1
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Varenyk Y, Theodorakis PE, Pham DQH, Li MS, Krupa P. Exploring Structural Insights of Aβ42 and α-Synuclein Monomers and Heterodimer: A Comparative Study Using Implicit and Explicit Solvent Simulations. J Phys Chem B 2024; 128:4655-4669. [PMID: 38700150 PMCID: PMC11103699 DOI: 10.1021/acs.jpcb.4c00503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 05/05/2024]
Abstract
Protein misfolding, aggregation, and fibril formation play a central role in the development of severe neurological disorders, including Alzheimer's and Parkinson's diseases. The structural stability of mature fibrils in these diseases is of great importance, as organisms struggle to effectively eliminate amyloid plaques. To address this issue, it is crucial to investigate the early stages of fibril formation when monomers aggregate into small, toxic, and soluble oligomers. However, these structures are inherently disordered, making them challenging to study through experimental approaches. Recently, it has been shown experimentally that amyloid-β 42 (Aβ42) and α-synuclein (α-Syn) can coassemble. This has motivated us to investigate the interaction between their monomers as a first step toward exploring the possibility of forming heterodimeric complexes. In particular, our study involves the utilization of various Amber and CHARMM force-fields, employing both implicit and explicit solvent models in replica exchange and conventional simulation modes. This comprehensive approach allowed us to assess the strengths and weaknesses of these solvent models and force fields in comparison to experimental and theoretical findings, ensuring the highest level of robustness. Our investigations revealed that Aβ42 and α-Syn monomers can indeed form stable heterodimers, and the resulting heterodimeric model exhibits stronger interactions compared to the Aβ42 dimer. The binding of α-Syn to Aβ42 reduces the propensity of Aβ42 to adopt fibril-prone conformations and induces significant changes in its conformational properties. Notably, in AMBER-FB15 and CHARMM36m force fields with the use of explicit solvent, the presence of Aβ42 significantly increases the β-content of α-Syn, consistent with the experiments showing that Aβ42 triggers α-Syn aggregation. Our analysis clearly shows that although the use of implicit solvent resulted in too large compactness of monomeric α-Syn, structural properties of monomeric Aβ42 and the heterodimer were preserved in explicit-solvent simulations. We anticipate that our study sheds light on the interaction between α-Syn and Aβ42 proteins, thus providing the atom-level model required to assess the initial stage of aggregation mechanisms related to Alzheimer's and Parkinson's diseases.
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Affiliation(s)
- Yuliia Varenyk
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Department
of Theoretical Chemistry, University of
Vienna, Vienna 1090, Austria
| | | | - Dinh Q. H. Pham
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Paweł Krupa
- Institute
of Physics Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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2
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Manathunga L, Akter R, Zhyvoloup A, Simmerling C, Raleigh DP. On the plasticity of amyloid formation: The impact of destabilizing small to large substitutions on islet amyloid polypeptide amyloid formation. Protein Sci 2023; 32:e4539. [PMID: 36484106 PMCID: PMC9847078 DOI: 10.1002/pro.4539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/19/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Amyloids are partially ordered, proteinaceous, β-sheet rich deposits that have been implicated in a wide range of diseases. An even larger set of proteins that do not normally form amyloid in vivo can be induced to do so in vitro. A growing number of structures of amyloid fibrils have been reported and a common feature is the presence of a tightly packed core region in which adjacent monomers pack together in extremely tight interfaces, often referred to as steric zippers. A second common feature of many amyloid fibrils is their polymorphous nature. We examine the consequences of disrupting the tight packing in amyloid fibrils on the kinetics of their formation using the 37 residue polypeptide hormone islet amyloid polypeptide (IAPP, amylin) as a model system. IAPP forms islet amyloid in vivo and is aggressively amyloidogenic in vitro. Six Cryo-EM structures of IAPP amyloid fibrils are available and in all Gly24 is in the core of the structured region and makes tight contacts with other residues. Calculations using the ff14SBonlysc forcefield in Amber20 show that substitutions with larger amino acids significantly disrupt close packing and are predicted to destabilize the various fibril structures. However, Gly to 2-amino butyric acid (2-carbon side chain) and Gly to Leu substitutions actually enhance the rate of amyloid formation. A Pro substitution slows, but does not prevent amyloid formation.
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Affiliation(s)
- Lakshan Manathunga
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookNew YorkUSA
| | - Rehana Akter
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
| | - Alexander Zhyvoloup
- Research Department of Structural and Molecular BiologyUniversity College LondonLondonUK
| | - Carlos Simmerling
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookNew YorkUSA
| | - Daniel P. Raleigh
- Department of ChemistryStony Brook UniversityStony BrookNew YorkUSA
- Laufer Center for Physical and Quantitative Biology, Stony Brook UniversityStony BrookNew YorkUSA
- Research Department of Structural and Molecular BiologyUniversity College LondonLondonUK
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3
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Baidya L, Reddy G. pH Induced Switch in the Conformational Ensemble of Intrinsically Disordered Protein Prothymosin-α and Its Implications for Amyloid Fibril Formation. J Phys Chem Lett 2022; 13:9589-9598. [PMID: 36206480 DOI: 10.1021/acs.jpclett.2c01972] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aggregation of intrinsically disordered proteins (IDPs) can lead to neurodegenerative diseases. Although there is experimental evidence that acidic pH promotes IDP monomer compaction leading to aggregation, the general mechanism is unclear. We studied the pH effect on the conformational ensemble of prothymosin-α (proTα), which is involved in multiple essential functions, and probed its role in aggregation using computer simulations. We show that compaction in the proTα dimension at low pH is due to the protein's collapse in the intermediate region (E41-D80) rich in glutamic acid residues, enhancing its β-sheet content. We observed by performing dimer simulations that the conformations with high β-sheet content could act as aggregation-prone (N*) states and nucleate the aggregation process. The simulations initiated using N* states form dimers within a microsecond time scale, whereas the non-N* states do not form dimers within this time scale. This study contributes to understanding the general principles of pH-induced IDP aggregation.
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Affiliation(s)
- Lipika Baidya
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka560012, India
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4
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Thu TTM, Li MS. Protein aggregation rate depends on mechanical stability of fibrillar structure . J Chem Phys 2022; 157:055101. [DOI: 10.1063/5.0088689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formation of the fibrillar structure of amyloid proteins/peptides is believed to be associated with neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, etc. Since the rate of aggregation can influence neurotoxicity, finding the key factors that control this rate is of paramount importance. It was recently found evidence that the rate of protein aggregation is related to the mechanical stability of the fibrillar structure, such that the higher the mechanical stability, the faster the fibril is formed. However, this conclusion was supported by a limited dataset. In this work, we expand the previous study to a larger dataset, including the wild type of Aβ42 peptide and its 20 mutants, the aggregation rate of which was measured experimentally. By using all-atom steered molecular dynamics (SMD) simulations we can access the mechanical stability of the fibril structure, which is characterized by the rupture force, pulling work and unbinding free energy barrier. Our result confirms that mechanical stability is indeed related to the aggregation rate. Since estimation of the aggregation rate using all-atom simulations is almost forbidden by the current computational capabilities, our result is useful for predicting it based on information obtained from fast SMD simulations for fibrils.
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Affiliation(s)
| | - Mai Suan Li
- Theoretical Physics, Institute of Physics, Polish Academy of Sciences, Poland
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5
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Co NT, Li MS, Krupa P. Computational Models for the Study of Protein Aggregation. Methods Mol Biol 2022; 2340:51-78. [PMID: 35167070 DOI: 10.1007/978-1-0716-1546-1_4] [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
Protein aggregation has been studied by many groups around the world for many years because it can be the cause of a number of neurodegenerative diseases that have no effective treatment. Obtaining the structure of related fibrils and toxic oligomers, as well as describing the pathways and main factors that govern the self-organization process, is of paramount importance, but it is also very difficult. To solve this problem, experimental and computational methods are often combined to get the most out of each method. The effectiveness of the computational approach largely depends on the construction of a reasonable molecular model. Here we discussed different versions of the four most popular all-atom force fields AMBER, CHARMM, GROMOS, and OPLS, which have been developed for folded and intrinsically disordered proteins, or both. Continuous and discrete coarse-grained models, which were mainly used to study the kinetics of aggregation, are also summarized.
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Affiliation(s)
- Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- Institute for Computational Science and Technology, Ho Chi Minh City, Vietnam
| | - Pawel Krupa
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
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6
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Kumar A, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D. Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. J Phys Chem Lett 2021; 12:9026-9032. [PMID: 34516126 PMCID: PMC8826754 DOI: 10.1021/acs.jpclett.1c02310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Residues spanning distinct regions of the low-complexity domain of the RNA-binding protein, Fused in Sarcoma (FUS-LC), form fibril structures with different core morphologies. Solid-state NMR experiments show that the 214-residue FUS-LC forms a fibril with an S-bend (core-1, residues 39-95), while the rest of the protein is disordered. In contrast, the fibrils of the C-terminal variant (FUS-LC-C; residues 111-214) have a U-bend topology (core-2, residues 112-150). Absence of the U-bend in FUS-LC implies that the two fibril cores do not coexist. Computer simulations show that these perplexing findings could be understood in terms of the population of sparsely populated fibril-like excited states in the monomer. The propensity to form core-1 is higher compared to core-2. We predict that core-2 forms only in truncated variants that do not contain the core-1 sequence. At the monomer level, sequence-dependent enthalpic effects determine the relative stabilities of the core-1 and core-2 topologies.
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Affiliation(s)
- Abhinaw Kumar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Mauro Lorenzo Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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7
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Poma AB, Thu TTM, Tri LTM, Nguyen HL, Li MS. Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations. J Phys Chem B 2021; 125:7628-7637. [PMID: 34253022 PMCID: PMC8389904 DOI: 10.1021/acs.jpcb.1c02322] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/25/2021] [Indexed: 02/07/2023]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder and one of the main causes of dementia. The disease is associated with amyloid beta (Aβ) peptide aggregation forming initial clusters and then fibril structure and plaques. Other neurodegenerative diseases such as type 2 diabetes, amyotrophic lateral sclerosis, and Parkinson's disease follow a similar mechanism. Therefore, inhibition of Aβ aggregation is considered an effective way to prevent AD. Recent experiments have provided evidence that oligomers are more toxic agents than mature fibrils, prompting researchers to investigate various factors that may influence their properties. One of these factors is nanomechanical stability, which plays an important role in the self-assembly of Aβ and possibly other proteins. This stability is also likely to be related to cell toxicity. In this work, we compare the mechanical stability of Aβ-tetramers and fibrillar structures using a structure-based coarse-grained (CG) approach and all-atom molecular dynamics simulation. Our results support the evidence for an increase in mechanical stability during the Aβ fibrillization process, which is consistent with in vitro AFM characterization of Aβ42 oligomers. Namely, using a CG model, we showed that the Young modulus of tetramers is lower than that of fibrils and, as follows from the experiment, is about 1 GPa. Hydrogen bonds are the dominant contribution to the detachment of one chain from the Aβ fibril fragment. They tend to be more organized along the pulling direction, whereas in the Aβ tetramers no preference is observed.
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Affiliation(s)
- Adolfo B. Poma
- Institute
of Fundamental Technological Research, Polish
Academy of Sciences, Pawińskiego 5B, 02-106 Warsaw, Poland
- International
Center for Research on Innovative Biobased Materials (ICRI-BioM)—International
Research Agenda, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland
| | - Tran Thi Minh Thu
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Faculty
of Materials Science and Technology, Ho
Chi Minh City University of Science - VNUHCM, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Lam Tang Minh Tri
- Faculty
of Materials Science and Technology, Ho
Chi Minh City University of Science - VNUHCM, 227 Nguyen Van Cu Street, District 5, Ho Chi Minh City, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Hoang Linh Nguyen
- Institute
for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh
Hiep Ward, District 12, Ho Chi Minh City, Vietnam
- Ho
Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 700000, Vietnam
- Vietnam
National University, Ho Chi Minh
City 700000, Vietnam
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
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8
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Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea JE, Dokholyan NV, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesné S, Wei G, Sterpone F, Doig AJ, Derreumaux P. Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis. Chem Rev 2021; 121:2545-2647. [PMID: 33543942 PMCID: PMC8836097 DOI: 10.1021/acs.chemrev.0c01122] [Citation(s) in RCA: 378] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein misfolding and aggregation is observed in many amyloidogenic diseases affecting either the central nervous system or a variety of peripheral tissues. Structural and dynamic characterization of all species along the pathways from monomers to fibrils is challenging by experimental and computational means because they involve intrinsically disordered proteins in most diseases. Yet understanding how amyloid species become toxic is the challenge in developing a treatment for these diseases. Here we review what computer, in vitro, in vivo, and pharmacological experiments tell us about the accumulation and deposition of the oligomers of the (Aβ, tau), α-synuclein, IAPP, and superoxide dismutase 1 proteins, which have been the mainstream concept underlying Alzheimer's disease (AD), Parkinson's disease (PD), type II diabetes (T2D), and amyotrophic lateral sclerosis (ALS) research, respectively, for many years.
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Affiliation(s)
- Phuong H Nguyen
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Bikash R Sahoo
- Biophysics and Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Jie Zheng
- Department of Chemical & Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Peter Faller
- Institut de Chimie, UMR 7177, CNRS-Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Laura Dominguez
- Facultad de Química, Departamento de Fisicoquímica, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Nikolay V Dokholyan
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
- Department of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Molecular Biology, University of Naples Federico II, Naples 80138, Italy
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc., Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, United States
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Saeed Najafi
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics & Faculty of Applied Sciences, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Mara Chiricotto
- Department of Chemical Engineering and Analytical Science, University of Manchester, Manchester M13 9PL, U.K
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - James McCarty
- Chemistry Department, Western Washington University, Bellingham, Washington 98225, United States
| | - Mai Suan Li
- Institute for Computational Science and Technology, SBI Building, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Carol Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yiming Wang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695-7905, United States
| | - Yifat Miller
- Department of Chemistry and The Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | | | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects, (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600 Pessac, France
| | - Stepan Timr
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Jiaxing Chen
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Brianna Hnath
- Department of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, Pennsylvania 17033, United States
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, and Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Sylvain Lesné
- Department of Neuroscience, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, and Key Laboratory for Computational Physical Science, Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200438, China
| | - Fabio Sterpone
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
| | - Andrew J Doig
- Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, U.K
| | - Philippe Derreumaux
- CNRS, UPR9080, Université de Paris, Laboratory of Theoretical Biochemistry, IBPC, Fondation Edmond de Rothschild, PSL Research University, Paris 75005, France
- Laboratory of Theoretical Chemistry, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
- Faculty of Pharmacy, Ton Duc Thang University, 33000 Ho Chi Minh City, Vietnam
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Saini R, Shuaib S, Goyal D, Goyal B. Impact of Mutations on the Conformational Transition from α-Helix to β-Sheet Structures in Arctic-Type Aβ 40: Insights from Molecular Dynamics Simulations. ACS OMEGA 2020; 5:23219-23228. [PMID: 32954172 PMCID: PMC7495726 DOI: 10.1021/acsomega.0c02983] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/13/2020] [Indexed: 05/13/2023]
Abstract
The amyloid-β (Aβ) protein aggregation into toxic oligomers and fibrils has been recognized as a key player in the pathogenesis of Alzheimer's disease. Recent experiments reported that a double alanine mutation (L17A/F19A) in the central hydrophobic core (CHC) region of [G22]Aβ40 (familial Arctic mutation) diminished the self-assembly propensity of [G22]Aβ40. However, the molecular mechanism behind the decreased aggregation tendency of [A17/A19/G22]Aβ40 is not well understood. Herein, we carried out molecular dynamics simulations to elucidate the structure and dynamics of [G22]Aβ40 and [A17/A19/G22]Aβ40. The results for the secondary structure analysis reveal a significantly increased amount of the helical content in the CHC and C-terminal region of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40. The bending free-energy analysis of D23-K28 salt bridge suggests that the double alanine mutation in the CHC region of [G22]Aβ40 has the potential to reduce the fibril formation rate by 0.57 times of [G22]Aβ40. Unlike [G22]Aβ40, [A17/A19/G22]Aβ40 largely sampled helical conformation, as determined by the minimum energy conformations extracted from the free-energy landscape. The present study provided atomic level details into the experimentally observed diminished aggregation tendency of [A17/A19/G22]Aβ40 as compared to [G22]Aβ40.
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Affiliation(s)
- Rajneet
Kaur Saini
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Suniba Shuaib
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Deepti Goyal
- Department
of Chemistry, Faculty of Basic and Applied Sciences, Sri Guru Granth Sahib World University, Fatehgarh Sahib 140406, Punjab, India
| | - Bhupesh Goyal
- School
of Chemistry & Biochemistry, Thapar
Institute of Engineering & Technology, Patiala 147004, Punjab, India
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10
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Differences in the free energies between the excited states of A β40 and A β42 monomers encode their aggregation propensities. Proc Natl Acad Sci U S A 2020; 117:19926-19937. [PMID: 32732434 DOI: 10.1073/pnas.2002570117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The early events in the aggregation of the intrinsically disordered peptide, amyloid-β (Aβ), involve transitions from the disordered free energy ground state to assembly-competent states. Are the fingerprints of order found in the amyloid fibrils encoded in the conformations that the monomers access at equilibrium? If so, could the enhanced aggregation rate of Aβ42 compared to Aβ40 be rationalized from the sparsely populated high free energy states of the monomers? Here, we answer these questions in the affirmative using coarse-grained simulations of the self-organized polymer-intrinsically disordered protein (SOP-IDP) model of Aβ40 and Aβ42. Although both the peptides have practically identical ensemble-averaged properties, characteristic of random coils (RCs), the conformational ensembles of the two monomers exhibit sequence-specific heterogeneity. Hierarchical clustering of conformations reveals that both the peptides populate high free energy aggregation-prone ([Formula: see text]) states, which resemble the monomers in the fibril structure. The free energy gap between the ground (RC) and the [Formula: see text] states of Aβ42 peptide is smaller than that for Aβ40. By relating the populations of excited states of the two peptides to the fibril formation time scales using an empirical formula, we explain nearly quantitatively the faster aggregation rate of Aβ42 relative to Aβ40. The [Formula: see text] concept accounts for fibril polymorphs, leading to the prediction that the less stable [Formula: see text] state of Aβ42, encoding for the U-bend fibril, should form earlier than the structure with the S-bend topology, which is in accord with Ostwald's rule rationalizing crystal polymorph formation.
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11
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Saranya V, Mary PV, Vijayakumar S, Shankar R. The hazardous effects of the environmental toxic gases on amyloid beta-peptide aggregation: A theoretical perspective. Biophys Chem 2020; 263:106394. [PMID: 32480019 DOI: 10.1016/j.bpc.2020.106394] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Alzheimer's disease (AD) is one of the leading causes of dementia in elderly people. It has been well documented that the exposure to environmental toxins such as CO, CO2, SO2 and NO2 that are present in the air is considered as a hallmark for the progression of Alzheimer's disease. However, their actual mechanism by which environmental toxin triggers the aggregation of Aβ42 peptide at the molecular and atomic levels remain unknown. In this study, molecular dynamics simulation was carried out to study the aggregation mechanism of the Aβ42 peptide due to its interaction of toxic gas (CO, CO2, SO2 and NO2). During the 400 ns simulation, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes have smaller Root Mean Square Deviation values when compared to the Aβ42 peptide, which shows that the interaction of toxic gases (CO, CO2, SO2, and NO2) would increase the Aβ42 peptide structural stability. The radius of gyration analysis also supports that Aβ42 interacted CO2 and SO2 complexes have the minimum value in the range of 0.95 nm and 1.5 nm. It is accounted that the Aβ42 interacted CO2 and SO2 complexes have a greater compact structure in comparison to Aβ42 interacted CO and NO2 complexes. Furthermore, all the Aβ42 interacted toxic gas (CO, CO2, SO2, and NO2) complexes exhibited an enhanced secondary structural probability for coil and turn regions with a reduced α-helix probability, which indicates that the interaction of toxic gases may enhance the toxicity and aggregation of Aβ42.
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Affiliation(s)
- Vasudevan Saranya
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India
| | - Pitchumani Violet Mary
- Department of Physics, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641 062, India
| | | | - Ramasamy Shankar
- Molecular Simulation Laboratory, Department of Physics, Bharathiar University, Coimbatore 641 046, India.
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12
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Krupa P, Quoc Huy PD, Li MS. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components. J Chem Phys 2019. [DOI: 10.1063/1.5093184] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Pawel Krupa
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Pham Dinh Quoc Huy
- Institute of Physics Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics Polish Academy of Sciences, Al. Lotników 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
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13
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Saini RK, Shuaib S, Goyal D, Goyal B. Molecular insights into the effect L17A/F19A double mutation on the structure and dynamics of Aβ
40
: A molecular dynamics simulation study. J Cell Biochem 2018; 119:8949-8961. [DOI: 10.1002/jcb.27149] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 05/18/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Rajneet Kaur Saini
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Suniba Shuaib
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Deepti Goyal
- Department of Chemistry, Faculty of Basic and Applied Sciences Sri Guru Granth Sahib World University Fatehgarh Sahib India
| | - Bhupesh Goyal
- School of Chemistry & Biochemistry Thapar Institute of Engineering & Technology Patiala India
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14
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Kouza M, Co NT, Li MS, Kmiecik S, Kolinski A, Kloczkowski A, Buhimschi IA. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study. J Chem Phys 2018; 148:215106. [PMID: 29884031 DOI: 10.1063/1.5028575] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Nguyen Truong Co
- Institute of Physics, Polish Academy of Sciences, Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Sebastian Kmiecik
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, The Research Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, Ohio 43215, USA
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15
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Boopathi S, Kolandaivel P. Effect of mutation on Aβ1-42-Heme complex in aggregation mechanism: Alzheimer’s disease. J Mol Graph Model 2017; 76:224-233. [DOI: 10.1016/j.jmgm.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 10/19/2022]
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16
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Kouza M, Banerji A, Kolinski A, Buhimschi IA, Kloczkowski A. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model. Phys Chem Chem Phys 2017; 19:2990-2999. [PMID: 28079198 PMCID: PMC5305032 DOI: 10.1039/c6cp07145g] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Preeclampsia, a pregnancy-specific disorder, shares typical pathophysiological features with protein misfolding disorders including Alzheimer's disease. Characteristic for preeclampsia is the involvement of multiple proteins of which fragments of SERPINA1 and β-amyloid co-aggregate in urine and placenta of preeclamptic women. To explore the biophysical basis of this interaction, we investigated the multidimensional efficacy of the FVFLM sequence in SERPINA1, as a model inhibitory agent of β-amyloid aggregation. After studying the oligomerization of FVFLM peptides using all-atom molecular dynamics simulations with the GROMOS43a1 force field and explicit water, we report that FVFLM can aggregate and its aggregation is spontaneous with a remarkably faster rate than that recorded for KLVFF (aggregation "hot-spot" from β-amyloid). The fast kinetics of FVFLM aggregation was found to be driven primarily by core-like aromatic interactions originating from the anti-parallel orientation of complementarily uncharged strands. The conspicuously stable aggregation mechanism observed for FVFLM peptides is found not to conform to the popular 'dock-lock' scheme. We also found high propensity of FVFLM for KLVFF binding. When present, FVFLM disrupts the β-amyloid aggregation pathway and we propose that FVFLM-like peptides might be used to prevent the assembly of full-length Aβ or other pro-amyloidogenic peptides into amyloid fibrils.
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Affiliation(s)
- M Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland. and Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Banerji
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA
| | - A Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - I A Buhimschi
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
| | - A Kloczkowski
- Nationwide Children's Hospital, Battelle Center for Mathematical Medicine, Columbus, OH 43215, USA and Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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17
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Faraggi E, Kouza M, Zhou Y, Kloczkowski A. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile. Methods Mol Biol 2017; 1484:127-136. [PMID: 27787824 DOI: 10.1007/978-1-4939-6406-2_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A fast accessible surface area (ASA) predictor is presented. In this new approach no residue mutation profiles generated by multiple sequence alignments are used as inputs. Instead, we use only single sequence information and global features such as single-residue and two-residue compositions of the chain. The resulting predictor is both highly more efficient than sequence alignment based predictors and of comparable accuracy to them. Introduction of the global inputs significantly helps achieve this comparable accuracy. The predictor, termed ASAquick, is found to perform similarly well for so-called easy and hard cases indicating generalizability and possible usability for de-novo protein structure prediction. The source code and a Linux executables for ASAquick are available from Research and Information Systems at http://mamiris.com and from the Battelle Center for Mathematical Medicine at http://mathmed.org .
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Affiliation(s)
- Eshel Faraggi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA.,Research and Information Systems, LLC, Indianapolis, IN, USA
| | - Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | - Yaoqi Zhou
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Parklands Drive, Southport, QLD 4222, Australia
| | - Andrzej Kloczkowski
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbu, OH 43205, USA. .,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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18
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Kouza M, Faraggi E, Kolinski A, Kloczkowski A. The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool. Methods Mol Biol 2017; 1484:7-24. [PMID: 27787816 DOI: 10.1007/978-1-4939-6406-2_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The GOR method of protein secondary structure prediction is described. The original method was published by Garnier, Osguthorpe, and Robson in 1978 and was one of the first successful methods to predict protein secondary structure from amino acid sequence. The method is based on information theory, and an assumption that information function of a protein chain can be approximated by a sum of information from single residues and pairs of residues. The analysis of frequencies of occurrence of secondary structure for singlets and doublets of residues in a protein database enables prediction of secondary structure for new amino acid sequences. Because of these simple physical assumptions the GOR method has a conceptual advantage over other later developed methods such as PHD, PSIPRED, and others that are based on Machine Learning methods (like Neural Networks), give slightly better predictions, but have a "black box" nature. The GOR method has been continuously improved and modified for 30 years with the last GOR V version published in 2002, and the GOR V server developed in 2005. We discuss here the original GOR method and the GOR V program and the web server. Additionally we discuss new highly interesting and important applications of the GOR method to chameleon sequences in protein folding simulations, and for prediction of protein aggregation propensities. Our preliminary studies show that the GOR method is a promising and efficient alternative to other protein aggregation predicting tools. This shows that the GOR method despite being almost 40 years old is still important and has significant potential in application to new scientific problems.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Eshel Faraggi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46032, USA.,Research and Information Systems, LLC, Indianapolis, Indiana, USA
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, 02-093, Poland
| | - Andrzej Kloczkowski
- Battelle Center for MathematicalMedicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43215, USA. .,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43215, USA.
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19
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Kashchiev D. Modeling the Effect of Monomer Conformational Change on the Early Stage of Protein Self-Assembly into Fibrils. J Phys Chem B 2016; 121:35-46. [PMID: 28029261 DOI: 10.1021/acs.jpcb.6b09302] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Filamentous self-assembly of proteins is an important process implicated in a plethora of human diseases and of interest for nanotechnology. Using rate equations, we analyze the early stage of the process in solutions that initially contain fibrillation-passive protein monomers and in which the nascent fibrils are practically insoluble. The analysis is based on a model accounting for the conformational and/or other changes the passive monomers experience to transform themselves into fibrillation-active monomers and thus become fibril nuclei. The model allows exact, comprehensive, and simple mathematical description of the early stage of fibrillation, which reveals the usually neglected role of the nucleation nonstationarity in this stage of fibrillation. We obtain exact and user-friendly expressions for experimentally accessible quantities such as the size distribution of fibrils, their number and mass concentrations, the rate and nonstationary period of fibril nucleation, and the delay time of fibril formation. Analyzing available experimental data, we find that the theory successfully describes the fibrillation time course of pathological and nonpathological ataxin-3, a protein involved in the neurodegenerative disorder spinocerebellar ataxia type-3. The analysis provides mechanistic insight into the reason for the higher fibril nucleation and elongation rates of the pathological ataxin-3.
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Affiliation(s)
- Dimo Kashchiev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences , ul. Acad. G. Bonchev 11, Sofia 1113, Bulgaria
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20
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Leahy CT, Murphy RD, Hummer G, Rosta E, Buchete NV. Coarse Master Equations for Binding Kinetics of Amyloid Peptide Dimers. J Phys Chem Lett 2016; 7:2676-2682. [PMID: 27323250 DOI: 10.1021/acs.jpclett.6b00518] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We characterize the kinetics of dimer formation of the short amyloid microcrystal-forming tetrapeptides NNQQ by constructing coarse master equations for the conformational dynamics of the system, using temperature replica-exchange molecular dynamics (REMD) simulations. We minimize the effects of Kramers-type recrossings by assigning conformational states based on their sequential time evolution. Transition rates are further estimated from short-time state propagators by maximizing the likelihood that the extracted rates agree with the observed atomistic trajectories without any a priori assumptions about their temperature dependence. Here, we evaluate the rates for both continuous replica trajectories that visit different temperatures and for discontinuous data corresponding to each REMD temperature. While the binding-unbinding kinetic process is clearly Markovian, the conformational dynamics of the bound NNQQ dimer has a complex character. Our kinetic analysis allows us to discriminate between short-lived encounter pairs and strongly bound conformational states. The conformational dynamics of NNQQ dimers supports a kinetically driven aggregation mechanism, in agreement with the polymorphic character reported for amyloid aggregates such as microcrystals and fibrils.
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Affiliation(s)
- Cathal T Leahy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Ronan D Murphy
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue-Straße 3, D-60438 Frankfurt am Main, Germany
| | - Edina Rosta
- Department of Chemistry, King's College London , London SE1 1DB, United Kingdom
| | - Nicolae-Viorel Buchete
- School of Physics, University College Dublin , Belfield, Dublin 4, Ireland
- Complex and Adaptive Systems Laboratory, University College Dublin , Belfield, Dublin 4, Ireland
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21
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Boopathi S, Kolandaivel P. Fe(2+) binding on amyloid β-peptide promotes aggregation. Proteins 2016; 84:1257-74. [PMID: 27214008 DOI: 10.1002/prot.25075] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 04/29/2016] [Accepted: 05/08/2016] [Indexed: 01/26/2023]
Abstract
The metal ions Zn(2+) , Cu(2+) , and Fe(2+) play a significant role in the aggregation mechanism of Aβ peptides. However, the nature of binding between metal and peptide has remained elusive; the detailed information on this from the experimental study is very difficult. Density functional theory (dft) (M06-2X/6-311++G (2df,2pd) +LANL2DZ) has employed to determine the force field resulting due to metal and histidine interaction. We performed 200 ns molecular dynamics (MD) simulation on Aβ1-42 -Zn(2+) , Aβ1-42 -Cu(2+) , and Aβ1-42 -Fe(2+) systems in explicit water with different combination of coordinating residues including the three Histidine residues in the N-terminal. The present investigation, the Aβ1-42 -Zn(2+) system possess three turn conformations separated by coil structure. Zn(2+) binding caused the loss of the helical structure of N-terminal residues which transformed into the S-shaped conformation. Zn(2+) has reduced the coil and increases the turn content of the peptide compared with experimental study. On the other hand, the Cu(2+) binds with peptide, β sheet formation is observed at the N-terminal residues of the peptide. Fe(2+) binding is to promote the formation of Glu22-Lys28 salt-bridge which stabilized the turn conformation in the Phe19-Gly25 residues, subsequently β sheets were observed at His13-Lys18 and Gly29-Gly37 residues. The turn conformation facilitates the β sheets are arranged in parallel by enhancing the hydrophobic contact between Gly25 and Met35, Lys16 and Met35, Leu17 and Leu34, Val18 and Leu34 residues. The Fe(2+) binding reduced the helix structure and increases the β sheet content in the peptide, which suggested, Fe(2+) promotes the oligomerization by enhancing the peptide-peptide interaction. Proteins 2016; 84:1257-1274. © 2016 Wiley Periodicals, Inc.
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22
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Kouza M, Co NT, Nguyen PH, Kolinski A, Li MS. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models. J Chem Phys 2016; 142:145104. [PMID: 25877597 DOI: 10.1063/1.4917073] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite the fact that the fibril formation process is very slow and thus poses a significant challenge for theoretical and experimental studies, a number of alternative pictures of molecular mechanisms of amyloid fibril formation have been recently proposed. What seems to be common for the majority of the proposed models is that fibril elongation involves the formation of pre-nucleus seeds prior to the creation of a critical nucleus. Once the size of the pre-nucleus seed reaches the critical nucleus size, its thermal fluctuations are expected to be small and the resulting nucleus provides a template for sequential (one-by-one) accommodation of added monomers. The effect of template fluctuations on fibril formation rates has not been explored either experimentally or theoretically so far. In this paper, we make the first attempt at solving this problem by two sets of simulations. To mimic small template fluctuations, in one set, monomers of the preformed template are kept fixed, while in the other set they are allowed to fluctuate. The kinetics of addition of a new peptide onto the template is explored using all-atom simulations with explicit water and the GROMOS96 43a1 force field and simple lattice models. Our result demonstrates that preformed template fluctuations can modulate protein aggregation rates and pathways. The association of a nascent monomer with the template obeys the kinetics partitioning mechanism where the intermediate state occurs in a fraction of routes to the protofibril. It was shown that template immobility greatly increases the time of incorporating a new peptide into the preformed template compared to the fluctuating template case. This observation has also been confirmed by simulation using lattice models and may be invoked to understand the role of template fluctuations in slowing down fibril elongation in vivo.
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Affiliation(s)
- Maksim Kouza
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw, Poland
| | - Nguyen Truong Co
- Department of Physics, Institute of Technology, National University of HCM City, 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
| | - Phuong H Nguyen
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Andrzej Kolinski
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warszaw, Poland
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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23
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Modeling of protein-peptide interactions using the CABS-dock web server for binding site search and flexible docking. Methods 2015; 93:72-83. [PMID: 26165956 DOI: 10.1016/j.ymeth.2015.07.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 07/06/2015] [Accepted: 07/08/2015] [Indexed: 11/22/2022] Open
Abstract
Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of protein-peptide interactions is usually divided into two stages: prediction of the binding site at a protein receptor surface, and then docking (and modeling) the peptide structure into the known binding site. This paper presents a comprehensive CABS-dock method for the simultaneous search of binding sites and flexible protein-peptide docking, available as a user's friendly web server. We present example CABS-dock results obtained in the default CABS-dock mode and using its advanced options that enable the user to increase the range of flexibility for chosen receptor fragments or to exclude user-selected binding modes from docking search. Furthermore, we demonstrate a strategy to improve CABS-dock performance by assessing the quality of models with classical molecular dynamics. Finally, we discuss the promising extensions and applications of the CABS-dock method and provide a tutorial appendix for the convenient analysis and visualization of CABS-dock results. The CABS-dock web server is freely available at http://biocomp.chem.uw.edu.pl/CABSdock/.
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24
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Keerthana SP, Kolandaivel P. Structural investigation on the electrostatic loop of native and mutated SOD1 and their interaction with therapeutic compounds. RSC Adv 2015. [DOI: 10.1039/c5ra00286a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The electrostatic loop of the native and mutated SOD1 protein with single point mutation in the loop is subjected to MD simulation. The structure and electrostatic properties of the native and mutated loops before/after interacting with small compounds are compared.
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Affiliation(s)
- S. P. Keerthana
- Department of Physics
- Bharathiar University
- Coimbatore
- India-641 046
| | - P. Kolandaivel
- Department of Physics
- Bharathiar University
- Coimbatore
- India-641 046
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25
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Ning L, Wang Q, Zheng Y, Liu H, Yao X. Effects of the A117V mutation on the folding and aggregation of palindromic sequences (PrP113–120) in prion: insights from replica exchange molecular dynamics simulations. MOLECULAR BIOSYSTEMS 2015; 11:647-55. [DOI: 10.1039/c4mb00546e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The A117V mutation enhances the aggregation propensity of the palindromic sequences in prion protein.
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Affiliation(s)
- Lulu Ning
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Qianqian Wang
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000
- China
| | - Yang Zheng
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
| | - Huanxiang Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- School of Pharmacy
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- State Key Laboratory of Quality Research in Chinese Medicine
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26
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Viet MH, Nguyen PH, Derreumaux P, Li MS. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2014; 5:646-57. [PMID: 24949887 DOI: 10.1021/cn500007j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The self-assembly of the amyloid beta (Aβ) peptides into senile plaques is the hallmark of Alzheimer's disease. Recent experiments have shown that the English familial disease mutation (H6R) speeds up the fibril formation process of alloforms Aβ40 and Aβ42 peptides altering their toxicity to cells. We used all-atom molecular dynamics simulations at microsecond time scales with the OPLS-AA force field and TIP4P explicit water model to study the structural dynamics of the monomer and dimer of H6R sequences of both peptides. The reason behind the self-assembly acceleration is common that upon mutation the net charge is reduced leading to the weaker repulsive interaction between chains that facilitates the peptide association. In addition, our estimation of the solvation free energy shows that the mutation enhances the hydrophobicity of both peptides speeding up their aggregation. However, we can show that the acceleration mechanisms are different for different peptides: the rate of fibril formation of Aβ42 increases due to increased β-structure at the C-terminal in both monomer and dimer and enhanced stability of salt bridge Asp23-Lys28 in monomer, while the enhancement of turn at residues 25-29 and reduction of coil in regions 10-13, 26-19, and 30-34 would play the key role for Aβ40. Overall, our study provides a detailed atomistic picture of the H6R-mediated conformational changes that are consistent with the experimental findings and highlights the important role of the N-terminal in Aβ peptide aggregation.
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Affiliation(s)
- Man Hoang Viet
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005 Paris, France
- Institut Universitaire de France, Bvd Saint Michel, 75005 Paris, France
| | - Mai Suan Li
- Institute
of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward,
District 12, Ho Chi Minh City, Vietnam
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27
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Nguyen PH, Li MS, Derreumaux P. Amyloid oligomer structure characterization from simulations: A general method. J Chem Phys 2014; 140:094105. [DOI: 10.1063/1.4866902] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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28
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Viet MH, Nguyen PH, Ngo ST, Li MS, Derreumaux P. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42. ACS Chem Neurosci 2013; 4:1446-57. [PMID: 24041307 DOI: 10.1021/cn400110d] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Recent experiments have shown that the mutation Tottori (D7N) alters the toxicity, assembly and rate of fibril formation of the wild type (WT) amyloid beta (Aβ) Aβ40 and Aβ42 peptides. We used all-atom molecular dynamics simulations in explicit solvent of the monomer and dimer of both alloforms with their WT and D7N sequences. The monomer simulations starting from a random coil and totaling 3 μs show that the D7N mutation changes the fold and the network of salt bridges in both alloforms. The dimer simulations starting from the amyloid fibrillar states and totaling 4.4 μs also reveal noticeable changes in terms of secondary structure, salt bridge, and topology. Overall, this study provides physical insights into the enhanced rate of fibril formation upon D7N mutation and an atomic picture of the D7N-mediated conformational change on Aβ40 and Aβ42 peptides.
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Affiliation(s)
- Man Hoang Viet
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Son Tung Ngo
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc
District, Ho Chi Minh City, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow
32/46, 02-668 Warsaw, Poland
| | - Philippe Derreumaux
- Laboratoire de Biochimie Theorique, UPR
9080 CNRS, IBPC, Universite Denis Diderot, Paris Sorbonne Cité 13 rue Pierre et Marie Curie, 75005, Paris, France
- Institut Universitaire de France, Bvd
Saint Michel, 75005, Paris, France
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29
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Chiang HL, Ngo ST, Chen CJ, Hu CK, Li MS. Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin. PLoS One 2013; 8:e65358. [PMID: 23805182 PMCID: PMC3689759 DOI: 10.1371/journal.pone.0065358] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 04/26/2013] [Indexed: 01/12/2023] Open
Abstract
Recently it has been proposed a model for fibrils of human insulin in which the fibril growth proceeds via stacking LVEALYL (fragment 11-17 from chain B of insulin) into pairs of tightly interdigitated [Formula: see text]-sheets. The experiments have also shown that LVEALYL has high propensity to self-assembly and binding to insulin. This necessitates study of oligomerization of LVEALYL and its binding affinity to full-length insulin. Using the all-atom simulations with Gromos96 43a1 force field and explicit water it is shown that LVEALYL can aggregate. Theoretical estimation of the binding free energy of LVEALYL to insulin by the molecular mechanic Poisson-Boltzmann surface area method reveals its strong binding affinity to chain B, implying that, in agreement with the experiments, LVEALYL can affect insulin aggregation via binding mechanism. We predict that, similar to LVEALYL, peptide RGFFYT (fragment B22-27) can self-assemble and bind to insulin modulating its fibril growth process. The binding affinity of RGFFYT is shown to be comparable with that of LVEALYL.
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Affiliation(s)
- Hsin-Lin Chiang
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan
| | - Son Tung Ngo
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Chun-Jung Chen
- Department of Physics, National Tsing Hua University, Hsinchu, Taiwan
- Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, Taiwan
- Institute of Biotechnology, National Cheng Kung University, Tainan City, Taiwan
| | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail: (CKH); (MSL)
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail: (CKH); (MSL)
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Saracino GAA, Gelain F. Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides. J Biomol Struct Dyn 2013; 32:759-75. [PMID: 23730849 DOI: 10.1080/07391102.2013.790848] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite the increasing use and development of peptide-based scaffolds in different fields including that of regenerative medicine, the understanding of the factors governing the self-assembly process and the relationship between sequence and properties have not yet been fully understood. BMHP1-derived self-assembling peptides (SAPs) have been developed and characterized showing that biotinylation at the N-terminal cap corresponds to better performing assembly and scaffold biomechanics. In this study, the effects of biotinylation on the self-assembly dynamics of seven BMHP1-derived SAPs have been investigated by molecular dynamics simulations. We confirmed that these SAPs self-assemble into β-structures and that proline acts as a β-breaker of the assembled aggregates. In biotinylated peptides, the formation of ordered β-structured aggregates is triggered by both the establishment of a dense and dynamic H-bonds network and the formation of a 'hydrophobic wall' available to interact with other peptides. Such conditions result from the peculiar chemical composition of the biotinyl-cap, given by the synergic cooperation of the uracil function of the ureido ring with the high hydrophobic portion consisting of the thiophenyl ring and valeryl chain. The inbuilt propensity of biotinylated peptides towards the formation of ordered small aggregates makes them ideal precursors of higher hierarchically organized self-assembled nanostructures as experimentally observed.
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Affiliation(s)
- Gloria Anna Ada Saracino
- a Center of Nanomedicine and Tissue Engineering A. O. Ospedale Niguarda Ca' Granda , Milan , 20162 Italy
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31
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Larini L, Gessel MM, LaPointe NE, Do TD, Bowers MT, Feinstein SC, Shea JE. Initiation of assembly of tau(273-284) and its ΔK280 mutant: an experimental and computational study. Phys Chem Chem Phys 2013; 15:8916-28. [PMID: 23515417 DOI: 10.1039/c3cp00063j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The microtubule associated protein tau is essential for the development and maintenance of the nervous system. Tau dysfunction is associated with a class of diseases called tauopathies, in which tau is found in an aggregated form. This paper focuses on a small aggregating fragment of tau, (273)GKVQIINKKLDL(284), encompassing the (PHF6*) region that plays a central role in tau aggregation. Using a combination of simulations and experiments, we probe the self-assembly of this peptide, with an emphasis on characterizing the early steps of aggregation. Ion-mobility mass spectrometry experiments provide a size distribution of early oligomers, TEM studies provide a time course of aggregation, and enhanced sampling molecular dynamics simulations provide atomistically detailed structural information about this intrinsically disordered peptide. Our studies indicate that a point mutation, as well the addition of heparin, lead to a shift in the conformations populated by the earliest oligomers, affecting the kinetics of subsequent fibril formation as well as the morphology of the resulting aggregates. In particular, a mutant associated with a K280 deletion (a mutation that causes a heritable form of neurodegeneration/dementia in the context of full length tau) is seen to aggregate more readily than its wild-type counterpart. Simulations and experiment reveal that the ΔK280 mutant peptide adopts extended conformations to a greater extent than the wild-type peptide, facilitating aggregation through the pre-structuring of the peptide into a fibril-competent structure.
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Affiliation(s)
- Luca Larini
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California 93106, USA
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32
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Lu Y, Wei G, Derreumaux P. Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations. J Chem Phys 2012; 137:025101. [PMID: 22803563 DOI: 10.1063/1.4732761] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Characterizing the early formed oligomeric intermediates of amyloid peptides is of particular interest due to their links with neurodegenerative diseases. Here we study the NNQQ peptide, known to display parallel β-strands in amyloid fibrils by x-ray microcrystallography, and investigate the structural, thermodynamical, and dynamical properties of 20 NNQQ peptides using molecular dynamics and replica exchange molecular dynamics simulations coupled to a coarse-grained force field. All simulations are initiated from randomized and fully dispersed monomeric conformations. Our simulations reveal that the phase transition is characterized by a change in the oligomer and β-sheet size distributions and the percentage of mixed parallel/antiparallel β-strands when the sheets are formed. At all temperatures, however, the fraction of parallel β-strands remains low, though there are many association/fragmentation events. This work and a growing body of computational studies provide strong evidence that the critical nucleus goes beyond 20 chains and reordering of the β-strands occurs in larger oligomers.
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Affiliation(s)
- Yan Lu
- State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China
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33
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Saracino GAA, Cigognini D, Silva D, Caprini A, Gelain F. Nanomaterials design and tests for neural tissue engineering. Chem Soc Rev 2012; 42:225-62. [PMID: 22990473 DOI: 10.1039/c2cs35065c] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nanostructured scaffolds recently showed great promise in tissue engineering: nanomaterials can be tailored at the molecular level and scaffold morphology may more closely resemble features of extracellular matrix components in terms of porosity, framing and biofunctionalities. As a consequence, both biomechanical properties of scaffold microenvironments and biomaterial-protein interactions can be tuned, allowing for improved transplanted cell engraftment and better controlled diffusion of drugs. Easier said than done, a nanotech-based regenerative approach encompasses different fields of know-how, ranging from in silico simulations, nanomaterial synthesis and characterization at the nano-, micro- and mesoscales to random library screening methods (e.g. phage display), in vitro cellular-based experiments and validation in animal models of the target injury. All of these steps of the "assembly line" of nanostructured scaffolds are tightly interconnected both in their standard analysis techniques and in their most recent breakthroughs: indeed their efforts have to jointly provide the deepest possible analyses of the diverse facets of the challenging field of neural tissue engineering. The purpose of this review is therefore to provide a critical overview of the recent advances in and drawbacks and potential of each mentioned field, contributing to the realization of effective nanotech-based therapies for the regeneration of peripheral nerve transections, spinal cord injuries and brain traumatic injuries. Far from being the ultimate overview of such a number of topics, the reader will acknowledge the intrinsic complexity of the goal of nanotech tissue engineering for a conscious approach to the development of a regenerative therapy and, by deciphering the thread connecting all steps of the research, will gain the necessary view of its tremendous potential if each piece of stone is correctly placed to work synergically in this impressive mosaic.
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Affiliation(s)
- Gloria A A Saracino
- Center for Nanomedicine and Tissue Engineering, A.O. Ospedale Niguarda Cà Granda, Milan, 20162, Italy
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Ngo ST, Li MS. Curcumin binds to Aβ1-40 peptides and fibrils stronger than ibuprofen and naproxen. J Phys Chem B 2012; 116:10165-75. [PMID: 22877239 DOI: 10.1021/jp302506a] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Binding of curcumin, naproxen, and ibuprofen to Aβ1-40 peptide and its fibrils is studied by docking method and all-atom molecular dynamics simulations. The Gromos96 43a1 force field and simple point charge model of water have been used for molecular dynamics simulations. It is shown that if the receptor is a monomer then naproxen and ibuprofen are bound to the same place that is different from the binding position of curcumin. However all of three ligands have the same binding pocket in fibrillar structures. The binding mechanism is studied in detail showing that the van der Waals interaction between ligand and receptor dominates over the electrostatic interaction. The binding free energies obtained by the molecular mechanic-Poisson-Boltzmann surface area method indicate that curcumin displays higher binding affinity than nonsteroidal anti-inflammatory drugs. Our results are in good agreement with the experiments.
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Affiliation(s)
- Son Tung Ngo
- Institute for Computational Science and Technology , 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam, and
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35
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Viet MH, Li MS. Amyloid peptide Aβ40 inhibits aggregation of Aβ42: Evidence from molecular dynamics simulations. J Chem Phys 2012; 136:245105. [DOI: 10.1063/1.4730410] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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36
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Viet MH, Ngo ST, Lam NS, Li MS. Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity. J Phys Chem B 2011; 115:7433-46. [DOI: 10.1021/jp1116728] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Man Hoang Viet
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw, Poland
| | - Son Tung Ngo
- Institute for Computational Science and Technology, 6 Quarter, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Vietnam
| | - Nguyen Sy Lam
- Computational Physics Laboratory, Vietnam National University, Ho Chi Minh City, 227 Nguyen Van Cu, District 5, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, 02-668 Warsaw, Poland
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37
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Wu C, Shea JE. Coarse-grained models for protein aggregation. Curr Opin Struct Biol 2011; 21:209-20. [DOI: 10.1016/j.sbi.2011.02.002] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 02/03/2011] [Accepted: 02/07/2011] [Indexed: 01/09/2023]
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38
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Nguyen PH, Li MS, Derreumaux P. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer. Phys Chem Chem Phys 2011; 13:9778-88. [DOI: 10.1039/c1cp20323a] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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