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Ni R, Chau Y. Tuning the Inter-nanofibril Interaction To Regulate the Morphology and Function of Peptide/DNA Co-assembled Viral Mimics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703596] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Rong Ni
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Institute for Advanced Study; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
| | - Ying Chau
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
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Ni R, Chau Y. Tuning the Inter-nanofibril Interaction To Regulate the Morphology and Function of Peptide/DNA Co-assembled Viral Mimics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201703596] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Rong Ni
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Institute for Advanced Study; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
| | - Ying Chau
- Division of Biomedical Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
- Department of Chemical and Biomolecular Engineering; The Hong Kong University of Science and Technology; Clearwater Bay, Kowloon Hong Kong Hong Kong
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3
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Brasili D, Watly J, Simonovsky E, Guerrini R, Barbosa NA, Wieczorek R, Remelli M, Kozlowski H, Miller Y. The unusual metal ion binding ability of histidyl tags and their mutated derivatives. Dalton Trans 2016; 45:5629-39. [DOI: 10.1039/c5dt04747a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Peptides that consist of repeated sequences of alternating histidines and alanines strongly bind Cu(ii) and form α-helical structures.
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Affiliation(s)
- Davide Brasili
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Joanna Watly
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Eyal Simonovsky
- Department of Chemistry
- Ben Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Nuno A. Barbosa
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Robert Wieczorek
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Maurizio Remelli
- Department of Chemical and Pharmaceutical Sciences
- University of Ferrara
- I-44121 Ferrara
- Italy
| | - Henryk Kozlowski
- Department of Chemistry
- University of Wroclaw
- 50-383 Wroclaw
- Poland
| | - Yifat Miller
- Department of Chemistry
- Ben Gurion University of the Negev
- Beer-Sheva 84105
- Israel
- Ilse Katz Institute for Nanoscale Science and Technology
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4
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Khavani M, Izadyar M. Implicit and explicit solvent effects on the selectivity of the cycloaddition reaction of cyclopentadiene and methyl acrylate; a theoretical study. PROGRESS IN REACTION KINETICS AND MECHANISM 2015. [DOI: 10.3184/146867815x14297104685269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The product selectivity of the Diels–Alder reaction between cyclopentadiene and methyl acrylate has been studied through a solvent effect analysis by implicit and explicit solvent models. Two paths for this reaction have been proposed and thermodynamic and kinetic parameters for each path were calculated by the B3LYP functional with 6-311++G(d,p) basis set at 298.15 K. In the explicit solvent model, hydrogen bonds were investigated by the QM/MM method. According to the results, the proportion of the exo product in the gas phase is more than for the endo one, which is in contrast to the solvent phase. HOMO–LUMO analyses in the gas phase and different solvents have been done and solvent effects on the energies of the HOMO–LUMO orbitals were investigated. According to the results, the band gap of the TSs was increased in the presence of the solvents. Finally, natural population analysis has been performed to calculate the electronic charges of some atoms that are involved in the centre of the reaction. The data obtained showed that different solvents, including polar and nonpolar solvents, have different effects on the electronic charges of the atoms. Topological analysis of the structures during the reaction by the quantum theory of atoms in molecules (QTAIM) method in the gas phase and different solvents confirmed a cyclic structure for the transition state.
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Affiliation(s)
- Mohammad Khavani
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Izadyar
- Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 743] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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Plumley JA, Ali-Torres J, Pohl G, Dannenberg JJ. Capping amyloid β-sheets of the tau-amyloid structure VQIVYK with hexapeptides designed to arrest growth. An ONIOM and density functional theory study. J Phys Chem B 2014; 118:3326-34. [PMID: 24601594 PMCID: PMC3983367 DOI: 10.1021/jp501890p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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We
present ONIOM calculations using density functional theory (DFT)
as the high and AM1 as the medium level that explore the abilities
of different hexapeptide sequences to terminate the growth of a model
for the tau-amyloid implicated in Alzheimer’s disease. We delineate
and explore several design principles (H-bonding in the side chains,
using antiparallel interactions on the growing edge of a parallel
sheet, using all-d residues to form rippled interactions
at the edge of the sheet, and replacing the H-bond donor N–H’s
that inhibit further growth) that can be used individually and in
combination to design such peptides that will have a greater affinity
for binding to the parallel β-sheet of acetyl-VQIVYK-NHCH3 than the natural sequence and will prevent another strand
from binding to the sheet, thus providing a cap to the growing sheet
that arrests further growth. We found peptides in which the Q is replaced
by an acetyllysine (aK) residue to be particularly promising candidates,
particularly if the reverse sequence (KYVIaKV) is used to form an
antiparallel interaction with the sheet.
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Affiliation(s)
- Joshua A Plumley
- Department of Chemistry Hunter College and the Graduate School, City University of New York , 695 Park Avenue, New York, New York 10065, United States
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