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1
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Park J, Lee HS, Kim H, Choi JM. Conformational landscapes of artificial peptides predicted by various force fields: are we ready to simulate β-amino acids? Phys Chem Chem Phys 2023; 25:7466-7476. [PMID: 36848062 DOI: 10.1039/d2cp05998c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
With the introduction of artificial peptides as antimicrobial agents and organic catalysts, numerous efforts have been made to design foldamers with desirable structures and functions. Computational tools are a helpful proxy for revealing the dynamic structures at atomic resolution and understanding foldamer's complex structure-function relationships. However, the performance of conventional force fields in predicting the structures of artificial peptides has not been systematically evaluated. In this study, we critically assessed three popular force fields, AMBER ff14SB, CHARMM36m, and OPLS-AA/L, in predicting conformational propensities of a β-peptide foldamer at monomer and hexamer levels. Simulation results were compared to those obtained from quantum chemistry calculations and experimental data. We also utilised replica exchange molecular dynamics simulations to investigate the energy landscape of each force field and assess the similarities and differences between force fields. We compared different solvent systems in the AMBER ff14SB and CHARMM36m frameworks and confirmed the unanimous role of hydrogen bonds in shaping energy landscapes. We anticipate that our data will pave the way for further improvements to force fields and for understanding the role of solvents in peptide folding, crystallisation, and engineering.
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Affiliation(s)
- Jihye Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Hee-Seung Lee
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea. .,Center for Multiscale Chiral Architectures, KAIST, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hyungjun Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon 34141, Republic of Korea.
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Geumjeong-gu, Busan 46241, Republic of Korea.
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2
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Miyagi Y, Sogawa H, Shiotsuki M, Sanda F. Synthesis of Optically Active Conjugated Polymers Bearing m-Terphenylene Moieties by Acetylenic Coupling Polymerization: Chiral Aggregation and Optical Properties of the Product Polymers. Macromolecules 2014. [DOI: 10.1021/ma402123w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Yu Miyagi
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University Katsura
Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hiromitsu Sogawa
- Department
of Organic and Polymeric Materials, Tokyo Institute of Technology, O-okayama, Meguro, Tokyo 152-8552, Japan
| | - Masashi Shiotsuki
- Molecular
Engineering Institute, Kinki University, Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Fumio Sanda
- Department
of Chemistry and Materials Engineering, Faculty of Chemistry, Materials
and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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3
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Sogawa H, Shiotsuki M, Hirao T, Haino T, Sanda F. Synthesis of Optically Active Poly(m-phenyleneethynylene–aryleneethynylene)s Bearing Hydroxy Groups and Examination of the Higher Order Structures. Macromolecules 2013. [DOI: 10.1021/ma4017295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiromitsu Sogawa
- Department of Polymer Chemistry, Graduate
School of Engineering, Kyoto University, Katsura
Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masashi Shiotsuki
- Molecular
Engineering Institute, Kinki University, Kayanomori, Iizuka, Fukuoka 820-8555, Japan
| | - Takehiro Hirao
- Graduate
School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Takeharu Haino
- Graduate
School of Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Fumio Sanda
- Department
of Chemistry and Materials Engineering, Faculty of Chemistry, Materials
and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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4
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Sogawa H, Shiotsuki M, Sanda F. Synthesis and Photoresponse of Helically Folded Poly(phenyleneethynylene)s Bearing Azobenzene Moieties in the Main Chains. Macromolecules 2013. [DOI: 10.1021/ma4002947] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Hiromitsu Sogawa
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto
615-8510, Japan
| | - Masashi Shiotsuki
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto
615-8510, Japan
| | - Fumio Sanda
- Department
of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto
615-8510, Japan
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5
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Banno M, Yamaguchi T, Nagai K, Kaiser C, Hecht S, Yashima E. Optically Active, Amphiphilic Poly(meta-phenylene ethynylene)s: Synthesis, Hydrogen-Bonding Enforced Helix Stability, and Direct AFM Observation of Their Helical Structures. J Am Chem Soc 2012; 134:8718-28. [DOI: 10.1021/ja303204m] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Motonori Banno
- Department of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Tomoko Yamaguchi
- Department of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Kanji Nagai
- Department of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Christian Kaiser
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse
2, 12489 Berlin, Germany
| | - Stefan Hecht
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse
2, 12489 Berlin, Germany
| | - Eiji Yashima
- Department of Molecular Design
and Engineering, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan
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6
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Wu C. Simulated Glass Transition of Poly(ethylene oxide) Bulk and Film: A Comparative Study. J Phys Chem B 2011; 115:11044-52. [DOI: 10.1021/jp205205x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chaofu Wu
- Department of Chemistry and Materials Science, Hunan University of Humanities, Science and Technology, Loudi 417000, the People’s Republic of China
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7
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Wu C. Competitive absorption of epoxy monomers on carbon nanotube: A molecular simulation study. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22287] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Sogawa H, Shiotsuki M, Matsuoka H, Sanda F. Synthesis, Chiroptical Properties, and Photoresponsiveness of Optically Active Poly(m-phenyleneethynylene)s Containing Azobenzene Moieties. Macromolecules 2011. [DOI: 10.1021/ma200281e] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiromitsu Sogawa
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masashi Shiotsuki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hideki Matsuoka
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Fumio Sanda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
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9
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Zhang J, Su J, Guo H. An Atomistic Simulation for 4-Cyano-4′-pentylbiphenyl and Its Homologue with a Reoptimized Force Field. J Phys Chem B 2011; 115:2214-27. [DOI: 10.1021/jp111408n] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jianguo Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jiaye Su
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongxia Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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10
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Nguyen HH, McAliley JH, Bruce DA. Controlling the m-Poly(phenylene ethynylene) Helical Cavity Environment: Hydrogen Bond Stabilized Helical Structures. Macromolecules 2010. [DOI: 10.1021/ma101514c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ha H. Nguyen
- Department of Chemical and Biomolecular Engineering, Clemson University Clemson, South Carolina 29634-0909, United States
| | - James H. McAliley
- Department of Chemical and Biomolecular Engineering, Clemson University Clemson, South Carolina 29634-0909, United States
| | - David A. Bruce
- Department of Chemical and Biomolecular Engineering, Clemson University Clemson, South Carolina 29634-0909, United States
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11
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Nguyen HH, McAliley JH, Batson, WR, Bruce DA. Molecular Design of Functionalized m-Poly(phenylene ethynylene) Foldamers: from Simulation to Synthesis. Macromolecules 2010. [DOI: 10.1021/ma100746x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ha H. Nguyen
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0909
| | - James H. McAliley
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0909
| | - William R. Batson,
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0909
| | - David A. Bruce
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634-0909
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12
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Liu R, Sogawa H, Shiotsuki M, Masuda T, Sanda F. Tyrosine-based poly(m-phenyleneethynylene-p-phenyleneethynylene)s. Helix folding and responsiveness to a base. POLYMER 2010. [DOI: 10.1016/j.polymer.2010.03.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Ni BB, Yan Q, Ma Y, Zhao D. Recent advances in arylene ethynylene folding systems: Toward functioning. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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14
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Tong L, Liu X, Deng J, Yang W. Effect of solvents on polymerization of N-propargylamide monomer and secondary structure of polymer. Polym Chem 2010. [DOI: 10.1039/c0py00116c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Liu R, Shiotsuki M, Masuda T, Sanda F. Synthesis and Chiroptical Properties of Hydroxyphenylglycine-Based Poly(m-phenyleneethynylene-p-phenyleneethynylene)s. Macromolecules 2009. [DOI: 10.1021/ma900910k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ruiyuan Liu
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
| | - Masashi Shiotsuki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
| | - Toshio Masuda
- Faculty of Engineering, Department of Environmental and Biological Chemistry, Fukui University of Technology, 3-6-1 Gakuen, Fukui 910-8505, Japan
| | - Fumio Sanda
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Kyoto 615-8510, Japan
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16
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Slutsky MM, Phillip JS, Tew GN. Synthesis and characterization of amphiphilic o-phenylene ethynylene oligomers. NEW J CHEM 2008. [DOI: 10.1039/b707618e] [Citation(s) in RCA: 16] [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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