 peptide. However, the underlying molecular mechanisms remain elusive. Herein, we investigated effects of D290V mutation on aggregation dynamics of hnRNPA2286-291 peptide and the conformational ensemble of hnRNPA2286-291 oligomers by performing all-atom molecular dynamic and replica-exchange molecular dynamic simulations. Our simulations demonstrate that D290V mutation greatly reduces the dynamics of hnRNPA2286-291 peptide and that D290V oligomers possess higher compactness and β-sheet content than WT, indicative of mutation-enhanced aggregation capability. Specifically, D290V mutation strengthens inter-peptide hydrophobic, main-chain hydrogen bonding and side-chain aromatic stacking interactions. Those interactions collectively lead to the enhancement of aggregation capability of hnRNPA2286-291 peptides. Overall, our study provides insights into the dynamics and thermodynamic mechanisms underlying D290V-induced disease-causing aggregation of hnRNPA2286-291, which could contribute to better understanding of the transitions from reversible condensates to irreversible pathogenic aggregates of hnRNPA2 LCD in ALS-related diseases.
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Affiliation(s)
- Yuan Tan
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yujie Chen
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Xianshi Liu
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Yiming Tang
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Zenghui Lao
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China
| | - Guanghong Wei
- Department of Physics, Fudan University, Shanghai 200438, People's Republic of China; State Key Laboratory of Surface Physics, Fudan University, Shanghai 200438, People's Republic of China; Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200438, People's Republic of China.
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8
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Disassembly of Amyloid Fibril with Infrared Free Electron Laser. Int J Mol Sci 2023; 24:ijms24043686. [PMID: 36835098 PMCID: PMC9967569 DOI: 10.3390/ijms24043686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 μm to 100 μm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10-50 mJ/cm2). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1-6.2 μm) where the abundance of β-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from β2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook.
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9
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Nguyen PH, Derreumaux P. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation. Methods Mol Biol 2022; 2340:175-196. [PMID: 35167075 DOI: 10.1007/978-1-0716-1546-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein aggregation can lead to well-defined structures that are functional, but is also the cause of the death of neuron cells in many neurodegenerative diseases. The complexity of the molecular events involved in the aggregation kinetics of amyloid proteins and the transient and heterogeneous characters of all oligomers prevent high-resolution structural experiments. As a result, computer simulations have been used to determine the atomic structures of amyloid proteins at different association stages as well as to understand fibril dissociation. In this chapter, we first review the current computer simulation methods used for aggregation with some atomistic and coarse-grained results aimed at better characterizing the early formed oligomers and amyloid fibril formation. Then we present the applications of non-equilibrium molecular dynamics simulations to comprehend the dissociation of protein assemblies.
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Affiliation(s)
- Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université de Paris, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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10
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Nguyen PH, Tufféry P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol 2022; 2405:95-113. [PMID: 35298810 DOI: 10.1007/978-1-0716-1855-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibril formation is an intrinsic property of short peptides, non-disease proteins, and proteins associated with neurodegenerative diseases. Aggregates of the Aβ and tau proteins, the α-synuclein protein, and the prion protein are observed in the brain of Alzheimer's, Parkinson's, and prion disease patients, respectively. Due to the transient short-range and long-range interactions of all species and their high aggregation propensities, the conformational ensemble of these devastating proteins, the exception being for the monomeric prion protein, remains elusive by standard structural biology methods in bulk solution and in lipid membranes. To overcome these limitations, an increasing number of simulations using different sampling methods and protein models have been performed. In this chapter, we first review our main contributions to the field of amyloid protein simulations aimed at understanding the early aggregation steps of short linear amyloid peptides, the conformational ensemble of the Aβ40/42 dimers in bulk solution, and the stability of Aβ aggregates in lipid membrane models. Then we focus on our studies on the interactions of amyloid peptides/inhibitors to prevent aggregation, and long amyloid sequences, including new results on a monomeric tau construct.
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Affiliation(s)
- Phuong Hoang Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Pierre Tufféry
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, RPBS, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France.
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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11
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Burra G, Maina MB, Serpell LC, Thakur AK. Nucleation-dependent Aggregation Kinetics of Yeast Sup35 Fragment GNNQQNY. J Mol Biol 2020; 433:166732. [PMID: 33279578 DOI: 10.1016/j.jmb.2020.166732] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
An N-terminal hepta-peptide sequence of yeast prion protein Sup35 with the sequence GNNQQNY is widely used as a model system for amyloid fibril formation. In this study, we used a reproducible solubilisation protocol that allows the generation of a homogenous monomeric solution of GNNQQNY to uncover the molecular details of its self-assembly mechanism. The aggregation kinetics data show that the GNNQQNY sequence follows nucleation-dependent aggregation kinetics with a critical nucleus of size ~7 monomers and that the efficiency of nucleation were found to be inversely related to the reaction temperature. The nucleus reduces the thermodynamic energy barrier by acting as a template for further self-assembly and results in highly ordered amyloid fibrils. The fibers grown at different temperatures showed similar Thioflavin T fluorescence, Congo-red binding and β-sheet rich structures displaying a characteristic cross-β diffraction pattern. These aggregates also share morphological and structural identity with those reported earlier. The mature GNNQQNY fibers did not exert significant oxidative stress or cytotoxicity upon incubating with differentiated SHSY5Y cells. To our knowledge, this is the first study to experimentally validate previous nucleus size predictions based on theoretical and molecular dynamics simulations. These findings provide the basis for understanding the kinetics and thermodynamics of amyloid nucleation and elongation of amyloidogenic proteins/peptides associated with many systemic and neurodegenerative diseases.
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Affiliation(s)
- Gunasekhar Burra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India; Sussex Neuroscience, School of Life Sciences, University of Sussex, UK.
| | - Mahmoud B Maina
- Sussex Neuroscience, School of Life Sciences, University of Sussex, UK; College of Medical Sciences, Yobe State University, Nigeria
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, UK
| | - Ashwani K Thakur
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, India.
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12
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Mushnoori S, Lu CY, Schmidt K, Zang E, Dutt M. Peptide-based vesicles and droplets: a review. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 33:053002. [PMID: 32942264 DOI: 10.1088/1361-648x/abb995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 09/17/2020] [Indexed: 06/11/2023]
Abstract
Peptide assembly is an increasingly important field of study due to the versatility, tunability and vast design space of amino acid based biomolecular assemblies. Peptides can be precisely engineered to possess various useful properties such as the ability to form supramolecular assemblies, desired response to pH, or thermal stability. These peptide supramolecular assemblies have diverse morphologies including vesicles, nanotubes, nanorods and ribbons. Of specific interest is the domain of engineering peptides that aggregate into spherical nanostructures due to their encapsulation properties: the ability to hold, transport and release chemical payloads in a controllable manner. This is invaluable to the fields of nanomedicine and targeted drug delivery. In this review, the state of the art in the domain of peptide-based vesicles and nanospheres is summarized. Specifically, an overview of the assembly of peptides into nanovesicles and nanospheres is provided. Both aromatic as well as aliphatic side chain amino acids are discussed. The domain of aromatic side chained amino acid residues is largely dominated by phenylalanine based peptides and variants thereof. Tyrosine also demonstrates similar aggregation properties. Both experimentally and computationally driven approaches are discussed. The domain of aliphatic amino acid residues based vesicles and droplets is broader, and details multiple amino acid residues such as alanine, valine, lysine, glycine, proline, and aspartic acid. Finally, a discussion on potential future directions is provided.
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Affiliation(s)
- Srinivas Mushnoori
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Chien Y Lu
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Kassandra Schmidt
- Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Ethan Zang
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
| | - Meenakshi Dutt
- Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States of America
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13
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Heilmann N, Wolf M, Kozlowska M, Sedghamiz E, Setzler J, Brieg M, Wenzel W. Sampling of the conformational landscape of small proteins with Monte Carlo methods. Sci Rep 2020; 10:18211. [PMID: 33097750 PMCID: PMC7585447 DOI: 10.1038/s41598-020-75239-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2020] [Indexed: 12/24/2022] Open
Abstract
Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the β-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.
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Affiliation(s)
- Nana Heilmann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Moritz Wolf
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Mariana Kozlowska
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Elaheh Sedghamiz
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Julia Setzler
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Martin Brieg
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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14
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Szała-Mendyk B, Molski A. Clustering and Fibril Formation during GNNQQNY Aggregation: A Molecular Dynamics Study. Biomolecules 2020; 10:biom10101362. [PMID: 32987720 PMCID: PMC7598727 DOI: 10.3390/biom10101362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 12/02/2022] Open
Abstract
The precise kinetic pathways of peptide clustering and fibril formation are not fully understood. Here we study the initial clustering kinetics and transient cluster morphologies during aggregation of the heptapeptide fragment GNNQQNY from the yeast prion protein Sup35. We use a mid-resolution coarse-grained molecular dynamics model of Bereau and Deserno to explore the aggregation pathways from the initial random distribution of free monomers to the formation of large clusters. By increasing the system size to 72 peptides we could follow directly the molecular events leading to the formation of stable fibril-like structures. To quantify those structures we developed a new cluster helicity parameter. We found that the formation of fibril-like structures is a cooperative processes that requires a critical number of monomers, M⋆≈25, in a cluster. The terminal tyrosine residue is the structural determinant in the formation of helical fibril-like structures. This work supports and quantifies the two-step aggregation model where the initially formed amorphous clusters grow and, when they are large enough, rearrange into mature twisted structures. However, in addition to the nucleated fibrillation, growing aggregates undergo further internal reorganization, which leads to more compact structures of large aggregates.
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15
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Ozgur B, Sayar M. Representation of the conformational ensemble of peptides in coarse grained simulations. J Chem Phys 2020; 153:054108. [DOI: 10.1063/5.0012391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Mehmet Sayar
- Chemical and Biological Engineering and Mechanical Engineering Departments, College of Engineering, Koç University, 34450 Istanbul, Turkey
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16
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Kawasaki T, Man VH, Sugimoto Y, Sugiyama N, Yamamoto H, Tsukiyama K, Wang J, Derreumaux P, Nguyen PH. Infrared Laser-Induced Amyloid Fibril Dissociation: A Joint Experimental/Theoretical Study on the GNNQQNY Peptide. J Phys Chem B 2020; 124:6266-6277. [PMID: 32560588 DOI: 10.1021/acs.jpcb.0c05385] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neurodegenerative diseases are usually characterized by plaques made of well-ordered aggregates of distinct amyloid proteins. Dissociating these very stable amyloid plaques is a critical clinical issue. In this study, we present a joint mid-infrared free electron laser experiment/nonequilibrium molecular dynamics simulation to understand the dissociation process of a representative example GNNQQNY fibril. By tuning the laser frequency to the amide I band of the fibril, the resonance takes place and dissociation is occurred. With the calculated and observed wide-angle X-ray scattering profiles and secondary structures before and after laser irradiation being identical, we can propose a dissociation mechanism with high confidence from our simulations. We find that dissociation starts in the core of the fibrils by fragmenting the intermolecular hydrogen bonds and separating the peptides and then propagates to the fibril extremities leading to the formation of unstructured expanded oligomers. We suggest that this should be a generic mechanism of the laser-induced dissociation of amyloid fibrils.
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Affiliation(s)
- Takayasu Kawasaki
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Viet Hoang Man
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Yasunobu Sugimoto
- Synchrotron Radiation Research Center, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8603, Japan
| | - Nobuyuki Sugiyama
- Aichi Synchrotron Radiation Center, 250-3 minamiyamaguchi-cho, Seto-shi, 489-0965, Japan
| | - Hiroko Yamamoto
- Aichi Synchrotron Radiation Center, 250-3 minamiyamaguchi-cho, Seto-shi, 489-0965, Japan
| | - Koichi Tsukiyama
- IR-FEL Research Center, Research Institute for Science and Technology, Organization for Research Advancement, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, United States
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh, Vietnam.,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh, Vietnam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR9080, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France
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17
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Structures of the intrinsically disordered Aβ, tau and α-synuclein proteins in aqueous solution from computer simulations. Biophys Chem 2020; 264:106421. [PMID: 32623047 DOI: 10.1016/j.bpc.2020.106421] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022]
Abstract
Intrinsically disordered proteins (IDPs) play many biological roles in the human proteome ranging from vesicular transport, signal transduction to neurodegenerative diseases. The Aβ and tau proteins, and the α-synuclein protein, key players in Alzheimer's and Parkinson's diseases, respectively are fully disordered at the monomer level. The structural heterogeneity of the monomeric and oligomeric states and the high self-assembly propensity of these three IDPs have precluded experimental structural determination. Simulations have been used to determine the atomic structures of these IDPs. In this article, we review recent computer models to capture the equilibrium ensemble of Aβ, tau and α-synuclein proteins at different association steps in aqueous solution and present new results of the PEP-FOLD framework on α-synuclein monomer.
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18
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Theoretical and computational advances in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:1-31. [PMID: 31928722 DOI: 10.1016/bs.apcsb.2019.08.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Misfolded proteins escape the cellular quality control mechanism and fail to fold properly or remain correctly folded leading to a loss in their functional specificity. Thus misfolding of proteins cause a large number of very different diseases ranging from errors in metabolism to various types of complex neurodegenerative diseases. A theoretical and computational perspective of protein misfolding is presented with a special emphasis on its salient features, mechanism and consequences. These insights quantitatively analyze different determinants of misfolding, that may be applied to design disease specific molecular targets.
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19
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Nguyen PH, Sterpone F, Derreumaux P. Aggregation of disease-related peptides. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:435-460. [PMID: 32145950 DOI: 10.1016/bs.pmbts.2019.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Protein misfolding and aggregation of amyloid proteins is the fundamental cause of more than 20 diseases. Molecular mechanisms of the self-assembly and the formation of the toxic aggregates are still elusive. Computer simulations have been intensively used to study the aggregation of amyloid peptides of various amino acid lengths related to neurodegenerative diseases. We review atomistic and coarse-grained simulations of short amyloid peptides aimed at determining their transient oligomeric structures and the early and late aggregation steps.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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20
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Katyal N, Deep S. A computational approach to get insights into multiple faces of additives in modulation of protein aggregation pathways. Phys Chem Chem Phys 2019; 21:24269-24285. [PMID: 31670327 DOI: 10.1039/c9cp03763b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enormous population worldwide is presently confronted with debilitating neurodegenerative diseases. The etiology of the disease is connected to protein aggregation and the events involved therein. Thus, a complete understanding of an inhibitor at different stages in the process is imperative for the formulation of a drug molecule. This review presents a detailed summary of the current status of different cosolvents. It further develops how the complex aggregation pathway can be simplified into three steps common to all proteins and the way computer simulations can be exploited to gain insights into the ways by which known inhibitors can affect all these stages. Computation of theoretical parameters in this regard and their correlation with experimental techniques is accentuated. In addition to providing an outline of the scope of different additives, this review showcases the way by which the problem of analyzing an effect of an additive can be addressed effectively via MD simulations.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi-110016, Delhi, India.
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21
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Crowet JM, Sinnaeve D, Fehér K, Laurin Y, Deleu M, Martins JC, Lins L. Molecular Model for the Self-Assembly of the Cyclic Lipodepsipeptide Pseudodesmin A. J Phys Chem B 2019; 123:8916-8922. [PMID: 31558021 DOI: 10.1021/acs.jpcb.9b08035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Self-assembly of peptides into supramolecular structures represents an active field of research with potential applications ranging from material science to medicine. Their study typically involves the application of a large toolbox of spectroscopic and imaging techniques. However, quite often, the structural aspects remain underexposed. Besides, molecular modeling of the self-assembly process is usually difficult to handle, since a vast conformational space has to be sampled. Here, we have used an approach that combines short molecular dynamics simulations for peptide dimerization and NMR restraints to build a model of the supramolecular structure from the dimeric units. Experimental NMR data notably provide crucial information about the conformation of the monomeric units, the supramolecular assembly dimensions, and the orientation of the individual peptides within the assembly. This in silico/in vitro mixed approach enables us to define accurate atomistic models of supramolecular structures of the bacterial cyclic lipodepsipeptide pseudodesmin A.
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Affiliation(s)
- Jean-Marc Crowet
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Davy Sinnaeve
- CNRS-Unité de Glycobiologie structurale et fonctionnelle (UGSF) UMR 8576 , 50, Avenue de Halley, Campus CNRS de la Haute Borne , 59658 Villeneuve d'Ascq , France
| | - Krisztina Fehér
- Heidelberg Institute for Theoretical Studies , Schloss-Wolfsbrunnenweg 35 , 69118 Heidelberg , Germany
| | - Yoann Laurin
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - Magali Deleu
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 S4 , B-9000 Gent , Belgium
| | - Laurence Lins
- Laboratory of Molecular Biophysics at Interfaces, TERRA Research Center, Gembloux Agro-Bio Tech , University of Liège , Passage des déportés 2 , B-5030 Gembloux , Belgium
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22
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Szała B, Molski A. Aggregation kinetics of short peptides: All-atom and coarse-grained molecular dynamics study. Biophys Chem 2019; 253:106219. [PMID: 31301554 DOI: 10.1016/j.bpc.2019.106219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/14/2019] [Accepted: 07/03/2019] [Indexed: 11/30/2022]
Abstract
Peptides can aggregate into ordered structures with different morphologies. The aggregation mechanism and evolving structures are the subject of intense research. In this paper we have used molecular dynamics to examine the sequence-dependence of aggregation kinetics for three short peptides: octaalanine (Ala8), octaasparagine (Asn8), and the heptapeptide GNNQQNY (abbreviated as GNN). First, we compared the aggregation of 20 randomly distributed peptides using the coarse-grained MARTINI force field and the atomistic OPLS-AA force field. We found that the MARTINI and OPLS-AA aggregation kinetics are similar for Ala8, Asn8, and GNN. Second, we used the MARTINI force field to study the early stages of aggregation kinetics for a larger system with 72 peptides. In the initial stage of aggregation small clusters grow by monomer addition. In the second stage, when the free monomers are depleted, the dominant cluster growth path is cluster-cluster coalescence. We quantified the aggregation kinetics in terms of rate equations. Our study shows that the initial aggregation kinetics are similar for Ala8, Asn8, and GNN but the molecular details can be different, especially for MARTINI Ala8. We hypothesize that peptide aggregation proceed in two steps. In the first step amorphous aggregates are formed, and then, in the second step, they reorganize into ordered structures. We conclude that sequence-specific differences show up in the second step of aggregation.
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Affiliation(s)
- Beata Szała
- Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
| | - Andrzej Molski
- Adam Mickiewicz University in Poznań, Faculty of Chemistry, Umultowska 89b, 61-614 Poznań, Poland.
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23
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Lu Y, Shi XF, Nguyen PH, Sterpone F, Salsbury FR, Derreumaux P. Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids. J Phys Chem B 2019; 123:2687-2696. [PMID: 30813725 DOI: 10.1021/acs.jpcb.9b00431] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The omega-3 and omega-6 polyunsaturated fatty acids are two important components of cell membranes in human brains. When incorporated into phospholipids, omega-3 slows the progression of Alzheimer's disease (AD), whereas omega-6 is linked to increased risk of AD. Little is known on the amyloid-β (Aβ) conformations in membranes rich in omega-3 and omega-6 phospholipids. Herein, the structural properties of the Aβ29-42 dimer embedded in both fatty acid membranes were comparatively studied to a 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) bilayer using all-atom molecular dynamics (MD) simulations. Starting from α-helix, both omega-6 and omega-3 membranes promote new orientations and conformations of the dimer, in agreement with the observed dependence of Aβ production upon addition of these two fatty acids. This conformational result is corroborated by atomistic MD simulations of the dimer of the 99 amino acid C-terminal fragment of amyloid precursor protein spanning the residues 15-55. Starting from β-sheet, omega-6 membrane promotes helical and disordered structures of Aβ29-42 dimer, whereas omega-3 membrane preserves the β-sheet structures differing however from those observed in POPC. Remarkably, the mixture of the two fatty acids and POPC depicts another conformational ensemble of the Aβ29-42 dimer. This finding demonstrates that variation in the abundance of the molecular phospholipids, which changes with age, modulates membrane-embedded Aβ oligomerization.
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Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering , Xidian University , Xi'an 710071 , China
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS , Université Paris Diderot, Sorbonne Paris Cite , 13 rue Pierre et Marie Curie , 75005 Paris , France
| | - Freddie R Salsbury
- Department of Physics , Wake Forest University , Winston-Salem , North Carolina 27106 , United States
| | - Philippe Derreumaux
- Laboratory of Theoretical Chemistry , Ton Duc Thang University , Ho Chi Minh City , Vietnam.,Faculty of Pharmacy , Ton Duc Thang University , Ho Chi Minh City , Vietnam
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24
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Nguyen PH, del Castillo-Frias MP, Berthoumieux O, Faller P, Doig AJ, Derreumaux P. Amyloid-β/Drug Interactions from Computer Simulations and Cell-Based Assays. J Alzheimers Dis 2018; 64:S659-S672. [DOI: 10.3233/jad-179902] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
| | - Maria P. del Castillo-Frias
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Olivia Berthoumieux
- CNRS, LCC (Laboratoire de Chimie de Coordination), Toulouse Cedex 4, France et Université de Toulouse, UPS, INPT, Toulouse Cedex 4, France
| | - Peter Faller
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, Strasbourg, France
| | - Andrew J. Doig
- Manchester Institute of Biotechnology and Department of Chemistry, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France
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25
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Katyal N, Deep S. Inhibition of GNNQQNY prion peptide aggregation by trehalose: a mechanistic view. Phys Chem Chem Phys 2018; 19:19120-19138. [PMID: 28702592 DOI: 10.1039/c7cp02912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Deposition of amyloid fibrils is the seminal event in the pathogenesis of numerous neurodegenerative diseases. The formation of this amyloid assembly is the manifestation of a cascade of structural transitions including toxic oligomer formation in the early stages of aggregation. Thus a viable therapeutic strategy involves the use of small molecular ligands to interfere with this assembly. In this perspective, we have explored the kinetics of aggregate formation of the fibril forming GNNQQNY peptide fragment from the yeast prion protein SUP35 using multiple all atom MD simulations with explicit solvent and provided mechanistic insights into the way trehalose, an experimentally known aggregation inhibitor, modulates the aggregation pathway. The results suggest that the assimilation process is impeded by different barriers at smaller and larger oligomeric sizes: the initial one being easily surpassed at higher temperatures and peptide concentrations. The kinetic profile demonstrates that trehalose delays the aggregation process by increasing both these activation barriers, specifically the latter one. It increases the sampling of small-sized aggregates that lack the beta sheet conformation. Analysis reveals that the barrier in the growth of larger stable oligomers causes the formation of multiple stable small oligomers which then fuse together bimolecularly. The PCA of 26 properties was carried out to deconvolute the events within the temporary lag phases, which suggested dynamism in lags involving an increase in interchain contacts and burial of SASA. The predominant growth route is monomer addition, which changes to condensation on account of a large number of depolymerisation events in the presence of trehalose. The favourable interaction of trehalose specifically with the sidechain of the peptide promotes crowding of trehalose molecules in its vicinity - the combination of both these factors imparts the observed behaviour. Furthermore, increasing trehalose concentration leads to faster expulsion of water molecules than interpeptide interactions. These expelled water molecules have larger translational movement, suggesting an entropy factor to favor the assembly process. Different conformations observed under this condition suggest the role of water molecules in guiding the morphology of the aggregates as well. A similar scenario exists on increasing peptide concentration.
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Affiliation(s)
- Nidhi Katyal
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology, Delhi, Hauzkhas, New Delhi, India.
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26
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Lu Y, Shi XF, Salsbury FR, Derreumaux P. Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer. J Chem Phys 2018; 148:045105. [DOI: 10.1063/1.5018459] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yan Lu
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Xiao-Feng Shi
- School of Physics and Optoelectronic Engineering, Xidian University, Xi’an 710071, China
| | - Freddie R. Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27106, USA
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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27
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Multi-scale simulations of biological systems using the OPEP coarse-grained model. Biochem Biophys Res Commun 2017; 498:296-304. [PMID: 28917842 DOI: 10.1016/j.bbrc.2017.08.165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/31/2017] [Indexed: 12/14/2022]
Abstract
Biomolecules are complex machines that are optimized by evolution to properly fulfill or contribute to a variety of biochemical tasks in the cellular environment. Computer simulations based on quantum mechanics and atomistic force fields have been proven to be a powerful microscope for obtaining valuable insights into many biological, physical, and chemical processes. Many interesting phenomena involve, however, a time scale and a number of degrees of freedom, notably if crowding is considered, that cannot be explored at an atomistic resolution. To bridge the gap between reality and simulation, many different advanced computational techniques and coarse-grained (CG) models have been developed. Here, we report some applications of the CG OPEP protein model to amyloid fibril formation, the response of catch-bond proteins to two types of fluid flow, and interactive simulations to fold peptides with well-defined 3D structures or with intrinsic disorder.
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28
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Patel S, Sasidhar YU, Chary KVR. Mechanism of Initiation, Association, and Formation of Amyloid Fibrils Modeled with the N-Terminal Peptide Fragment, IKYLEFIS, of Myoglobin G-Helix. J Phys Chem B 2017; 121:7536-7549. [PMID: 28707888 DOI: 10.1021/acs.jpcb.7b02205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Some peptides and proteins undergo self-aggregation under certain conditions, leading to amyloid fibrils formation, which is related to many disease conditions. It is important to understand such amyloid fibrils formation to provide mechanistic detail that governs the process. A predominantly α-helical myoglobin has been reported recently to readily form amyloid fibrils at a higher temperature, similar to its G-helix segment. Here, we have investigated the mechanism of amyloid fibrils formation by performing multiple long molecular dynamics simulations (27 μs) on the N-terminal segment of the G-helix of myoglobin. These simulations resulted in the formation of a single-layered tetrameric β-sheet with mixed parallel and antiparallel β-strands and this is the most common event irrespective of many different starting structures. Formation of the single-layered tetrameric β-sheet takes place following three distinctive pathways. The process of fibril initiation is dependent on temperature. Further, this study provides mechanistic insights into the formation of multilayered fibrilar structure, which could be applicable to a wider variety of peptides or proteins to understand the amyloidogenesis.
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Affiliation(s)
- Sunita Patel
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,UM-DAE Centre for Excellence in Basic Sciences , Mumbai University Campus, Mumbai 400098, India
| | - Yellamraju U Sasidhar
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Kandala V R Chary
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences , Hyderabad 500075, India.,Tata Institute of Fundamental Research , Mumbai 400005, India
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29
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Tran TT, Nguyen PH, Derreumaux P. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides. J Chem Phys 2017; 144:205103. [PMID: 27250331 DOI: 10.1063/1.4951739] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Coarse-grained protein lattice models approximate atomistic details and keep the essential interactions. They are, therefore, suitable for capturing generic features of protein folding and amyloid formation at low computational cost. As our aim is to study the critical nucleus sizes of two experimentally well-characterized peptide fragments Aβ16-22 and Aβ37-42 of the full length Aβ1-42 Alzheimer's peptide, it is important that simulations with the lattice model reproduce all-atom simulations. In this study, we present a comprehensive force field parameterization based on the OPEP (Optimized Potential for Efficient protein structure Prediction) force field for an on-lattice protein model, which incorporates explicitly the formation of hydrogen bonds and directions of side-chains. Our bottom-up approach starts with the determination of the best lattice force parameters for the Aβ16-22 dimer by fitting its equilibrium parallel and anti-parallel β-sheet populations to all-atom simulation results. Surprisingly, the calibrated force field is transferable to the trimer of Aβ16-22 and the dimer and trimer of Aβ37-42. Encouraged by this finding, we characterized the free energy landscapes of the two decamers. The dominant structure of the Aβ16-22 decamer matches the microcrystal structure. Pushing the simulations for aggregates between 4-mer and 12-mer suggests a nucleus size for fibril formation of 10 chains. In contrast, the Aβ37-42 decamer is largely disordered with mixed by parallel and antiparallel chains, suggesting that the nucleus size is >10 peptides. Our refined force field coupled to this on-lattice model should provide useful insights into the critical nucleation number associated with neurodegenerative diseases.
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Affiliation(s)
- Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France
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30
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Chiricotto M, Melchionna S, Derreumaux P, Sterpone F. Hydrodynamic effects on β-amyloid (16-22) peptide aggregation. J Chem Phys 2017; 145:035102. [PMID: 27448906 DOI: 10.1063/1.4958323] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Computer simulations based on simplified representations are routinely used to explore the early steps of amyloid aggregation. However, when protein models with implicit solvent are employed, these simulations miss the effect of solvent induced correlations on the aggregation kinetics and lifetimes of metastable states. In this work, we apply the multi-scale Lattice Boltzmann Molecular Dynamics technique (LBMD) to investigate the initial aggregation phases of the amyloid Aβ16-22 peptide. LBMD includes naturally hydrodynamic interactions (HIs) via a kinetic on-lattice representation of the fluid kinetics. The peptides are represented by the flexible OPEP coarse-grained force field. First, we have tuned the essential parameters that control the coupling between the molecular and fluid evolutions in order to reproduce the experimental diffusivity of elementary species. The method is then deployed to investigate the effect of HIs on the aggregation of 100 and 1000 Aβ16-22 peptides. We show that HIs clearly impact the aggregation process and the fluctuations of the oligomer sizes by favouring the fusion and exchange dynamics of oligomers between aggregates. HIs also guide the growth of the leading largest cluster. For the 100 Aβ16-22 peptide system, the simulation of ∼300 ns allowed us to observe the transition from ellipsoidal assemblies to an elongated and slightly twisted aggregate involving almost the totality of the peptides. For the 1000 Aβ16-22 peptides, a system of unprecedented size at quasi-atomistic resolution, we were able to explore a branched disordered fibril-like structure that has never been described by other computer simulations, but has been observed experimentally.
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Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Simone Melchionna
- CNR-ISC, Institute for Complex System, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
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31
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Lei J, Qi R, Xie L, Xi W, Wei G. Inhibitory effect of hydrophobic fullerenes on the β-sheet-rich oligomers of a hydrophilic GNNQQNY peptide revealed by atomistic simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27608c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Fullerenes suppress fibril-like β-sheet oligomers by interacting strongly with the nonpolar aliphatic groups of polar residues of GNNQQNY peptide, thus inhibit peptide aggregation.
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Affiliation(s)
- Jiangtao Lei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Ruxi Qi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Luogang Xie
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Wenhui Xi
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
| | - Guanghong Wei
- State Key Laboratory of Surface Physics
- Key Laboratory for Computational Physical Sciences (Ministry of Education)
- Department of Physics
- Fudan University
- Shanghai
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32
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Ozgur B, Sayar M. Assembly of Triblock Amphiphilic Peptides into One-Dimensional Aggregates and Network Formation. J Phys Chem B 2016; 120:10243-10257. [PMID: 27635660 DOI: 10.1021/acs.jpcb.6b07545] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Peptide assembly plays a key role in both neurological diseases and development of novel biomaterials with well-defined nanostructures. Synthetic model peptides provide a unique platform to explore the role of intermolecular interactions in the assembly process. A triblock peptide architecture designed by the Hartgerink group is a versatile system which relies on Coulomb interactions, hydrogen bonding, and hydrophobicity to guide these peptides' assembly at three different length scales: β-sheets, double-wall ribbon-like aggregates, and finally a highly porous network structure which can support gels with ≤1% by weight peptide concentration. In this study, by using molecular dynamics simulations of a structure based implicit solvent coarse grained model, we analyzed this hierarchical assembly process. Parametrization of our CG model is based on multiple-state points from atomistic simulations, which enables this model to represent the conformational adaptability of the triblock peptide molecule based on the surrounding medium. Our results indicate that emergence of the double-wall β-sheet packing mechanism, proposed in light of the experimental evidence, strongly depends on the subtle balance of the intermolecular forces. We demonstrate that, even though backbone hydrogen bonding dominates the early nucleation stages, depending on the strength of the hydrophobic and Coulomb forces, alternative structures such as zero-dimensional aggregates with two β-sheets oriented orthogonally (which we refer to as a cross-packed structure) and β-sheets with misoriented hydrophobic side chains are also feasible. We discuss the implications of these competing structures for the three different length scales of assembly by systematically investigating the influence of density, counterion valency, and hydrophobicity.
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Affiliation(s)
| | - Mehmet Sayar
- College of Engineering, Koc University , Istanbul, Turkey.,Chemical & Biological Engineering and Mechanical Engineering Departments, Koc University , Istanbul, Turkey
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33
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Matthes D, Gapsys V, Brennecke JT, de Groot BL. An Atomistic View of Amyloidogenic Self-assembly: Structure and Dynamics of Heterogeneous Conformational States in the Pre-nucleation Phase. Sci Rep 2016; 6:33156. [PMID: 27616019 PMCID: PMC5018807 DOI: 10.1038/srep33156] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
The formation of well-defined filamentous amyloid structures involves a polydisperse collection of oligomeric states for which relatively little is known in terms of structural organization. Here we use extensive, unbiased explicit solvent molecular dynamics (MD) simulations to investigate the structural and dynamical features of oligomeric aggregates formed by a number of highly amyloidogenic peptides at atomistic resolution on the μs time scale. A consensus approach has been adopted to analyse the simulations in multiple force fields, yielding an in-depth characterization of pre-fibrillar oligomers and their global and local structure properties. A collision cross section analysis revealed structurally heterogeneous aggregate ensembles for the individual oligomeric states that lack a single defined quaternary structure during the pre-nucleation phase. To gain insight into the conformational space sampled in early aggregates, we probed their substructure and found emerging β-sheet subunit layers and a multitude of ordered intermolecular β-structure motifs with growing aggregate size. Among those, anti-parallel out-of-register β-strands compatible with toxic β-barrel oligomers were particularly prevalent already in smaller aggregates and formed prior to ordered fibrillar structure elements. Notably, also distinct fibril-like conformations emerged in the oligomeric state and underscore the notion that pre-nucleated oligomers serve as a critical intermediate step on-pathway to fibrils.
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Affiliation(s)
- Dirk Matthes
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Julian T Brennecke
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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34
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Chiricotto M, Tran TT, Nguyen PH, Melchionna S, Sterpone F, Derreumaux P. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Simone Melchionna
- Istituto Sistemi Complessi; Consiglio Nazionale delle Ricerche; P. le A. Moro 2 00185 Rome Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
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35
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Kmiecik S, Gront D, Kolinski M, Wieteska L, Dawid AE, Kolinski A. Coarse-Grained Protein Models and Their Applications. Chem Rev 2016; 116:7898-936. [DOI: 10.1021/acs.chemrev.6b00163] [Citation(s) in RCA: 555] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sebastian Kmiecik
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Dominik Gront
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Michal Kolinski
- Bioinformatics
Laboratory, Mossakowski Medical Research Center of the Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
| | - Lukasz Wieteska
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
- Department
of Medical Biochemistry, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
| | | | - Andrzej Kolinski
- Faculty
of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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36
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Barz B, Strodel B. Understanding Amyloid-β Oligomerization at the Molecular Level: The Role of the Fibril Surface. Chemistry 2016; 22:8768-72. [PMID: 27135646 DOI: 10.1002/chem.201601701] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 12/11/2022]
Abstract
The aggregation of the amyloid β-peptide into fibrils is a complex process that involves mechanisms such as primary and secondary nucleation, fibril elongation and fibril fragmentation. Some of these processes generate neurotoxic Aβ oligomers, which are involved in the development of Alzheimer's disease. Recent experimental studies have emphasized the role of the fibril as a catalytic surface for the production of highly toxic oligomers during secondary nucleation. By using molecular dynamics simulations, we show that it is the hydrophobic fibril region that causes the structural changes required for catalyzing the formation of β-sheet-rich Aβ1-42 oligomers on the fibril surface. These results reveal, for the first time, the molecular basis of the secondary nucleation pathway.
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Affiliation(s)
- Bogdan Barz
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätstrasse 1, 40225, Düsseldorf, Germany. , .,Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany. ,
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37
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Luiken JA, Bolhuis PG. Prediction of a stable associated liquid of short amyloidogenic peptides. Phys Chem Chem Phys 2016; 17:10556-67. [PMID: 25804723 DOI: 10.1039/c5cp00284b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Amyloid fibril formation is believed to be a nucleation-controlled process. Depending on the nature of peptide sequence, fibril nucleation can occur in one step, straight from a dilute solution, or in multiple steps via oligomers or disordered aggregates. What determines this process is poorly understood. Since the fibril formation kinetics is driven by thermodynamic forces, knowledge of the phase behavior is crucial. Here, we investigated the phase behavior of three short peptide sequences of varying side-chain hydrophobicity. Replica exchange molecular dynamics simulations of a mid-resolution model indicate that the weakly hydrophobic peptide forms fibrils directly from solution, whereas the most hydrophobic peptide forms a dense liquid phase before crystallizing into ordered fibrils at low temperatures. For the medium hydrophobic peptide we found evidence of a novel additional transition to a liquid phase consisting of clusters of aligned peptides, implying a three-step nucleation process. We tested the robustness of this prediction by applying Wertheim's theory and statistical associating fluid theory to a hard-sphere model dressed with isotropic and anisotropic attractions. We found that the ratio of interaction strengths strongly affects the phase behavior, and under certain conditions indeed gives rise to a stable polymerized liquid phase. The peptide clusters in the associated liquid tend to be slow and long-lived, which may give the oligomer droplet more time to act as a toxic oligomer, before turning into a fibril.
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Affiliation(s)
- Jurriaan A Luiken
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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38
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Srivastava A, Balaji PV. Molecular events during the early stages of aggregation of GNNQQNY: An all atom MD simulation study of randomly dispersed peptides. J Struct Biol 2015; 192:376-391. [DOI: 10.1016/j.jsb.2015.09.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 09/26/2015] [Accepted: 09/30/2015] [Indexed: 12/11/2022]
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39
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Nochebuena J, Ireta J. On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides. J Chem Phys 2015; 143:135103. [DOI: 10.1063/1.4932083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jorge Nochebuena
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
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40
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Luiken JA, Bolhuis PG. Primary Nucleation Kinetics of Short Fibril-Forming Amyloidogenic Peptides. J Phys Chem B 2015; 119:12568-79. [DOI: 10.1021/acs.jpcb.5b05799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jurriaan A. Luiken
- van ’t
Hoff Institute
for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, Netherlands
| | - Peter G. Bolhuis
- van ’t
Hoff Institute
for Molecular Sciences, University of Amsterdam, P.O. Box 94157, 1090 GD Amsterdam, Netherlands
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41
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Martinez AV, Małolepsza E, Rivera E, Lu Q, Straub JE. Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles. J Chem Phys 2015; 141:22D530. [PMID: 25494801 DOI: 10.1063/1.4902550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Knowledge of how intermolecular interactions of amyloid-forming proteins cause protein aggregation and how those interactions are affected by sequence and solution conditions is essential to our understanding of the onset of many degenerative diseases. Of particular interest is the aggregation of the amyloid-β (Aβ) peptide, linked to Alzheimer's disease, and the aggregation of the Sup35 yeast prion peptide, which resembles the mammalian prion protein linked to spongiform encephalopathies. To facilitate the study of these important peptides, experimentalists have identified small peptide congeners of the full-length proteins that exhibit amyloidogenic behavior, including the KLVFFAE sub-sequence, Aβ16-22, and the GNNQQNY subsequence, Sup357-13. In this study, molecular dynamics simulations were used to examine these peptide fragments encapsulated in reverse micelles (RMs) in order to identify the fundamental principles that govern how sequence and solution environment influence peptide aggregation. Aβ16-22 and Sup357-13 are observed to organize into anti-parallel and parallel β-sheet arrangements. Confinement in the sodium bis(2-ethylhexyl) sulfosuccinate (AOT) reverse micelles is shown to stabilize extended peptide conformations and enhance peptide aggregation. Substantial fluctuations in the reverse micelle shape are observed, in agreement with earlier studies. Shape fluctuations are found to facilitate peptide solvation through interactions between the peptide and AOT surfactant, including direct interaction between non-polar peptide residues and the aliphatic surfactant tails. Computed amide I IR spectra are compared with experimental spectra and found to reflect changes in the peptide structures induced by confinement in the RM environment. Furthermore, examination of the rotational anisotropy decay of water in the RM demonstrates that the water dynamics are sensitive to the presence of peptide as well as the peptide sequence. Overall, our results demonstrate that the RM is a complex confining environment where substantial direct interaction between the surfactant and peptides plays an important role in determining the resulting ensemble of peptide conformations. By extension the results suggest that similarly complex sequence-dependent interactions may determine conformational ensembles of amyloid-forming peptides in a cellular environment.
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Affiliation(s)
| | - Edyta Małolepsza
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Eva Rivera
- Department of Chemistry and Biochemistry, Queens College, City University of New York (CUNY), Flushing, New York 11791, USA
| | - Qing Lu
- Division of Materials Science and Engineering, Boston University, Brookline, Massachusetts 02446, USA
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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42
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Sterpone F, Derreumaux P, Melchionna S. Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics. J Chem Theory Comput 2015; 11:1843-53. [PMID: 26574390 PMCID: PMC5242371 DOI: 10.1021/ct501015h] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A novel simulation framework that integrates the OPEP coarse-grained (CG) model for proteins with the Lattice Boltzmann (LB) methodology to account for the fluid solvent at mesoscale level is presented. OPEP is a very efficient, water-free and electrostatic-free force field that reproduces at quasi-atomistic detail processes like peptide folding, structural rearrangements, and aggregation dynamics. The LB method is based on the kinetic description of the solvent in order to solve the fluid mechanics under a wide range of conditions, with the further advantage of being highly scalable on parallel architectures. The capabilities of the approach are presented, and it is shown that the strategy is effective in exploring the role of hydrodynamics on protein relaxation and peptide aggregation. The end result is a strategy for modeling systems of thousands of proteins, such as in the case of dense protein suspensions. The future perspectives of the multiscale approach are also discussed.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France
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43
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Langkilde AE, Morris KL, Serpell LC, Svergun DI, Vestergaard B. The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:882-95. [PMID: 25849399 PMCID: PMC4388266 DOI: 10.1107/s1399004715001674] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 01/25/2015] [Indexed: 11/12/2022]
Abstract
Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.
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Affiliation(s)
- Annette E. Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Kyle L. Morris
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, Brighton, England
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22607 Hamburg, Germany
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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44
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Morriss-Andrews A, Shea JE. Computational Studies of Protein Aggregation: Methods and Applications. Annu Rev Phys Chem 2015; 66:643-66. [DOI: 10.1146/annurev-physchem-040513-103738] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joan-Emma Shea
- Department of Physics and
- Department of Chemistry, University of California, Santa Barbara, California 93106;
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45
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Nasica-Labouze J, Nguyen PH, Sterpone F, Berthoumieu O, Buchete NV, Coté S, De Simone A, Doig AJ, Faller P, Garcia A, Laio A, Li MS, Melchionna S, Mousseau N, Mu Y, Paravastu A, Pasquali S, Rosenman DJ, Strodel B, Tarus B, Viles JH, Zhang T, Wang C, Derreumaux P. Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies. Chem Rev 2015; 115:3518-63. [PMID: 25789869 DOI: 10.1021/cr500638n] [Citation(s) in RCA: 478] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jessica Nasica-Labouze
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Phuong H Nguyen
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Fabio Sterpone
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Olivia Berthoumieu
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Sébastien Coté
- ∥Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, C.P. 6128, succursale Centre-ville, Montréal, Québec H3C 3T5, Canada
| | - Alfonso De Simone
- ⊥Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Andrew J Doig
- #Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Faller
- ‡LCC (Laboratoire de Chimie de Coordination), CNRS, Université de Toulouse, Université Paul Sabatier (UPS), Institut National Polytechnique de Toulouse (INPT), 205 route de Narbonne, BP 44099, Toulouse F-31077 Cedex 4, France
| | | | - Alessandro Laio
- ○The International School for Advanced Studies (SISSA), Via Bonomea 265, 34136 Trieste, Italy
| | - Mai Suan Li
- ◆Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland.,¶Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City, Vietnam
| | - Simone Melchionna
- ⬠Instituto Processi Chimico-Fisici, CNR-IPCF, Consiglio Nazionale delle Ricerche, 00185 Roma, Italy
| | | | - Yuguang Mu
- ▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Anant Paravastu
- ⊕National High Magnetic Field Laboratory, 1800 East Paul Dirac Drive, Tallahassee, Florida 32310, United States
| | - Samuela Pasquali
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | | | - Birgit Strodel
- △Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Bogdan Tarus
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - John H Viles
- ▼School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Tong Zhang
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,▲School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | | | - Philippe Derreumaux
- †Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.,□Institut Universitaire de France, 75005 Paris, France
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Portillo A, Hashemi M, Zhang Y, Breydo L, Uversky VN, Lyubchenko YL. Role of monomer arrangement in the amyloid self-assembly. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:218-28. [PMID: 25542374 DOI: 10.1016/j.bbapap.2014.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 11/24/2014] [Accepted: 12/10/2014] [Indexed: 02/05/2023]
Abstract
Assembly of amyloid proteins into aggregates requires the ordering of the monomers in oligomers and especially in such highly organized structures as fibrils. This ordering is accompanied by structural transitions leading to the formation of ordered β-structural motifs in proteins and peptides lacking secondary structures. To characterize the effect of the monomer arrangements on the aggregation process at various stages, we performed comparative studies of the yeast prion protein Sup35 heptapeptide (GNNQQNY) along with its dimeric form CGNNQQNY-(d-Pro)-G-GNNQQNY. The (d-Pro)-G linker in this construct is capable of adopting a β-turn, facilitating the assembly of the dimer into the dimeric antiparallel hairpin structure (AP-hairpin). We applied Atomic Force Microscopy (AFM) techniques to follow peptide-peptide interactions at the single molecule level, to visualize the morphology of aggregates formed by both constructs, thioflavin T (ThT) fluorescence to follow the aggregation kinetics, and circular dichroism (CD) spectroscopy to characterize the secondary structure of the constructs. The ThT fluorescence data showed that the AP-hairpin aggregation kinetics is insensitive to the external environment such as ionic strength and pH contrary to the monomers the kinetics of which depends dramatically on the ionic strength and pH. The AFM topographic imaging revealed that AP-hairpins primarily assemble into globular aggregates, whereas linear fibrils are primary assemblies of the monomers suggesting that both constructs follow different aggregation pathways during the self-assembly. These morphological differences are in line with the AFM force spectroscopy experiments and CD spectroscopy measurements, suggesting that the AP-hairpin is structurally rigid regardless of changes of environmental factors.
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Affiliation(s)
- Alexander Portillo
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Yuliang Zhang
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Leonid Breydo
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd. MDC07, Tampa, FL 33647, USA; Department of Biological Science, Faculty of Science, King Abdulaziz University, PO Box 80203, Jeddah 21589, Saudi Arabia; Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA.
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Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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50
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Yang YI, Gao YQ. Computer Simulation Studies of Aβ37–42 Aggregation Thermodynamics and Kinetics in Water and Salt Solution. J Phys Chem B 2014; 119:662-70. [DOI: 10.1021/jp502169b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Y. Isaac Yang
- Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yi Qin Gao
- Institute of Theoretical
and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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