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Kanematsu Y, Kondo HX, Takano Y. Computational Exploration of Minimum Energy Reaction Pathway of N 2O Formation from Intermediate I of P450nor Using an Active Center Model. Int J Mol Sci 2023; 24:17172. [PMID: 38139001 PMCID: PMC10743073 DOI: 10.3390/ijms242417172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
P450nor is a heme-containing enzyme that catalyzes the conversion of nitric oxide (NO) to nitrous oxide (N2O). Its catalytic mechanism has attracted attention in chemistry, biology, and environmental engineering. The catalytic cycle of P450nor is proposed to consist of three major steps. The reaction mechanism for the last step, N2O generation, remains unknown. In this study, the reaction pathway of the N2O generation from the intermediate I was explored with the B3LYP calculations using an active center model after the examination of the validity of the model. In the validation, we compared the heme distortions between P450nor and other oxidoreductases, suggesting a small effect of protein environment on the N2O generation reaction in P450nor. We then evaluated the electrostatic environment effect of P450nor on the hydride affinity to the active site with quantum mechanics/molecular mechanics (QM/MM) calculations, confirming that the affinity was unchanged with or without the protein environment. The active center model for P450nor showed that the N2O generation process in the enzymatic reaction undergoes a reasonable barrier height without protein environment. Consequently, our findings strongly suggest that the N2O generation reaction from the intermediate I depends sorely on the intrinsic reactivity of the heme cofactor bound on cysteine residue.
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Affiliation(s)
- Yusuke Kanematsu
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
| | - Hiroko X. Kondo
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan;
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Kondo HX, Nakamura H, Takano Y. Negative fragmentation approach for investigating the depolarization effect of neighboring residues on hydrogen bonds in π-helix. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Kondo HX, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y. Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network. Biomolecules 2023; 13:biom13010137. [PMID: 36671521 PMCID: PMC9855806 DOI: 10.3390/biom13010137] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023] Open
Abstract
Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure-function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure-function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB-OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure-function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.
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Affiliation(s)
- Hiroko X. Kondo
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita 565-0874, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
| | - Hiroyuki Iizuka
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14, Nishi 9, Kitaku, Sapporo 060-0814, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Information R&D and Strategy Headquarters, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yuichi Kabaya
- Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami 090-8507, Japan
| | - Yusuke Kanematsu
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima 739-8527, Japan
| | - Yu Takano
- Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Correspondence: (H.X.K.); (Y.T.); Tel.: +81-157-26-9401 (H.X.K.); +81-82-830-1825 (Y.T.)
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Affiliation(s)
- Hiroko X. Kondo
- Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
| | - Yusuke Kanematsu
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
- Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Yu Takano
- Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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Kondo HX, Fujii M, Tanioka T, Kanematsu Y, Yoshida T, Takano Y. Global Analysis of Heme Proteins Elucidates the Correlation between Heme Distortion and the Heme-Binding Pocket. J Chem Inf Model 2022; 62:775-784. [PMID: 35157473 DOI: 10.1021/acs.jcim.1c01315] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Heme proteins play diverse and important biological roles, from electron transfer and chemical catalysis to oxygen transport and/or storage. Although the distortion of heme porphyrin correlates with the physical properties of heme, such as the redox potential and oxygen affinity, the relationship between heme distortion and the heme protein environment is unclear. Here, we tested the hypothesis that the protein environment of the heme-binding pocket determines heme distortion (conformation). We analyzed the correlations between the amino acid composition of the heme-binding pocket and the magnitude of heme distortion along 12 vibrational modes using machine learning. A correlation was detected in the three lowest vibrational modes. Analysis of heme distortions in nearly the same environments of the heme-binding pocket supported this notion. Our analyses indicate that the heme-binding pocket environment is a major factor impacting the distortion of heme porphyrin along the three lowest vibrational modes. In addition, statistical analysis of the distortion of heme porphyrin revealed that the peaks of distributions of the ruffling and breathing distortions are shifted from 0 (the equilibrium structure). Both the ruffling and breathing distortions are correlated with the redox potential of heme, so that heme molecules with these distortions have a lower redox potential than planar molecules. These findings explain the structure-function relationship of heme.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan.,Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan
| | - Masanori Fujii
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Takuma Tanioka
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan.,Department of Applied Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Takashi Yoshida
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima, Hiroshima 731-3194, Japan
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Kondo HX, Kanematsu Y, Masumoto G, Takano Y. PyDISH: database and analysis tools for heme porphyrin distortion in heme proteins. Database (Oxford) 2020; 2023:baaa066. [PMID: 33002111 PMCID: PMC10755257 DOI: 10.1093/database/baaa066] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/24/2020] [Indexed: 11/14/2022]
Abstract
Heme participates in a wide range of biological functions such as oxygen transport, electron transport, oxygen reduction, transcriptional regulation and so on. While the mechanism of each function has been investigated for many heme proteins, the origin of the diversity of the heme functions is still unclear and a crucial scientific issue. We have constructed a database of heme proteins, named Python-based database and analyzer for DIStortion of Heme porphyrin (PyDISH), which also contains some analysis tools. The aim of PyDISH is to integrate the information on the structures of hemes and heme proteins and the functions of heme proteins. This database will provide the structure-function relationships focusing on heme porphyrin distortion and lead to the elucidation of the origin of the functional diversity of heme proteins. In addition, the insights obtained from the database can be used for the design of protein function. PyDISH contains the structural data of more than 13 000 hemes extracted from the Protein Data Bank, including heme porphyrin distortion, axial ligands coordinating to the heme and the orientation of the propionate sidechains of heme. PyDISH also has information about the protein domains, including Uniprot ID, protein fold by CATH ID, organism, coordination distance and so on. The analytical tools implemented in PyDISH allow users to not only browse and download the data but also analyze the structures of heme porphyrin by using the analytical tools implemented in PyDISH. PyDISH users will be able to utilize the obtained results for the design of protein function. Database URL: http://pydish.bio.info.hiroshima-cu.ac.jp/.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido 090-8507, Japan
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita 565-0874, Japan and
| | - Yusuke Kanematsu
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
| | - Gen Masumoto
- Information Systems Division, RIKEN Head Office for Information Systems and Cybersecurity, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozukahigashi Asaminamiku, Hiroshima 731-3194, Japan
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Kondo HX, Kiribayashi R, Kuroda D, Kohda J, Kugimiya A, Nakano Y, Tsumoto K, Takano Y. Effects of a remote mutation from the contact paratope on the structure of CDR-H3 in the anti-HIV neutralizing antibody PG16. Sci Rep 2019; 9:19840. [PMID: 31882602 PMCID: PMC6934664 DOI: 10.1038/s41598-019-56154-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/06/2019] [Indexed: 11/22/2022] Open
Abstract
PG16 is a broadly neutralizing antibody to the human immunodeficiency virus (HIV). A crystal structure of PG16 revealed that the unusually long 28-residue complementarity determining region (CDR) H3 forms a unique subdomain, referred to as a "hammerhead", that directly contacts the antigen. The hammerhead apparently governs the function of PG16 while a previous experimental assay showed that the mutation of TyrH100Q to Ala, which does not directly contact the antigen, decreased the neutralization ability of PG16. However, the molecular mechanism by which a remote mutation from the hammerhead or contact paratope affects the neutralization potency has remained unclear. Here, we performed molecular dynamics simulations of the wild-type and variants (TyrH100Q to Ala, and TyrH100Q to Phe) of PG16, to clarify the effects of these mutations on the dynamics of CDR-H3. Our simulations revealed that the structural rigidity of the CDR-H3 in PG16 is attributable to the hydrogen bond interaction between TyrH100Q and ProH99, as well as the steric support by TyrH100Q. The loss of both interactions increases the intrinsic fluctuations of the CDR-H3 in PG16, leading to a conformational transition of CDR-H3 toward an inactive state.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, Kitami, 090-8507, Japan.
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan.
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, Suita, 565-0874, Japan.
| | - Ryo Kiribayashi
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan.
| | - Jiro Kohda
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Akimitsu Kugimiya
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Yasuhisa Nakano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 113-8656, Japan
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, Hiroshima, 731-3194, Japan.
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Kondo HX, Kusaka A, Kitakawa CK, Onari J, Yamanaka S, Nakamura H, Takano Y. Hydrogen bond donors and acceptors are generally depolarized in α-helices as revealed by a molecular tailoring approach. J Comput Chem 2019; 40:2043-2052. [PMID: 31099907 PMCID: PMC6767508 DOI: 10.1002/jcc.25859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 11/24/2022]
Abstract
Hydrogen‐bond (H‐bond) interaction energies in α‐helices of short alanine peptides were systematically examined by precise density functional theory calculations, followed by a molecular tailoring approach. The contribution of each H‐bond interaction in α‐helices was estimated in detail from the entire conformation energies, and the results were compared with those in the minimal H‐bond models, in which only H‐bond donors and acceptors exist with the capping methyl groups. The former interaction energies were always significantly weaker than the latter energies, when the same geometries of the H‐bond donors and acceptors were applied. The chemical origin of this phenomenon was investigated by analyzing the differences among the electronic structures of the local peptide backbones of the α‐helices and those of the minimal H‐bond models. Consequently, we found that the reduced H‐bond energy originated from the depolarizations of both the H‐bond donor and acceptor groups, due to the repulsive interactions with the neighboring polar peptide groups in the α‐helix backbone. The classical force fields provide similar H‐bond energies to those in the minimal H‐bond models, which ignore the current depolarization effect, and thus they overestimate the actual H‐bond energies in α‐helices. © 2019 The Authors. Journal of Computational Chemistry published by Wiley Periodicals, Inc.
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Affiliation(s)
- Hiroko X Kondo
- School of Regional Innovation and Social Design Engineering, Faculty of Engineering, Kitami Institute of Technology, 165 Koen-cho, Kitami, Hokkaido, 090-8507, Japan
| | - Ayumi Kusaka
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Colin K Kitakawa
- Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka, 560-0043, Japan
| | - Jinta Onari
- Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka, 560-0043, Japan
| | - Shusuke Yamanaka
- Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka, 560-0043, Japan
| | - Haruki Nakamura
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yu Takano
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi Asa-Minami-Ku, Hiroshima, 731-3194, Japan
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Kondo HX, Yoshida N, Shirota M, Kinoshita K. Molecular Mechanism of Depolarization-Dependent Inactivation in W366F Mutant of Kv1.2. J Phys Chem B 2018; 122:10825-10833. [PMID: 30395463 DOI: 10.1021/acs.jpcb.8b09446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Voltage-gated potassium channels play crucial roles in regulating membrane potential. They are activated by membrane depolarization, allowing the selective permeation of K+ ions across the plasma membrane, and enter a nonconducting state after lasting depolarization, a process known as inactivation. Inactivation in voltage-activated potassium channels occurs through two distinct mechanisms, N-type and C-type inactivation. C-type inactivation is caused by conformational changes in the extracellular mouth of the channel, whereas N-type inactivation is elicited by changes in the cytoplasmic mouth of the protein. The W434F-mutated Shaker channel is known as a nonconducting mutant and is in a C-type inactivation state at a depolarizing membrane potential. To clarify the structural properties of C-type inactivated protein, we performed molecular dynamics simulations of the wild-type and W366F (corresponding to W434F in Shaker) mutant of the Kv1.2-2.1 chimera channel. The W366F mutant was in a nearly nonconducting state with a depolarizing voltage and recovered from inactivation with a reverse voltage. Our simulations and three-dimensional reference interaction site model analysis suggested that structural changes in the selectivity filter upon membrane depolarization trap K+ ions around the inner mouth of the selectivity filter and prevent ion permeation. This pore restriction is involved in the molecular mechanism of C-type inactivation.
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Affiliation(s)
- Hiroko X Kondo
- Department of Applied Information Sciences, Graduate School of Information Sciences , Tohoku University , 6-3-09 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8579 , Japan.,Laboratory for Computational Molecular Design , RIKEN Center for Biosystems Dynamics Research , 6-2-3, Furuedai , Suita 565-0874 , Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science , Kyushu University , 744, Motooka , Nishi-ku, Fukuoka 819-0395 , Japan
| | - Matsuyuki Shirota
- Department of Applied Information Sciences, Graduate School of Information Sciences , Tohoku University , 6-3-09 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8579 , Japan.,Graduate School of Medicine , Tohoku University , 2-1 Seiryo-machi , Aoba-ku, Sendai 980-8575 , Japan.,Tohoku Medical Megabank Organization , Tohoku University , 2-1 Seiryo-machi , Aoba-ku, Sendai 980-8573 , Japan
| | - Kengo Kinoshita
- Department of Applied Information Sciences, Graduate School of Information Sciences , Tohoku University , 6-3-09 Aramaki-Aza-Aoba , Aoba-ku, Sendai 980-8579 , Japan.,Tohoku Medical Megabank Organization , Tohoku University , 2-1 Seiryo-machi , Aoba-ku, Sendai 980-8573 , Japan.,Institute of Development, Aging and Cancer , Tohoku University , 4-1 Seiryocho, Aoba-ku , Sendai 980-8575 , Japan
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Kanematsu Y, Kondo HX, Imada Y, Takano Y. Statistical and quantum-chemical analysis of the effect of heme porphyrin distortion in heme proteins: Differences between oxidoreductases and oxygen carrier proteins. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Iwaki M, Takeshita K, Kondo HX, Kinoshita K, Okamura Y, Takano Y, Nakagawa A, Kandori H. Zn2+-Binding to the Voltage-Gated Proton Channel Hv1/VSOP. J Phys Chem B 2018; 122:9076-9080. [DOI: 10.1021/acs.jpcb.8b04890] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Hiroko X. Kondo
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
- Laboratory for Computational Molecular Design, RIKEN Center for Biosystems Dynamics Research, 6-2-3, Furuedai, Suita, 565-0874, Japan
| | - Kengo Kinoshita
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seityo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryocho, Aoba-ku, Sendai, 980-8575, Japan
| | | | - Yu Takano
- Department of Biomedical Information Sciences, Graduate School of Information Sciences, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, Hiroshima 731-3194, Japan
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Katsura Y, Kondo HX, Ryan J, Harley V, Satta Y. The evolutionary process of mammalian sex determination genes focusing on marsupial SRYs. BMC Evol Biol 2018; 18:3. [PMID: 29338681 PMCID: PMC5771129 DOI: 10.1186/s12862-018-1119-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 01/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Maleness in mammals is genetically determined by the Y chromosome. On the Y chromosome SRY is known as the mammalian male-determining gene. Both placental mammals (Eutheria) and marsupial mammals (Metatheria) have SRY genes. However, only eutherian SRY genes have been empirically examined by functional analyses, and the involvement of marsupial SRY in male gonad development remains speculative. RESULTS In order to demonstrate that the marsupial SRY gene is similar to the eutherian SRY gene in function, we first examined the sequence differences between marsupial and eutherian SRY genes. Then, using a parsimony method, we identify 7 marsupial-specific ancestral substitutions, 13 eutherian-specific ancestral substitutions, and 4 substitutions that occurred at the stem lineage of therian SRY genes. A literature search and molecular dynamics computational simulations support that the lineage-specific ancestral substitutions might be involved with the functional differentiation between marsupial and eutherian SRY genes. To address the function of the marsupial SRY gene in male determination, we performed luciferase assays on the testis enhancer of Sox9 core (TESCO) using the marsupial SRY. The functional assay shows that marsupial SRY gene can weakly up-regulate the luciferase expression via TESCO. CONCLUSIONS Despite the sequence differences between the marsupial and eutherian SRY genes, our functional assay indicates that the marsupial SRY gene regulates SOX9 as a transcription factor in a similar way to the eutherian SRY gene. Our results suggest that SRY genes obtained the function of male determination in the common ancestor of Theria (placental mammals and marsupials). This suggests that the marsupial SRY gene has a function in male determination, but additional experiments are needed to be conclusive.
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Affiliation(s)
- Yukako Katsura
- Department of Biology, The Pennsylvania State University, State College, USA
- Department of Biology, Temple University, Philadelphia, USA
- Department of Biomedical Sciences, Nihon University, Tokyo, Japan
| | - Hiroko X. Kondo
- Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan
- Laboratory for Computational Molecular Design, RIKEN Quantitative Biology Center, Osaka, Japan
| | - Janelle Ryan
- Hudson Institute of Medical Research, Melbourne, Australia
| | - Vincent Harley
- Hudson Institute of Medical Research, Melbourne, Australia
| | - Yoko Satta
- Department of Evolutionary Study of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
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Fujiwara Y, Kondo HX, Shirota M, Kobayashi M, Takeshita K, Nakagawa A, Okamura Y, Kinoshita K. Structural basis for the membrane association of ankyrinG via palmitoylation. Sci Rep 2016; 6:23981. [PMID: 27046665 PMCID: PMC4820748 DOI: 10.1038/srep23981] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/17/2016] [Indexed: 12/03/2022] Open
Abstract
By clustering various ion channels and transporters, ankyrin-G (AnkG) configures the membrane-excitation platforms in neurons and cardiomyocytes. AnkG itself localizes to specific areas on the plasma membrane via s-palmitoylation of Cys. However, the structural mechanism by which AnkG anchors to the membrane is not understood. In this study, we solved the crystal structures of the reduced and oxidized forms of the AnkG s-palmitoylation domain and used multiple long-term coarse-grained molecular dynamics simulations to analyze their membrane association. Here we report that the membrane anchoring of AnkG was facilitated by s-palmitoylation, defining a stable binding interface on the lipid membrane, and that AnkG without s-palmitoylation also preferred to stay near the membrane but did not have a unique binding interface. This suggests that AnkG in the juxtamembrane region is primed to accept lipid modification at Cys, and once that happens AnkG constitutes a rigid structural base upon which a membrane-excitation platform can be assembled.
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Affiliation(s)
- Yuichiro Fujiwara
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, JAPAN
| | - Hiroko X Kondo
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, JAPAN.,Graduate School of Information Sciences, Hiroshima City University, Hiroshima, JAPAN
| | - Matsuyuki Shirota
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, JAPAN.,Systems Bioinformatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, JAPAN.,United Centers for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Sendai, JAPAN
| | - Megumi Kobayashi
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, JAPAN
| | - Kohei Takeshita
- Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, JAPAN
| | - Atsushi Nakagawa
- Supramolecular Crystallography, Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, Suita, JAPAN.,Graduate School of Frontier Biosciences, Osaka University, Suita, JAPAN
| | - Yasushi Okamura
- Integrative Physiology, Department of Physiology, Graduate School of Medicine, Osaka University, Suita, JAPAN.,Graduate School of Frontier Biosciences, Osaka University, Suita, JAPAN
| | - Kengo Kinoshita
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, JAPAN.,Systems Bioinformatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, JAPAN.,Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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Abstract
The replica exchange method (REM) is a powerful tool for the conformational sampling of biomolecules. In this study, we propose an enhanced exchange algorithm for REM not meeting the detailed balance condition (DBC), but satisfying the balance condition in all considered exchanges between two replicas. Breaking the DBC can minimize the rejection rate and make an exchange process rejection-free as the number of replicas increases. To enhance the efficiency of REM, all possible pairs--not only the nearest neighbor--were considered in the exchange process. The test simulations of the alanine dipeptide confirmed the correctness of our method. The average traveling distance of each replica in the temperature distribution was also increased in proportion to an increase in the exchange rate. Furthermore, we applied our algorithm to the conformational sampling of the 10-residue miniprotein, chignolin, with an implicit solvent model. The results showed a faster convergence in the calculation of its free energy landscape, compared to that achieved using the normal exchange method of adjacent pairs. This algorithm can also be applied to the conventional near neighbor method and is expected to reduce the required number of replicas.
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Affiliation(s)
- Hiroko X Kondo
- Laboratory for Computational Molecular Design, RIKEN QBiC (Quantitative Biology Center), 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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Affiliation(s)
- Hiroko X. Kondo
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
- Department of Computational Biology, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan 277-8561
| | - Noriaki Okimoto
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
| | - Gentaro Morimoto
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
| | - Makoto Taiji
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
- Department of Computational Biology, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan 277-8561
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