Faculty of Pharmacy, Widya Mandala Catholic University, Surabaya, East Java, Indonesia
BibTex Citation Data :
@article{JKSA55079, author = {Elisabeth Widjajakusuma and Monica Frederica and Kornelius Kaweono}, title = {Combined Classical and Flooding Molecular Dynamics Simulations of The Mip-Rapamycin and FKBP12-Rapamycin Complexes}, journal = {Jurnal Kimia Sains dan Aplikasi}, volume = {26}, number = {8}, year = {2023}, keywords = {macrophage infectivity potentiator; Legionella pneumophila; FKBP12, conformational flooding; dihedral angle principal component analysis}, abstract = { Macrophage infectivity potentiator (Mip) protein, an essential virulence factor encoded by pathogenic bacteria such as Legionella pneumophila , arises as an interesting new therapeutic target for novel antimicrobials. However, Mip- ligands also interact with FKBP12 protein, a human FKBP exhibiting immunosuppressive effects. Therefore, these ligands are unsuitable antibiotics. Understanding the dynamics and conformations of proteins in the binding pocket is important to predict binding properties and to design new binders for different FKBPs. We performed the 40 ns combined classical and flooding molecular dynamics simulations using additional flooding potential for Mip-rapamycin and FKBP12-rapamycin complexes. Both complexes have different flexibilities and dihedral angle principal component analysis calculated from MD trajectories. As a result, the Mip-rapamycin complex had more conformations than the FKBP12-rapamycin complex. These different features of both complexes at the binding pocket will provide new dues for the design of selective inhibitors of Mip proteins }, issn = {2597-9914}, pages = {300--309} doi = {10.14710/jksa.26.8.300-309}, url = {https://ejournal.undip.ac.id/index.php/ksa/article/view/55079} }
Refworks Citation Data :
Macrophage infectivity potentiator (Mip) protein, an essential virulence factor encoded by pathogenic bacteria such as Legionella pneumophila, arises as an interesting new therapeutic target for novel antimicrobials. However, Mip- ligands also interact with FKBP12 protein, a human FKBP exhibiting immunosuppressive effects. Therefore, these ligands are unsuitable antibiotics. Understanding the dynamics and conformations of proteins in the binding pocket is important to predict binding properties and to design new binders for different FKBPs. We performed the 40 ns combined classical and flooding molecular dynamics simulations using additional flooding potential for Mip-rapamycin and FKBP12-rapamycin complexes. Both complexes have different flexibilities and dihedral angle principal component analysis calculated from MD trajectories. As a result, the Mip-rapamycin complex had more conformations than the FKBP12-rapamycin complex. These different features of both complexes at the binding pocket will provide new dues for the design of selective inhibitors of Mip proteins
Note: This article has supplementary file(s).
Article Metrics:
Last update:
Last update: 2024-11-13 10:16:51
As an article writer, the author has the right to use their articles for various purposes, including use by institutions that employ authors or institutions that provide funding for research. Author rights are granted without special permission.
Author who publishes a paper at JKSA has the broad right to use their work for teaching and scientific purposes without the need to ask permission, including: used for (i) teaching in the author's class or institution, (ii) presentation at meetings or conferences and distributing copies to participants ; (iii) training conducted by the author or author's institution; (iv) distribution to colleagues for research use; (v) use in the compilation of subsequent authors' works; (vi) inclusion in a thesis or dissertation; (vi) reuse of part of the article in another work (with citation); (vii) preparation of derivative works (with citation); (viii) voluntary posting on open websites operated by authors or author institutions for scientific purposes (follow the CC BY-SA License).
Authors and readers can copy and redistribute material in any media or format, and mix, modify, and build material for any purpose but they must provide appropriate credit (provide article citation or content), providing links to the license, and indicate if there are changes.
The authors submitting a manuscript do so on the understanding that if accepted for publication, copyright of the article shall be assigned to Jurnal Kimia Sains dan Aplikasi (JKSA). Copyright encompasses rights to reproduce and deliver the article in all form and media, including reprints, photographs, microfilms and any other similar reproductions, as well as translations.
Reproduce any part of this journal, its storage in the database or its transmission by all forms or media is permitted does not need for written permission from JKSA. However, it should be cited as an honor in academic manners
JKSA and the Chemistry Department of Diponegoro University and the Editor make every effort to ensure that there are no data, opinions, or false or misleading statements published in JKSA. However, the content of the article is the sole and exclusive responsibility of each author.
The Copyright Transfer Form can be downloaded here: [Copyright Transfer Form - Indonesian] [Copyright Transfer Form - English]. The copyright form should be signed originally and send to the Editor in the form of printed letters, scanned documents sent via email or fax.
Adi Darmawan, Ph.D (Editor in Chief)
Editor in chief of Jurnal Kimia Sains dan Aplikasi (JKSA)
Chemistry Department, Faculty of Sciences and Mathematics, Diponegoro University
Visitor: View My Stats
Jurnal Kimia Sains dan Aplikasi is indexed in:
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.