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Zhu M, Zeng L, Li Z, Wang C, Wu L, Jiang X. Revealing the Nanoarchitectonics of Amyloid β-Aggregation on Two-Dimensional Biomimetic Membranes by Surface-Enhanced Infrared Absorption Spectroscopy. ChemistryOpen 2023; 12:e202200253. [PMID: 36744594 PMCID: PMC9906390 DOI: 10.1002/open.202200253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Indexed: 02/07/2023] Open
Abstract
The in vivo folding of amyloid β (Aβ) is influenced by many factors among which biomembrane interfaces play an important role. Here, using surface-enhanced infrared absorption (SEIRA) spectroscopy and atomic force microscopy (AFM), the adsorption, structure, and morphology of Aβ42 aggregating on different two-dimensional interfaces were investigated. Results show that interfaces facilitate the aggregation of Aβ42 and are conducive to the formation of homogeneous aggregates, while the aggregates vary on different interfaces. On hydrophobic interfaces, strong hydrophobic interactions with the C-terminus of Aβ42 result in the formation of small oligomers with a small proportion of the β-sheet structure. On hydrophilic interfaces, hydrogen-bonding interactions and electrostatic interactions promote the formation of large aggregate particles with β-sheet structure. The hydration repulsion plays an important role in the interaction of Aβ42 with interfaces. These findings help to understand the nature of Aβ42 adsorption and aggregation on the biomembrane interface and the origin of heterogeneity and polymorphism of Aβ42 aggregates.
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Affiliation(s)
- Manyu Zhu
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Li Zeng
- State Key Laboratory of Environmental Chemistry and EcotoxicologyResearch Center for Eco-Environmental SciencesChinese Academy of SciencesBeijing100085P. R. China
| | - Zihao Li
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Chen Wang
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
| | - Lie Wu
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied ChemistryChinese Academy of SciencesChangchunJilin130022P. R. China
- School of Applied Chemistry and EngineeringUniversity of Science & Technology of ChinaHefeiAnhui230026P. R. China
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2
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Coskuner-Weber O, Uversky VN. Insights into the Molecular Mechanisms of Alzheimer's and Parkinson's Diseases with Molecular Simulations: Understanding the Roles of Artificial and Pathological Missense Mutations in Intrinsically Disordered Proteins Related to Pathology. Int J Mol Sci 2018; 19:E336. [PMID: 29364151 PMCID: PMC5855558 DOI: 10.3390/ijms19020336] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β and α-synuclein are intrinsically disordered proteins (IDPs), which are at the center of Alzheimer's and Parkinson's disease pathologies, respectively. These IDPs are extremely flexible and do not adopt stable structures. Furthermore, both amyloid-β and α-synuclein can form toxic oligomers, amyloid fibrils and other type of aggregates in Alzheimer's and Parkinson's diseases. Experimentalists face challenges in investigating the structures and thermodynamic properties of these IDPs in their monomeric and oligomeric forms due to the rapid conformational changes, fast aggregation processes and strong solvent effects. Classical molecular dynamics simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β and α-synuclein in relation to the pathologies of Alzheimer's and Parkinson's diseases. Furthermore, there are several natural genetic variations that play a role in the pathogenesis of familial cases of Alzheimer's and Parkinson's diseases, which are related to specific genetic defects inherited in dominant or recessive patterns. The present review summarizes the current understanding of monomeric and oligomeric forms of amyloid-β and α-synuclein, as well as the impacts of artificial and pathological missense mutations on the structural ensembles of these IDPs using molecular dynamics simulations. We also emphasize the recent investigations on residual secondary structure formation in dynamic conformational ensembles of amyloid-β and α-synuclein, such as β-structure linked to the oligomerization and fibrillation mechanisms related to the pathologies of Alzheimer's and Parkinson's diseases. This information represents an important foundation for the successful and efficient drug design studies.
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Affiliation(s)
- Orkid Coskuner-Weber
- Türkisch-Deutsche Universität, Theoretical and Computational Biophysics Group, Molecular Biotechnology, Sahinkaya Caddesi, No. 86, Beykoz, Istanbul 34820, Turkey.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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3
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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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4
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Siwy CM, Lockhart C, Klimov DK. Is the Conformational Ensemble of Alzheimer's Aβ10-40 Peptide Force Field Dependent? PLoS Comput Biol 2017; 13:e1005314. [PMID: 28085875 PMCID: PMC5279813 DOI: 10.1371/journal.pcbi.1005314] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/30/2017] [Accepted: 12/16/2016] [Indexed: 11/21/2022] Open
Abstract
By applying REMD simulations we have performed comparative analysis of the conformational ensembles of amino-truncated Aβ10-40 peptide produced with five force fields, which combine four protein parameterizations (CHARMM36, CHARMM22*, CHARMM22/cmap, and OPLS-AA) and two water models (standard and modified TIP3P). Aβ10-40 conformations were analyzed by computing secondary structure, backbone fluctuations, tertiary interactions, and radius of gyration. We have also calculated Aβ10-40 3JHNHα-coupling and RDC constants and compared them with their experimental counterparts obtained for the full-length Aβ1-40 peptide. Our study led us to several conclusions. First, all force fields predict that Aβ adopts unfolded structure dominated by turn and random coil conformations. Second, specific TIP3P water model does not dramatically affect secondary or tertiary Aβ10-40 structure, albeit standard TIP3P model favors slightly more compact states. Third, although the secondary structures observed in CHARMM36 and CHARMM22/cmap simulations are qualitatively similar, their tertiary interactions show little consistency. Fourth, two force fields, OPLS-AA and CHARMM22* have unique features setting them apart from CHARMM36 or CHARMM22/cmap. OPLS-AA reveals moderate β-structure propensity coupled with extensive, but weak long-range tertiary interactions leading to Aβ collapsed conformations. CHARMM22* exhibits moderate helix propensity and generates multiple exceptionally stable long- and short-range interactions. Our investigation suggests that among all force fields CHARMM22* differs the most from CHARMM36. Fifth, the analysis of 3JHNHα-coupling and RDC constants based on CHARMM36 force field with standard TIP3P model led us to an unexpected finding that in silico Aβ10-40 and experimental Aβ1-40 constants are generally in better agreement than these quantities computed and measured for identical peptides, such as Aβ1-40 or Aβ1-42. This observation suggests that the differences in the conformational ensembles of Aβ10-40 and Aβ1-40 are small and the former can be used as proxy of the full-length peptide. Based on this argument, we concluded that CHARMM36 force field with standard TIP3P model produces the most accurate representation of Aβ10-40 conformational ensemble. Dependence of protein conformational ensembles on force field parameterizations limits the predictive power of molecular dynamics simulations. To address this problem, we evaluated five all-atom force fields for their consistency in reproducing the conformational ensemble of Alzheimer’s Aβ10-40 peptide. To generate conformational ensembles, we have used replica exchange molecular dynamics and computed Aβ10-40 secondary and tertiary structures. We found that, although all force fields predict Aβ10-40 unfolded structure, they strongly disagree on helix and β propensities and tertiary structure distributions. We have also calculated Aβ10-40 J-coupling and residual dipolar coupling constants and compared them with the experimental data for the full-length Aβ1-40 peptide. Unexpectedly, we determined that in silico Aβ10-40 and experimental Aβ1-40 constants are in better agreement than these quantities computed and measured previously for identical peptides, such as Aβ1-40 or Aβ1-42. We then concluded that the conformational ensembles of Aβ10-40 and Aβ1-40 are similar and on this basis argue that CHARMM36 force field with standard TIP3P water model provides the most accurate description of Aβ10-40. Although our objective was not to evaluate the biomolecular force fields in general, our study is expected to facilitate their proper selection for the simulations of Alzheimer’s peptides.
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Affiliation(s)
- Christopher M. Siwy
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
| | - Dmitri K. Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia, United States of America
- * E-mail:
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5
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Zhang Z, Murakami Y, Taniguchi T, Sohgawa M, Yamashita K, Noda M. A Cantilever-based Biosensor for Real-time Monitoring of Interactions between Amyloid-β(1-40) and Membranes Comprised of Phosphatidylcholine Lipids with Different Hydrophobic Acyl Chains. ELECTROANAL 2016. [DOI: 10.1002/elan.201600416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ziyang Zhang
- Graduate School of Science and Technology; Kyoto Institute of Technology; Matsugasaki, Sakyo-ku Kyoto 606-8585 Japan
| | - Yuki Murakami
- Graduate School of Science and Technology; Kyoto Institute of Technology; Matsugasaki, Sakyo-ku Kyoto 606-8585 Japan
| | - Tomoya Taniguchi
- Graduate School of Science and Technology; Kyoto Institute of Technology; Matsugasaki, Sakyo-ku Kyoto 606-8585 Japan
| | - Masayuki Sohgawa
- Graduate School of Science and Technology; Niigata University; 8050 Ikarashi 2-no-cho, Nishi-ku Niigata 950-2181 Japan
| | - Kaoru Yamashita
- Graduate School of Science and Technology; Kyoto Institute of Technology; Matsugasaki, Sakyo-ku Kyoto 606-8585 Japan
| | - Minoru Noda
- Graduate School of Science and Technology; Kyoto Institute of Technology; Matsugasaki, Sakyo-ku Kyoto 606-8585 Japan
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6
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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: 475] [Impact Index Per Article: 52.8] [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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7
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Gao G, Zhang M, Lu P, Guo G, Wang D, Sun T. Chirality-Assisted Ring-Like Aggregation of Aβ(1-40) at Liquid-Solid Interfaces: A Stereoselective Two-Step Assembly Process. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410768] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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8
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Gao G, Zhang M, Lu P, Guo G, Wang D, Sun T. Chirality-assisted ring-like aggregation of aβ(1-40) at liquid-solid interfaces: a stereoselective two-step assembly process. Angew Chem Int Ed Engl 2014; 54:2245-50. [PMID: 25533756 DOI: 10.1002/anie.201410768] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 11/29/2014] [Indexed: 11/07/2022]
Abstract
Molecular chirality is introduced at liquid-solid interfaces. A ring-like aggregation of amyloid Aβ(1-40) on N-isobutyryl-L-cysteine (L-NIBC)-modified gold substrate occurs at low Aβ(1-40) concentration, while D-NIBC modification only results in rod-like aggregation. Utilizing atomic force microscope controlled tip-enhanced Raman scattering, we directly observe the secondary structure information for Aβ(1-40) assembly in situ at the nanoscale. D- or L-NIBC on the surface can guide parallel or nonparallel alignment of β-hairpins through a two-step process based on electrostatic-interaction-enhanced adsorption and subsequent stereoselective recognition. Possible electrostatic interaction sites (R5 and K16) and a chiral recognition site (H14) of Aβ(1-40) are proposed, which may provide insight into the understanding of this effect.
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Affiliation(s)
- Guanbin Gao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, Wuhan 430070 (PR China)
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9
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Srivastava A, Balaji PV. Interplay of sequence, topology and termini charge in determining the stability of the aggregates of GNNQQNY mutants: a molecular dynamics study. PLoS One 2014; 9:e96660. [PMID: 24817093 PMCID: PMC4015988 DOI: 10.1371/journal.pone.0096660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 04/11/2014] [Indexed: 01/16/2023] Open
Abstract
This study explores the stabilities of single sheet parallel systems of three sequence variants of 1GNNQQNY7, N2D, N2S and N6D, with variations in aggregate size (5–8) and termini charge (charged or neutral). The aggregates were simulated at 300 and 330 K. These mutations decrease amyloid formation in the yeast prion protein Sup35. The present study finds that these mutations cause instability even in the peptide context. The protonation status of termini is found to be a key determinant of stabilities; other determinants are sequence, position of mutation and aggregate size. All systems with charged termini are unstable, whereas both stable and unstable systems are found when the termini are neutral. When termini are charged, the largest stable aggregate for the N2S and N6D systems has 3 to 4 peptides whereas N2D mutation supports oligomers of larger size (5-and 6-mers) as well. Mutation at 2nd position (N2S and N2D) results in fewer H-bonds at the mutated as well as neighboring (Gly1/Gln4) positions. However, no such effect is found if mutation is at 6th position (N6D). The effect of Asn→Asp mutation depends on the position and termini charge: it is more destabilizing at the 2nd position than at the 6th in case of neutral termini, however, the opposite is true in case of charged termini. Appearance of twist in stable systems and in smaller aggregates formed in unstable systems suggests that twist is integral to amyloid arrangement. Disorder, dissociation or rearrangement of peptides, disintegration or collapse of aggregates and formation of amorphous aggregates observed in these simulations are likely to occur during the early stages of aggregation also. The smaller aggregates formed due to such events have a variety of arrangements of peptides. This suggests polymorphic nature of oligomers and presence of a heterogeneous mixture of oligomers during early stages of aggregation.
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Affiliation(s)
- Alka Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Petety V. Balaji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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10
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Kahler A, Sticht H, Horn AHC. Conformational stability of fibrillar amyloid-beta oligomers via protofilament pair formation - a systematic computational study. PLoS One 2013; 8:e70521. [PMID: 23936224 PMCID: PMC3729696 DOI: 10.1371/journal.pone.0070521] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 06/19/2013] [Indexed: 11/18/2022] Open
Abstract
Amyloid-[Formula: see text] (A[Formula: see text]) oligomers play a crucial role in Alzheimer's disease due to their neurotoxic aggregation properties. Fibrillar A[Formula: see text] oligomerization can lead to protofilaments and protofilament pairs via oligomer elongation and oligomer association, respectively. Small fibrillar oligomers adopt the protofilament topology, whereas fibrils contain at least protofilament pairs. To date, the underlying growth mechanism from oligomers to the mature fibril still remains to be elucidated. Here, we performed all-atom molecular dynamics simulations in explicit solvent on single layer-like protofilaments and fibril-like protofilament pairs of different size ranging from the tetramer to the 48-mer. We found that the initial U-shaped topology per monomer is maintained over time in all oligomers. The observed deviations of protofilaments from the starting structure increase significantly with size due to the twisting of the in-register parallel [Formula: see text]-sheets. This twist causes long protofilaments to be unstable and leads to a breakage. Protofilament pairs, which are stabilized by a hydrophobic interface, exhibit more fibril-like properties such as the overall structure and the twist angle. Thus, they can act as stable conformational templates for further fibril growth. Key properties like the twist angle, shape complementarity, and energetics show a size-dependent behavior so that small oligomers favor the protofilament topology, whereas large oligomers favor the protofilament pair topology. The region for this conformational transition is at the size of approximately twelve A[Formula: see text] monomers. From that, we propose the following growth mechanism from A[Formula: see text] oligomers to fibrils: (1) elongation of short protofilaments; (2) breakage of large protofilaments; (3) formation of short protofilament pairs; and (4) elongation of protofilament pairs.
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Affiliation(s)
- Anna Kahler
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anselm H. C. Horn
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- * E-mail:
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11
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Xi W, Li W, Wang W. Template induced conformational change of amyloid-β monomer. J Phys Chem B 2012; 116:7398-405. [PMID: 22670893 DOI: 10.1021/jp300389g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Population of aggregation-prone conformers for the monomeric amyloid-β (Aβ) can dramatically speed up its fibrillar aggregation. In this work, we study the effect of preformed template on the conformational distributions of the monomeric Aβ by replica exchange molecular dynamics. Our results show that the template consisting of Aβ peptides with cross-β structure can induce the formation of β-rich conformations for the monomeric Aβ, which is the key feature of the aggregation-prone conformers. Similar effect is observed when the hIAPP peptides and poly alanine peptides were used as templates, suggesting that the template effect is insensitive to the sequence details of the template peptides. In comparison, the template with helical structure has no significant effects on the β-propensity of the monomeric Aβ. Analysis to the interaction details revealed that the template tends to disrupt the intrapeptide interactions of the monomeric Aβ, which are absent in the fibrillar state, suggesting that the preformed template can reorganize the intrapeptide interactions of the monomeric Aβ during the capturing stage and reduce the energy frustrations for the fibrillar aggregations.
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Affiliation(s)
- Wenhui Xi
- National Laboratory of Solid State Microstructure, and Department of Physics, Nanjing University, Nanjing 210093, China
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12
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Masters CL, Selkoe DJ. Biochemistry of amyloid β-protein and amyloid deposits in Alzheimer disease. Cold Spring Harb Perspect Med 2012; 2:a006262. [PMID: 22675658 PMCID: PMC3367542 DOI: 10.1101/cshperspect.a006262] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Progressive cerebral deposition of the amyloid β-protein (Aβ) in brain regions serving memory and cognition is an invariant and defining feature of Alzheimer disease. A highly similar but less robust process accompanies brain aging in many nondemented humans, lower primates, and some other mammals. The discovery of Aβ as the subunit of the amyloid fibrils in meningocerebral blood vessels and parenchymal plaques has led to innumerable studies of its biochemistry and potential cytotoxic properties. Here we will review the discovery of Aβ, numerous aspects of its complex biochemistry, and current attempts to understand how a range of Aβ assemblies, including soluble oligomers and insoluble fibrils, may precipitate and promote neuronal and glial alterations that underlie the development of dementia. Although the role of Aβ as a key molecular factor in the etiology of Alzheimer disease remains controversial, clinical trials of amyloid-lowering agents, reviewed elsewhere in this book, are poised to resolve the question of its pathogenic primacy.
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Affiliation(s)
- Colin L Masters
- The Mental Health Research Institute, The University of Melbourne, Parkville 3010, Australia.
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13
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Abstract
Protein aggregation is believed to be responsible for a number of human diseases and limits the yields of pharmaceutical proteins during production. Computer simulations can be used to develop novel experimentally testable hypotheses pertaining to aggregation. While all-atom simulations with explicit solvent are too computationally intensive to address the multitude of relevant time scales, coarse-grained models make it possible to observe the transition of monomers to an equilibrium containing aggregates. Here, we provide the reader with background information and a list of steps for setting up, performing, and analyzing computer simulations of aggregating coarse-grained (CG) proteins.
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Affiliation(s)
- Troy Cellmer
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
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14
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Kim S, Takeda T, Klimov DK. Mapping conformational ensembles of aβ oligomers in molecular dynamics simulations. Biophys J 2011; 99:1949-58. [PMID: 20858441 DOI: 10.1016/j.bpj.2010.07.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/27/2010] [Accepted: 07/07/2010] [Indexed: 11/30/2022] Open
Abstract
Although the oligomers formed by Aβ peptides appear to be the primary cytotoxic species in Alzheimer's disease, detailed information about their structures appears to be lacking. In this article, we use exhaustive replica exchange molecular dynamics and an implicit solvent united-atom model to study the structural properties of Aβ monomers, dimers, and tetramers. Our analysis suggests that the conformational ensembles of Aβ dimers and tetramers are very similar, but sharply distinct from those sampled by the monomers. The key conformational difference between monomers and oligomers is the formation of β-structure in the oligomers occurring together with the loss of intrapeptide interactions and helix structure. Our simulations indicate that, independent of oligomer order, the Aβ aggregation interface is largely confined to the sequence region 10-23, which forms the bulk of interpeptide interactions. We show that the fractions of β structure computed in our simulations and measured experimentally are in good agreement.
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Affiliation(s)
- Seongwon Kim
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, USA
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15
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Straub JE, Thirumalai D. Toward a molecular theory of early and late events in monomer to amyloid fibril formation. Annu Rev Phys Chem 2011; 62:437-63. [PMID: 21219143 PMCID: PMC11237996 DOI: 10.1146/annurev-physchem-032210-103526] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of transition from monomers to fibrils is needed to obtain insights into the growth of amyloid fibrils and more generally self-assembly multisubunit protein complexes. Significant advances using computations of protein aggregation in a number of systems have established generic and sequence-specific aspects of the early steps in oligomer formation. Theoretical considerations, which view oligomer and fibril growth as diffusion in a complex energy landscape, and computational studies, involving minimal lattice and coarse-grained models, have revealed general principles governing the transition from monomeric protein to ordered fibrillar aggregates. Detailed atomistic calculations have explored the early stages of the protein aggregation pathway for a number of amyloidogenic proteins, most notably amyloid β- (Aβ-) protein and fragments from proteins linked to various diseases. These computational studies have provided insights into the role of sequence, role of water, and specific interatomic interactions underlying the thermodynamics and dynamics of elementary kinetic steps in the aggregation pathway. Novel methods are beginning to illustrate the structural basis for the production of Aβ-peptides through interactions with secretases in the presence of membranes. We show that a variety of theoretical approaches, ranging from scaling arguments to minimal models to atomistic simulations, are needed as a complement to experimental studies probing the principles governing protein aggregation.
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Affiliation(s)
- John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA.
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16
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Miller Y, Ma B, Nussinov R. Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape. Chem Rev 2010; 110:4820-38. [PMID: 20402519 PMCID: PMC2920034 DOI: 10.1021/cr900377t] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Indexed: 01/13/2023]
Affiliation(s)
| | | | - Ruth Nussinov
- To whom correspondence should be addressed. Tel.: (301) 846-5579. Fax: (301) 846-5598. E-mail:
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17
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Takeda T, Klimov DK. Computational backbone mutagenesis of Abeta peptides: probing the role of backbone hydrogen bonds in aggregation. J Phys Chem B 2010; 114:4755-62. [PMID: 20302321 DOI: 10.1021/jp911533q] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Using replica exchange molecular dynamics (REMD) and united atom implicit solvent model we examine the role of backbone hydrogen bonds (HBs) in Abeta aggregation. The importance of HBs appears to depend on the aggregation stage. The backbone HBs have little effect on the stability of Abeta dimers or on their aggregation interface. The HBs also do not play a critical role in initial binding of Abeta peptides to the amyloid fibril. Their elimination does not change the continuous character of Abeta binding nor its temperature. However, cancellation of HBs forming between incoming Abeta peptides and the fibril disrupts the locked fibril-like states in the bound peptides. Without the support of HBs, bound Abeta peptides form few long beta-strands on the fibril edge. As a result, the deletion of peptide-fibril HBs is expected to impede fibril growth. As for the peptides bound to Abeta fibril the deletion of interpeptide HBs reduces the beta propensity in the dimers making them less competent for amyloid assembly. These simulation findings together with the backbone mutagenesis experiments suggest that a viable strategy for arresting fibril growth is the disruption of interpeptide HBs.
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Affiliation(s)
- Takako Takeda
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA
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18
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Kim S, Takeda T, Klimov DK. Globular state in the oligomers formed by Abeta peptides. J Chem Phys 2010; 132:225101. [PMID: 20550420 PMCID: PMC2896418 DOI: 10.1063/1.3447894] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Accepted: 05/14/2010] [Indexed: 01/04/2023] Open
Abstract
Replica exchange molecular dynamics and implicit solvent model are used to study two oligomeric species of Abeta peptides, dimer and tetramer, which are typically observed in in vitro experiments. Based on the analysis of free energy landscapes, density distributions, and chain flexibility, we propose that the oligomer formation is a continuous transition occurring without metastable states. The density distribution computations suggest that Abeta oligomer consists of two volume regions-the core with fairly flat density profile and the surface layer with rapidly decreasing density. The core is mostly formed by the N-terminal residues, whereas the C-terminal tends to occur in the surface layer. Lowering the temperature results in the redistribution of peptide atoms from the surface layer into the core. Using these findings, we argue that Abeta oligomer resembles polymer globule in poor solvent. Abeta dimers and tetramers are found to be structurally similar suggesting that the conformations of Abeta peptides do not depend on the order of small oligomers.
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Affiliation(s)
- Seongwon Kim
- Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia 20110, USA
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19
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Horn AHC, Sticht H. Amyloid-beta42 oligomer structures from fibrils: a systematic molecular dynamics study. J Phys Chem B 2010; 114:2219-26. [PMID: 20104925 DOI: 10.1021/jp100023q] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Recent experimental data demonstrate that small, soluble amyloid-beta42 oligomers play an important role in Alzheimer's disease because they exhibit neurotoxic properties and also act as seed for fibril growth. We performed all-atom molecular dynamics simulations in explicit solvent of 0.7 micros in total on five Abeta9-42 oligomers (monomer through pentamer) starting from the fibril conformation. The initial conformation proves to be stable in the trimer to pentamer, and the two parallel in-register beta-sheets as well as the connecting turn are preserved. The dimer undergoes larger conformational changes in its C-terminus, and the predominant conformation detected exhibits an additional antiparallel beta-sheet in one of the subunits. This conformational rearrangement allows efficient shielding of hydrophobic residues from the solvent, which is not possible for a dimer in the fibril conformation. In addition to the presence of the hydrogen bonds in the beta-sheets, the larger oligomers are stabilized by interchain D23-K28 salt bridges, whereas a D23-N27 interaction is found in the dimer. The degree of structural similarity to the fibril conformation detected for the oligomers in the simulation may also offer a structural explanation for the experimental finding that trimers and tetramers act as more potent seeds in fibril formation than dimers because only small conformational changes will be required for fibril growth. The fact that the dimer predominantly exists in conformations distinct from the larger oligomers and the fibril is also interesting for the design of anti-Alzheimer drugs, because it suggests that multiple drugs might be required to target the structurally different neurotoxic oligomers.
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Affiliation(s)
- Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Zentrum, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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Lemkul JA, Bevan DR. Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics. J Phys Chem B 2010; 114:1652-60. [DOI: 10.1021/jp9110794] [Citation(s) in RCA: 318] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Justin A. Lemkul
- Department of Biochemistry, 111 Engel Hall, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308
| | - David R. Bevan
- Department of Biochemistry, 111 Engel Hall, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0308
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