1
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Sugisaki K, Nakano T, Mochizuki Y. Size-consistency and orbital-invariance issues revealed by VQE-UCCSD calculations with the FMO scheme. J Comput Chem 2024. [PMID: 38795375 DOI: 10.1002/jcc.27438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/27/2024]
Abstract
The fragment molecular orbital (FMO) scheme is one of the popular fragmentation-based methods and has the potential advantage of making the circuit shallow for quantum chemical calculations on quantum computers. In this study, we used a GPU-accelerated quantum simulator (cuQuantum) to perform the electron correlation part of the FMO calculation as unitary coupled-cluster singles and doubles (UCCSD) with the variational quantum eigensolver (VQE) for hydrogen-bonded (FH)3 $$ {}_3 $$ and (FH)2 $$ {}_2 $$ -H2 $$ {}_2 $$ O systems with the STO-3G basis set. VQE-UCCSD calculations were performed using both canonical and localized MO sets, and the results were examined from the point of view of size-consistency and orbital-invariance affected by the Trotter error. It was found that the use of localized MO leads to better results, especially for (FH)2 $$ {}_2 $$ -H2 $$ {}_2 $$ O. The GPU acceleration was substantial for the simulations with larger numbers of qubits, and was about a factor of 6.7-7.7 for 18 qubit systems.
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Affiliation(s)
- Kenji Sugisaki
- Graduate School of Science and Technology, Keio University, Kawasaki, Japan
- Quantum Computing Center, Keio University, Yokohama, Japan
- Centre for Quantum Engineering, Research and Education, TCG Centres for Research and Education in Science and Technology, Kolkata, India
| | - Tatsuya Nakano
- Division of Medicinal Safety Science, National Institute of Health Sciences, Kawasaki, Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University, Toshima-ku, Japan
- Institute of Industrial Science, The University of Tokyo, Meguro-ku, Japan
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2
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MOCHIZUKI Y, NAKANO T, SATO S, SAKAKURA K, WATANABE H, OKUWAKI K, OHSHIMA S, KATAGIRI T. Development Status of ABINIT-MP in 2021. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2021. [DOI: 10.2477/jccj.2022-0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuji MOCHIZUKI
- Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
| | - Tatsuya NAKANO
- National Institute of Health Sciences (Tonomachi 3-25-26, Kawasaki-ku, Kawasaki-shi Kanagawa, 210-951, Japan)
| | - Shinya SATO
- NEC Solution Innovators, Ltd. (Shiromi 1-4-24, NEC Kansai Building, Chuo-ku, Osaka, 540-8551, Japan)
| | - Kota SAKAKURA
- Foundation for Computational Science (Minatojima Minamicho 7-1-28 Computational Science Center Building 1F, Chuo-ku, Kobe, 650-0047, Japan)
| | - Hiromasa WATANABE
- HPC Systems Inc. (Kaigan 3-9-15 LOOP-X 8F, Minato-ku, Tokyo, 108-0022, Japan)
| | - Koji OKUWAKI
- Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
| | - Satoshi OHSHIMA
- Information Technology Center, Nagoya University (Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan)
| | - Takahiro KATAGIRI
- Information Technology Center, Nagoya University (Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan)
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3
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Watanabe C, Okiyama Y, Tanaka S, Fukuzawa K, Honma T. Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses. Chem Sci 2021; 12:4722-4739. [PMID: 35355624 PMCID: PMC8892577 DOI: 10.1039/d0sc06528e] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the COVID-19 pandemic, researchers have attempted to identify complex structures of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike glycoprotein (S-protein) with angiotensin-converting enzyme 2 (ACE2) or a blocking antibody. However, the molecular recognition mechanism—critical information for drug and antibody design—has not been fully clarified at the amino acid residue level. Elucidating such a microscopic mechanism in detail requires a more accurate molecular interpretation that includes quantum mechanics to quantitatively evaluate hydrogen bonds, XH/π interactions (X = N, O, and C), and salt bridges. In this study, we applied the fragment molecular orbital (FMO) method to characterize the SARS-CoV-2 S-protein binding interactions with not only ACE2 but also the B38 Fab antibody involved in ACE2-inhibitory binding. By analyzing FMO-based interaction energies along a wide range of binding interfaces carefully, we identified amino acid residues critical for molecular recognition between S-protein and ACE2 or B38 Fab antibody. Importantly, hydrophobic residues that are involved in weak interactions such as CH–O hydrogen bond and XH/π interactions, as well as polar residues that construct conspicuous hydrogen bonds, play important roles in molecular recognition and binding ability. Moreover, through these FMO-based analyses, we also clarified novel hot spots and epitopes that had been overlooked in previous studies by structural and molecular mechanical approaches. Altogether, these hot spots/epitopes identified between S-protein and ACE2/B38 Fab antibody may provide useful information for future antibody design, evaluation of the binding property of the SARS-CoV-2 variants including its N501Y, and small or medium drug design against the SARS-CoV-2. Quantum chemical calculations investigated molecular recognition of SARS-CoV-2 spike glycoproteins including its N501Y variant for ACE2 and antibody. Hot spot and epitope analyses revealed key residues to design drugs and antibodies against COVID-19.![]()
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Affiliation(s)
| | - Yoshio Okiyama
- Division of Medicinal Safety Science
- National Institute of Health Sciences
- Kawasaki
- Japan
| | - Shigenori Tanaka
- Department of Computational Science
- Graduate School of System Informatics
- Kobe University
- Kobe
- Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences
- Hoshi University
- Tokyo 142-8501
- Japan
- Department of Biomolecular Engineering
| | - Teruki Honma
- Center for Biosystems Dynamics Research
- RIKEN
- Yokohama
- Japan
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4
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Akisawa K, Hatada R, Okuwaki K, Mochizuki Y, Fukuzawa K, Komeiji Y, Tanaka S. Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations. RSC Adv 2021; 11:3272-3279. [PMID: 35424290 PMCID: PMC8694004 DOI: 10.1039/d0ra09555a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/06/2021] [Indexed: 12/13/2022] Open
Abstract
At the stage of SARS-CoV-2 infection in human cells, the spike protein consisting of three chains, A, B, and C, with a total of 3300 residues plays a key role, and thus its structural properties and the binding nature of receptor proteins to host human cells or neutralizing antibodies has attracted considerable interest. Here, we report on interaction analyses of the spike protein in both closed (PDB-ID: 6VXX) and open (6VYB) structures, based on large-scale fragment molecular orbital (FMO) calculations at the level of up to the fourth-order Møller–Plesset perturbation with singles, doubles, and quadruples (MP4(SDQ)). Inter-chain interaction energies were evaluated for both structures, and a mutual comparison indicated considerable losses of stabilization energies in the open structure, especially in the receptor binding domain (RBD) of chain-B. The role of charged residues in inter-chain interactions was illuminated as well. By two separate calculations for the RBD complexes with angiotensin-converting enzyme 2 (ACE2) (6M0J) and B38 Fab antibody (7BZ5), it was found that the binding with ACE2 or antibody partially compensated for this stabilization loss of RBD. Visualized IFIE results seen from chain-B of spike protein.![]()
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Affiliation(s)
- Kazuki Akisawa
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Ryo Hatada
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules
- Faculty of Science
- Rikkyo University
- Toshima-ku
- Japan
| | - Kaori Fukuzawa
- Institute of Industrial Science
- The University of Tokyo
- Meguro-ku
- Japan
- School of Pharmacy and Pharmaceutical Sciences
| | - Yuto Komeiji
- Health and Medical Research Institute
- AIST
- Tsukuba
- Japan
| | - Shigenori Tanaka
- Graduate School of System Informatics
- Department of Computational Science
- Kobe University
- Kobe 657-8501
- Japan
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5
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Ishikawa T. A novel method for analysis of the electrostatic complementarity of protein-protein interaction based on fragment molecular orbital method. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.138103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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MOCHIZUKI Y, SAKAKURA K, WATANABE H, OKUWAKI K, KATO K, WATANABE N, OKIYAMA Y, FUKUZAWA K, NAKANO T. Development Status of ABINIT-MP in 2020. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2020. [DOI: 10.2477/jccj.2021-0015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yuji MOCHIZUKI
- Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
- Institute of Industrial Science, The University of Tokyo (Komaba 4-6-1, Meguro-ku, Tokyo, 153-8505, Japan)
| | - Kota SAKAKURA
- Foundation for Computational Science (Minatojima Minamicho 7-1-28 Computational Science Center Building 1F, Chuo-ku, Kobe, 650-0047, Japan)
| | - Hiromasa WATANABE
- HPC Systems Inc. (Kaigan 3-9-15 LOOP-X 8F, Minato-ku, Tokyo, 108-0022, Japan)
| | - Koji OKUWAKI
- Department of Chemistry, Rikkyo University (Nishi-Ikebukuro 3-34-1, Toshima-ku, Tokyo, 171-8501, Japan)
| | - Koichiro KATO
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University (744 Moto-oka, Nishi-ku, Fukuoka, 819-0395, Japan)
| | - Naoki WATANABE
- Mizuho Information & Research Institute, Inc. (Kanda-Nishikicho 2-3, Chiyoda-ku, Tokyo, 101-8443, Japan)
| | - Yoshio OKIYAMA
- National Institute of Health Sciences (Tonomachi 3-25-26, Kawasaki-ku, Kawasaki-shi Kanagawa, 210-951, Japan)
| | - Kaori FUKUZAWA
- Institute of Industrial Science, The University of Tokyo (Komaba 4-6-1, Meguro-ku, Tokyo, 153-8505, Japan)
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University (Ebara 2-4-41, Shinagawa-ku, Tokyo, 142-8501, Japan)
| | - Tatsuya NAKANO
- National Institute of Health Sciences (Tonomachi 3-25-26, Kawasaki-ku, Kawasaki-shi Kanagawa, 210-951, Japan)
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7
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Ishikawa T, Sakakura K, Mochizuki Y. RI-MP3 calculations of biomolecules based on the fragment molecular orbital method. J Comput Chem 2018; 39:1970-1978. [PMID: 30277590 DOI: 10.1002/jcc.25368] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/04/2018] [Accepted: 05/09/2018] [Indexed: 12/24/2022]
Abstract
In this study, the third-order Møller-Plesset perturbation (MP3) theory using the resolution of the identity (RI) approximation was combined with the fragment molecular orbital (FMO) method to efficiently calculate a high-order electron correlation energy of biomolecular systems. We developed a new algorithm for the RI-MP3 calculation, which can be used with the FMO scheme. After test calculations using a small molecule, the FMO-RI-MP3 calculations were performed for two biomolecular systems comprising a protein and a ligand. The computational cost of these calculations was only around 5 and 4 times higher than those of the FMO-RHF calculations. The error associated with the RI approximation was around 2.0% of the third-order correlation contribution to the total energy. However, the RI approximation error in the interaction energy between the protein and ligand molecule was insignificantly small, which reflected the negligible error in the inter fragment interaction energy. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Takeshi Ishikawa
- Department of Molecular Microbiology and Immunology, Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Kota Sakakura
- 1st Government and Public Solutions Division, NEC Corporation, 7-1, Shiba 5-chome, Minato-ku, Tokyo, 108-8001, Japan
| | - Yuji Mochizuki
- 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.,Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, 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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Yamada H, Mochizuki Y, Fukuzawa K, Okiyama Y, Komeiji Y. Fragment molecular orbital (FMO) calculations on DNA by a scaled third-order Møller-Plesset perturbation (MP2.5) scheme. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Nebgen B, Prezhdo OV. Fragment Molecular Orbital Nonadiabatic Molecular Dynamics for Condensed Phase Systems. J Phys Chem A 2016; 120:7205-12. [DOI: 10.1021/acs.jpca.6b05607] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ben Nebgen
- Department
of Chemistry, University of Southern California, Los Angeles, California 90037, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of Southern California, Los Angeles, California 90037, United States
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11
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SAITOU S, MOCHIZUKI Y, YAMAZAKI Y, ISHIMURA K. Performance Evaluations of Parallelized DFT Calculations with SMASH on Intel Xeon Phi Processor. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2016. [DOI: 10.2477/jccj.2016-0047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Sona SAITOU
- Department of Chemistry and Research Center for Smart Molecules, College of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Yuji MOCHIZUKI
- Department of Chemistry and Research Center for Smart Molecules, College of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8503, Japan
| | - Yutaka YAMAZAKI
- Department of Chemistry and Research Center for Smart Molecules, College of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Kazuya ISHIMURA
- Institute of Molecular Science, 38 Saigonaka, Myodaiji-cho, Okazaki, Aichi 444-8585, Japan
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12
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Tanaka S, Mochizuki Y, Komeiji Y, Okiyama Y, Fukuzawa K. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems. Phys Chem Chem Phys 2015; 16:10310-44. [PMID: 24740821 DOI: 10.1039/c4cp00316k] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.
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Affiliation(s)
- Shigenori Tanaka
- Graduate School of System Informatics, Kobe University, 1-1 Rokkodai, Nada-ku, Kobe 657-8501, Japan.
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13
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14
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Affiliation(s)
- Michael A Collins
- †Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ryan P A Bettens
- ‡Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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15
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TSUKAMOTO T, KATO K, KATO A, NAKANO T, MOCHIZUKI Y, FUKUZAWA K. Implementation of Pair Interaction Energy DecompositionAnalysis and Its Applications to Protein-Ligand Systems. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2015. [DOI: 10.2477/jccj.2014-0039] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Takayuki TSUKAMOTO
- Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda Tokyo 101-5494 Japan
| | - Koichiro KATO
- Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda Tokyo 101-5494 Japan
| | - Akifumi KATO
- Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda Tokyo 101-5494 Japan
| | - Tatsuya NAKANO
- University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505 Japan
- National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya, Tokyo 158-8501, Japan
| | - Yuji MOCHIZUKI
- University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505 Japan
- Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima, Tokyo 171-8501, Japan
| | - Kaori FUKUZAWA
- University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8505 Japan
- Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda Tokyo 101-5494 Japan
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16
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Baba T, Boero M, Kamiya K, Ando H, Negoro S, Nakano M, Shigeta Y. Unraveling the degradation of artificial amide bonds in nylon oligomer hydrolase: from induced-fit to acylation processes. Phys Chem Chem Phys 2015; 17:4492-504. [DOI: 10.1039/c4cp04419c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To unravel the factor that provides the ability to degrade non-biological amide bond with nylon oligomer hydrolase, we investigated the process from induced-fit to acylation by a combination of different theoretical methods.
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Affiliation(s)
- Takeshi Baba
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Mauro Boero
- Institut de Physique et Chimie des Matériaux de Strasbourg
- UMR 7504 CNRS and University of Strasbourg
- 67034 Strasbourg
- France
| | - Katsumasa Kamiya
- Center for Basic Education and Integrated Learning
- Kanagawa Institute of Technology
- Atsugi
- Japan
| | - Hiroyuki Ando
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Seiji Negoro
- Department of Material Science and Chemistry
- Graduate School of Engineering
- University of Hyogo
- Himeji
- Japan
| | - Masayoshi Nakano
- Department of Materials Engineering Science
- Graduate School of Engineering Science
- Osaka University
- Toyonaka
- Japan
| | - Yasuteru Shigeta
- Department of Physics
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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17
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Phipps MJS, Fox T, Tautermann CS, Skylaris CK. Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns. Chem Soc Rev 2015; 44:3177-211. [DOI: 10.1039/c4cs00375f] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.
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Affiliation(s)
| | - Thomas Fox
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
| | - Christofer S. Tautermann
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
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18
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Nishimoto Y, Fedorov DG, Irle S. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:4801-12. [DOI: 10.1021/ct500489d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
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19
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Ando H, Shigeta Y, Baba T, Watanabe C, Okiyama Y, Mochizuki Y, Nakano M. Hydration effects on enzyme–substrate complex of nylon oligomer hydrolase: inter-fragment interaction energy study by the fragment molecular orbital method. Mol Phys 2014. [DOI: 10.1080/00268976.2014.941311] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Yamamoto JI, Mochizuki Y. Optimal damping algorithm for unrestricted Hartree-Fock calculations. CHEM-BIO INFORMATICS JOURNAL 2014. [DOI: 10.1273/cbij.14.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Yuji Mochizuki
- Department of Chemistry and Research Center for Smart Molecules, Faculty of Science, Rikkyo University
- Institute of Industrial Science, The University of Tokyo
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21
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Brorsen KR, Minezawa N, Xu F, Windus TL, Gordon MS. Fragment Molecular Orbital Molecular Dynamics with the Fully Analytic Energy Gradient. J Chem Theory Comput 2012; 8:5008-12. [DOI: 10.1021/ct3007869] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kurt R. Brorsen
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
| | - Noriyuki Minezawa
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
| | - Feng Xu
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
| | - Theresa L. Windus
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department
of Chemistry and Ames Laboratory, Iowa State
University, Ames, Iowa 50011, United States
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22
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient for the embedding potential with approximations in the fragment molecular orbital method. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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23
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Nagata T, Fedorov DG, Li H, Kitaura K. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method. J Chem Phys 2012; 136:204112. [DOI: 10.1063/1.4714601] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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24
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Nagata T, Fedorov DG, Kitaura K. Analytic gradient and molecular dynamics simulations using the fragment molecular orbital method combined with effective potentials. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1136-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Fedorov DG, Nagata T, Kitaura K. Exploring chemistry with the fragment molecular orbital method. Phys Chem Chem Phys 2012; 14:7562-77. [DOI: 10.1039/c2cp23784a] [Citation(s) in RCA: 290] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Mochizuki Y, Yamashita K, Nakano T, Okiyama Y, Fukuzawa K, Taguchi N, Tanaka S. Higher-order correlated calculations based on fragment molecular orbital scheme. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1036-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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27
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Yoshioka A, Takematsu K, Kurisaki I, Fukuzawa K, Mochizuki Y, Nakano T, Nobusawa E, Nakajima K, Tanaka S. Antigen–antibody interactions of influenza virus hemagglutinin revealed by the fragment molecular orbital calculation. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-1048-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hitaoka S, Matoba H, Harada M, Yoshida T, Tsuji D, Hirokawa T, Itoh K, Chuman H. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures – LERE-QSAR Analysis (IV). J Chem Inf Model 2011; 51:2706-16. [DOI: 10.1021/ci2002395] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Seiji Hitaoka
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Matoba
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Masataka Harada
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Daisuke Tsuji
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Takatsugu Hirokawa
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Kohji Itoh
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
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Prediction of probable mutations in influenza virus hemagglutinin protein based on large-scale ab initio fragment molecular orbital calculations. J Mol Graph Model 2011; 30:110-9. [DOI: 10.1016/j.jmgm.2011.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/24/2011] [Accepted: 06/27/2011] [Indexed: 11/22/2022]
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30
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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Nagata T, Fedorov DG, Ishimura K, Kitaura K. Analytic energy gradient for second-order Møller-Plesset perturbation theory based on the fragment molecular orbital method. J Chem Phys 2011; 135:044110. [DOI: 10.1063/1.3611020] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Okiyama Y, Fukuzawa K, Yamada H, Mochizuki Y, Nakano T, Tanaka S. Counterpoise-corrected interaction energy analysis based on the fragment molecular orbital scheme. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.070] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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33
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Tanaka S. Modulation of excitation energy transfer by conformational oscillations in biomolecular systems. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.04.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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34
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Brorsen K, Fedorov DG. Fully analytic energy gradient in the fragment molecular orbital method. J Chem Phys 2011; 134:124115. [DOI: 10.1063/1.3568010] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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35
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Sawada T, Fedorov DG, Kitaura K. Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect. J Phys Chem B 2010; 114:15700-5. [DOI: 10.1021/jp1068895] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Toshihiko Sawada
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuo Kitaura
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan, Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan, and Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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