1
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Firouzi R, Noohi B. Identification of key stabilizing interactions of amyloid-β oligomers based on fragment molecular orbital calculations on macrocyclic β-hairpin peptides. Proteins 2021; 90:229-238. [PMID: 34387401 DOI: 10.1002/prot.26212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/01/2021] [Accepted: 08/06/2021] [Indexed: 11/10/2022]
Abstract
Analyzing the electronic states and inter-/intra-molecular interactions of amyloid oligomers expand our understanding of the molecular basis of Alzheimer's disease and other amyloid diseases. In the current study, several high-resolution crystal structures of oligomeric assemblies of Aβ-derived peptides have been studied by the ab initio fragment molecular orbital (FMO) method. The FMO method provides comprehensive details of the molecular interactions between the residues of the amyloid oligomers at the quantum mechanical level. Based on the calculations, two sequential aromatic residues (F19 and F20) and negatively charged E22 on the central region of Aβ have been identified as key residues in oligomer stabilization and potential interesting pharmacophores for preventing oligomer formation.
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Affiliation(s)
- Rohoullah Firouzi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Bahare Noohi
- Department of Physical Chemistry, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
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2
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Shinzato T, Sato R, Suzuki K, Tomioka S, Sogawa H, Shulga S, Blume Y, Kurita N. Proposal of therapeutic curcumin derivatives for Alzheimer’s disease based on ab initio molecular simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136883] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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3
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Khatua P, Mondal S, Bandyopadhyay S. Effects of Metal Ions on Aβ 42 Peptide Conformations from Molecular Simulation Studies. J Chem Inf Model 2019; 59:2879-2893. [PMID: 31095382 DOI: 10.1021/acs.jcim.9b00098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study, we investigate the conformational characteristics of full-length Aβ42 peptide monomers in the presence of Na+ and Zn2+ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aβ structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na+ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn2+ ion to Aβ peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aβ peptides is higher in the presence of divalent Zn2+ ions than monovalent Na+ ions. Relatively higher overall stability of the most populated Aβ peptide monomers in the presence of Zn2+ ions has been found to be associated with specific Zn2+-Aβ binding and significant free energy gain.
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Affiliation(s)
- Prabir Khatua
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
| | - Souvik Mondal
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory, Department of Chemistry , Indian Institute of Technology , Kharagpur 721302 , India.,Centre for Computational and Data Sciences , Indian Institute of Technology , Kharagpur 721302 , India
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4
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Okiyama Y, Watanabe C, Fukuzawa K, Mochizuki Y, Nakano T, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson-Boltzmann Equation: II. Protein and Its Ligand-Binding System Studies. J Phys Chem B 2018; 123:957-973. [PMID: 30532968 DOI: 10.1021/acs.jpcb.8b09326] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution: coupling with an implicit solvent model based on the Poisson-Boltzmann surface area called as FMO-PBSA. We investigated the solvent effects on practical and heterogeneous targets with uneven exposure to solvents unlike deoxyribonucleic acid analyzed in our recent study. Interfragment interaction energy (IFIE) and its decomposition analyses by FMO-PBSA revealed solvent-screening mechanisms that affect local stability inside ubiquitin protein: the screening suppresses excessiveness in bare charge-charge interactions and enables an intuitive IFIE analysis. The electrostatic character and associated solvation free energy also give consistent results as a whole to previous studies on the explicit solvent model. Moreover, by using the estrogen receptor alpha (ERα) protein bound to ligands, we elucidated the importance of specific interactions that depend on the electric charge and activatability as agonism/antagonism of the ligand while estimating the influences of the implicit solvent on the ligand and helix-12 bindings. The predicted ligand-binding affinities of bioactive compounds to ERα also show a good correlation with their in vitro activities. The FMO-PBSA approach would thus be a promising tool both for biological and pharmaceutical research targeting proteins.
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Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Chiduru Watanabe
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,RIKEN Center for Biosystems Dynamics Research , 1-7-22 Suehiro-cho , Tsurumi-ku, Yokohama , Kanagawa 230-0045 , Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Faculty of Pharmaceutical Sciences , Hoshi University , 2-4-41 Ebara , Shinagawa-ku, Tokyo 142-8501 , Japan
| | - Yuji Mochizuki
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Department of Chemistry and Research Center for Smart Molecules, Faculty of Science , Rikkyo University , 3-34-1 Nishi-ikebukuro , Toshima-ku, Tokyo 171-8501 , Japan
| | - Tatsuya Nakano
- Institute of Industrial Science , The University of Tokyo , 4-6-1 Komaba , Meguro-ku, Tokyo 153-8505 , Japan.,Division of Medicinal Safety Science , National Institute of Health Sciences , 3-25-26 Tonomachi , Kawasaki-ku, Kawasaki , Kanagawa 210-9501 , Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics , Kobe University , 1-1 Rokkodai, Nada-ku, Kobe , Hyogo 657-8501 , Japan
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5
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018; 57:8519-8524. [DOI: 10.1002/anie.201803234] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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6
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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7
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Okiyama Y, Nakano T, Watanabe C, Fukuzawa K, Mochizuki Y, Tanaka S. Fragment Molecular Orbital Calculations with Implicit Solvent Based on the Poisson–Boltzmann Equation: Implementation and DNA Study. J Phys Chem B 2018; 122:4457-4471. [DOI: 10.1021/acs.jpcb.8b01172] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Yoshio Okiyama
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Tatsuya Nakano
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan
| | - Chiduru Watanabe
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Faculty of Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
| | - Yuji Mochizuki
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe, Hyogo 657-8501, Japan
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8
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Specific interactions between amyloid-β peptides in an amyloid-β hexamer with three-fold symmetry: Ab initio fragment molecular orbital calculations in water. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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9
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Ngo ST, Hung HM, Tran KN, Nguyen MT. Replica exchange molecular dynamics study of the amyloid beta (11–40) trimer penetrating a membrane. RSC Adv 2017. [DOI: 10.1039/c6ra26461a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The transmembrane Aβ11–40 trimer is investigated for the first time using REMD and FEP.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Khoa Nhat Tran
- Department of Biological Sciences
- University of Maryland Baltimore County
- 21250 Baltimore
- USA
| | - Minh Tho Nguyen
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
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10
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Ngo ST, Hung HM, Truong DT, Nguyen MT. Replica exchange molecular dynamics study of the truncated amyloid beta (11–40) trimer in solution. Phys Chem Chem Phys 2017; 19:1909-1919. [DOI: 10.1039/c6cp05511g] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure of the 3Aβ11–40 oligomer is determined for the first time using T-REMD simulations.
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Affiliation(s)
- Son Tung Ngo
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | | | - Duc Toan Truong
- Department of Theoretical Physics
- Ho Chi Minh City University of Science
- Ho Chi Minh City
- Vietnam
| | - Minh Tho Nguyen
- Computational Chemistry Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
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11
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Conformational transition of Aβ 42 inhibited by a mimetic peptide. A molecular modeling study using QM/MM calculations and QTAIM analysis. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.02.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments. Sci Rep 2015; 5:15449. [PMID: 26498066 PMCID: PMC4620491 DOI: 10.1038/srep15449] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 06/22/2015] [Indexed: 11/24/2022] Open
Abstract
The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer’s disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.
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13
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The binding of small carbazole derivative (P7C3) to protofibrils of the Alzheimer’s disease and β-secretase: Molecular dynamics simulation studies. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.07.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Jose JC, Khatua P, Bansal N, Sengupta N, Bandyopadhyay S. Microscopic Hydration Properties of the Aβ1–42 Peptide Monomer and the Globular Protein Ubiquitin: A Comparative Molecular Dynamics Study. J Phys Chem B 2014; 118:11591-604. [DOI: 10.1021/jp505629q] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Jaya C. Jose
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Prabir Khatua
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
| | - Nupur Bansal
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhaba Road, Pune 411008, India
| | - Sanjoy Bandyopadhyay
- Molecular
Modeling
Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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15
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Yano A, Okamoto A, Nomura K, Higai S, Kurita N. Difference in dimer conformation between amyloid-β(1–42) and (1–43) proteins: Replica exchange molecular dynamics simulations in water. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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