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Journal of Biomolecular Structure and Dynamics Volume 36, 2018 - Issue 10
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Research Article

Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases

Wei YangInfection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, Australia
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Blake T. RileyInfection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, AustraliaORCID Iconhttp://orcid.org/0000-0003-2176-0503
ORCID Icon,
Xiangyun LeiSchool of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive N.W., Atlanta, GA, 30332-0100, USA
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Benjamin T. PorebskiInfection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, Australia;Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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Itamar KassInfection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, Australia;Victorian Life Sciences Computation Centre, Monash University, Clayton3800, Victoria, Australia
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Ashley M. BuckleInfection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, AustraliaORCID Iconhttp://orcid.org/0000-0003-2943-9044
ORCID Icon &
Sheena McGowanInfection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria3800, AustraliaCorrespondence[email protected]
ORCID Iconhttp://orcid.org/0000-0001-6863-1106
ORCID Icon show all
Pages 2595-2604 | Received 05 Jun 2017, Accepted 31 Jul 2017, Published online: 28 Aug 2017

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Talis Uelisson da Silva, Karina de Carvalho Pougy, Magaly Girão Albuquerque, Camilo Henrique da Silva Lima & Sérgio de Paula Machado. (2022) Development of parameters compatible with the CHARMM36 force field for [Fe4S4]2+ clusters and molecular dynamics simulations of adenosine-5’-phosphosulfate reductase in GROMACS 2019. Journal of Biomolecular Structure and Dynamics 40:8, pages 3481-3491.
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Gazal Kalyan, Vivek Junghare, Sourya Bhattacharya & Saugata Hazra. (2021) Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources. Journal of Biomolecular Structure and Dynamics 39:2, pages 635-649.
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Articles from other publishers (10)

Mahta Mansouri, Kajal Daware, Chaille T. Webb & Sheena McGowan. (2023) Understanding the structure and function of Plasmodium aminopeptidases to facilitate drug discovery. Current Opinion in Structural Biology 82, pages 102693.
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Wei Yang, Jingyuan Zhuang, Chen Li, Chen Bai & Guijuan Cheng. (2023) Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A. International Journal of Molecular Sciences 24:16, pages 12652.
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Zsolt Fazekas, Dóra K. Menyhárd & András Perczel. (2022) Omicron Binding Mode: Contact Analysis and Dynamics of the Omicron Receptor-Binding Domain in Complex with ACE2. Journal of Chemical Information and Modeling 62:16, pages 3844-3853.
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Chaille T. Webb, Wei Yang, Blake T. Riley, Brooke K. Hayes, Komagal Kannan Sivaraman, Tess R. Malcolm, Stephen Harrop, Sarah C. Atkinson, Itamar Kass, Ashley M. Buckle, Nyssa Drinkwater & Sheena McGowan. (2022) A metal ion–dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase. Journal of Biological Chemistry 298:7, pages 102119.
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Saman Sargazi, Sheida Shahraki, Omolbanin Shahraki, Farshid Zargari, Roghayeh Sheervalilou, Saeid Maghsoudi, Mohammad Navid Soltani Rad & Ramin Saravani. (2021) 8-Alkylmercaptocaffeine derivatives: antioxidant, molecular docking, and in-vitro cytotoxicity studies. Bioorganic Chemistry 111, pages 104900.
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Zahra Nikfarjam, Omid Bavi & Saeed K. Amini. (2021) Potential effective inhibitory compounds against Prostate Specific Membrane Antigen (PSMA): A molecular docking and molecular dynamics study. Archives of Biochemistry and Biophysics 699, pages 108747.
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Qin Qin, Chengye Tang, Jing Wu, Sheng Chen & Zhengfei Yan. (2021) A dual-functional aminopeptidase from Streptomyces canus T20 and its application in the preparation of small rice peptides. International Journal of Biological Macromolecules 167, pages 214-222.
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Antonija Tomić, Gordan Horvat, Michael Ramek, Dejan Agić, Hrvoje Brkić & Sanja Tomić. (2019) New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. Journal of Chemical Information and Modeling 59:8, pages 3437-3453.
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Jisook Lee, Natalie B. Vinh, Nyssa Drinkwater, Wei Yang, Komagal Kannan Sivaraman, Luke S. Schembri, Michelle Gazdik, Peter M. Grin, Georgina S. Butler, Christopher M. Overall, Susan A. Charman, Sheena McGowan & Peter J. Scammells. (2019) Novel Human Aminopeptidase N Inhibitors: Discovery and Optimization of Subsite Binding Interactions. Journal of Medicinal Chemistry 62:15, pages 7185-7209.
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Wei Yang, Blake T. Riley, Xiangyun Lei, Benjamin T. Porebski, Itamar Kass, Ashley M. Buckle & Sheena McGowan. (2018) Mapping the Pathway and Dynamics of Bestatin Inhibition of the Plasmodium falciparum M1 Aminopeptidase Pf A‐M1 . ChemMedChem 13:23, pages 2504-2513.
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