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Wang Z, Liu YF, Yan H, Tong H, Mei Z. Theoretical Investigations of the Chiral Transition of α-Amino Acid Confined in Various Sized Armchair Boron-Nitride Nanotubes. J Phys Chem A 2017; 121:1833-1840. [PMID: 28139928 DOI: 10.1021/acs.jpca.7b00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We computationally study the chiral transition process of the α-Ala molecule under confined different sizes of armchair SWBNNTs to explore the confinement effect. We find that the influence of a confinement environment (in armchair SWBNNTs) on the α-Ala molecule would lead to different reaction pathways. Meanwhile, the preferred reaction pathway is also different in various sizes of armchair SWBNNTs, and their energy barriers for the rate-limiting step decrease rapidly with the decreasing of the diameters of the nanotubes. It is obvious that significant decrease of the chiral transition energy barrier occurs compared with the isolated α-Ala molecule chirality conversion mechanism, by ∼15.6 kcal mol-1, highlighting the improvement in the activity the enantiomers of α-Ala molecule. We concluded that the confinement environment has a significant impact at the nanoscale on the enantiomer transformation process of the chiral molecule.
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Affiliation(s)
- Zuocheng Wang
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Yan Fang Liu
- The Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, Shandong 266101, P.R. China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101, Shandong, P.R. China
| | - Honyan Yan
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Computer Science, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Hua Tong
- The Department of Physics, Baicheng Normal University , Baicheng 137000, P.R. China.,The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China
| | - Zemin Mei
- The Institute of Theoretical and Computational Research, Baicheng Normal University , Baicheng 137000, P.R. China.,Department of Chemistry, Baicheng Normal University , Baicheng 137000, P.R. China
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Lintuluoto M, Lintuluoto JM. DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase. Biochemistry 2015; 55:210-23. [DOI: 10.1021/acs.biochem.5b00542] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Masami Lintuluoto
- Graduate
School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamohanki-cho, Sakyo, Kyoto 606-8522, Japan
| | - Juha M. Lintuluoto
- Graduate
School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8530, Japan
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Maekawa S, Matsui T, Hirao K, Shigeta Y. Theoretical Study on Reaction Mechanisms of Nitrite Reduction by Copper Nitrite Complexes: Toward Understanding and Controlling Possible Mechanisms of Copper Nitrite Reductase. J Phys Chem B 2015; 119:5392-403. [DOI: 10.1021/acs.jpcb.5b01356] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shintaro Maekawa
- Computational
Science Group, Mitsui Chemicals, Inc., 580-32 Nagaura, Sodegaura, Chiba 299-0265, Japan
| | - Toru Matsui
- RIKEN, Advanced
Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Kimihiko Hirao
- RIKEN, Advanced
Institute for Computational Science, 7-1-26, Minatojima-minami, Chuo-ku, Kobe, 650-0047, Japan
| | - Yasuteru Shigeta
- Graduate
School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawagoe, Saitama 332-0012, Japan
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Kamiya K, Baba T, Boero M, Matsui T, Negoro S, Shigeta Y. Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds. J Phys Chem Lett 2014; 5:1210-1216. [PMID: 26274473 DOI: 10.1021/jz500323y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The active site of 6-aminohexanoate-dimer hydrolase, a nylon-6 byproduct-degrading enzyme with a β-lactamase fold, possesses a Ser112/Lys115/Tyr215 catalytic triad similar to the one of penicillin-recognizing family of serine-reactive hydrolases but includes a unique Tyr170 residue. By using a reactive quantum mechanics/molecular mechanics (QM/MM) approach, we work out its catalytic mechanism and related functional/structural specificities. At variance with other peptidases, we show that the involvement of Tyr170 in the enzyme-substrate interactions is responsible for a structural variation in the substrate-binding state. The acylation via a tetrahedral intermediate is the rate-limiting step, with a free-energy barrier of ∼21 kcal/mol, driven by the catalytic triad Ser112, Lys115, and Tyr215, acting as a nucleophile, general base, and general acid, respectively. The functional interaction of Tyr170 with this triad leads to an efficient disruption of the tetrahedral intermediate, promoting a conformational change of the substrate favorable for proton donation from the general acid.
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Affiliation(s)
- Katsumasa Kamiya
- †Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Takeshi Baba
- ‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Mauro Boero
- §Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23 rue du Loess, 67034 Strasbourg, France
| | - Toru Matsui
- ∥RIKEN, Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Seiji Negoro
- ⊥Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Yasuteru Shigeta
- ‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- #CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 Japan
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Kamiya K, Shigeta Y. First-principles molecular dynamics study on the atomistic behavior of His503 in bovine cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2011; 1807:1328-35. [PMID: 21565155 DOI: 10.1016/j.bbabio.2011.03.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 03/29/2011] [Accepted: 03/30/2011] [Indexed: 11/26/2022]
Abstract
We report first-principles molecular dynamics calculations based on density functional theory performed on the entrance part of the D-path pathway in bovine cytochrome c oxidase. Our models, which are extracted from the fully reduced and oxidized X-ray structures, include His503 as a protonatable site. We find that the protonated His503 with the deprotonated Asp91 [H503-N(δ1)H(+) and D91-C(γ)OO(γ)] are more energetically favorable than other protonation states, [H503-N(δ1) and D91-C(γ)OOH], with an energy difference of about -5kcal/mol in reduced case, while the [H503-N(δ1)H+ and D91-C(γ)OO(-)] state is energetically unstable, about +3kcal/mol higher in energy in the oxidized case. The local interaction of His503 with the surrounding polar residues is necessary and sufficient for determining the energetics. The redox-coupled rotation of His503 is found to change the energetics of the protonation states. We also find that this rotation is coupled with the proton transfer from His503 and Asp91, which leads to the transition between the two different protonation states. This study suggests that His503 is involved in the proton supply to the D-path as a proton acceptor and that the redox-controlled proton-transfer-coupled rotation of His503 is a key process for an effective proton supply to the D-path from water bulk. This article is part of a Special Issue entitled: Allosteric cooperativity in respiratory proteins.
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