Applications of knot theory: chirality and the p53 protein
DOI:
https://doi.org/10.61117/ipsumtec.v6i4.271Keywords:
Knot, Chilarity, P53, DNA, Oncology drugsAbstract
In this paper we introduce some classic concepts of knot theory such as torsion, link number, mirror image, unknot number and quilarid of a knot, as well as the twist of a band. Later we translate these concepts to DNA modeling and similar molecules such as the P53 protein, which is synthesized from the DNA molecule and is known as the guardian of the genome, since it has a protocol to prevent the growth of damaged cells. Finally we established the quilarity of the P53 protein and discussed some uses in drug design.
Downloads
Metrics
References
Edward Witten, Fivebranes and Knots, http://arxiv.org/abs/1101.3216
Christopher C. Walker, Theodore L. Fobe, Michael R. Shirts, How cooperatively folding are homopolymer molecular knots? Macromolecules 2022, 55, 19, 8419–8437. DOI: https://doi.org/10.1021/acs.macromol.2c00881
Joseph L Sleiman, Robin H Burton, Michele Caraglio, Yair Augusto Gutierrez Fosado, Davide Michieletto, Geometric Predictors of Knotted and Linked Arcs. ACS Polym Au. 2022, volume 2(5), pages 341-350. DOI: https://doi.org/10.1021/acspolymersau.2c00021
Shensheng Chen, Tingtao Zhou, Polyelectrolyte Knot Delocalization Induced by Counterion Condensation, ArXiv
Levinthal, Cyrus (1968) Are there pathways for protein folding?. Journal de Chimie Physique et de Physico-Chimie Biologique 65: 44-45. DOI: https://doi.org/10.1051/jcp/1968650044
De J Alas-Guardado, S., Rojo, A., & Merino, G. (2011). La paradoja de Levinthal: cuando una contradicción se vuelve lógica. Educación Química, 22(1), 51-54. DOI: https://doi.org/10.1016/S0187-893X(18)30114-9
Curso en línea sobre codificación genética. https://www.youtube.com/playlist?list=PL2mpR0RYFsBiCWVJSvVAO3OJ2t7DzoHA
Bruno Contreras Moreira (2022) Algoritmos en Bioinformática Estructural. http://eead-csic-compbio.github.io/bioinformatica_estructural/#foldit
Database, A. P. S. (s. f.). AlphaFold Protein Structure Database. https://alphafold.ebi.ac.uk/
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583-589. DOI: https://doi.org/10.1038/s41586-021-03819-2
Efstratia Kalfagianni, Rob Mcconkey. (2023) Crossing numbers of cable knots. DOI: https://doi.org/10.1112/blms.13140
Vassily Manturoy. (2018) Knot Theory, second edition. CRC Press.
Reidemeister, Kurt (1927), Elementare Begründung der Knotentheorie, Abh. Math. Sem. Univ. Hamburg, 5 (1): 24–32, doi:10.1007/BF02952507, MR 3069462, S2CID 120149796 DOI: https://doi.org/10.1007/BF02952507
Alexander, James W.; Briggs, Garland B. (1926), On types of knotted curves, Annals of Mathematics, 28 (1/4): 562–586, doi:10.2307/1968399, JSTOR 1968399, MR 1502807 DOI: https://doi.org/10.2307/1968399
Gilberto Pardo Andreu, Patricia Hernández Casaña y Dr. René Delgado Hernández (2005) La apoptosis y la senescencia celular: mecanismos supresores de tumores Rev cubana med v.44 n.1-2 Ciudad de la Habana.
Joaquín Jordán. (2003), Apoptosis: muerte celular programada. Volo22, Num 6
Jian Dong Chen. (2016, marzo). The Cell-Cycle Arrest and Apoptotic Functions of p53 in Tumor Initiation and Progression. PubMed Central. Recuperado 10 de junio de 2023, de
Basu, S., & Murphy, M. E. (2016). Genetic modifiers of the P53 pathway. Cold Spring Harbor Perspectives in Medicine, 6(4), a026302. DOI: https://doi.org/10.1101/cshperspect.a026302
Chen, J. (2016). The Cell-Cycle arrest and apoptotic functions of P53 in tumor initiation and progression. Cold Spring Harbor Perspectives in Medicine, 6(3), a026104. DOI: https://doi.org/10.1101/cshperspect.a026104
D. Quintela Senra, JJB López Sáez, A. Senra Varela (2001) La proteína p53 y el cáncer de mama. Revisión crítica Revista de Senología y Patología Mamaria - Journal of Breast Science. Vol 14. Num 2. Pag 71-77
Ghatak, D., Ghosh, D. D., & Roychoudhury, S. (2021). Cancer stemness: p53 at the wheel. Frontiers in Oncology, 10 DOI: https://doi.org/10.3389/fonc.2020.604124
Erica Flapan, (2016). Knot, molecules and the universe. An introduction to topology. AMS DOI: https://doi.org/10.1090/mbk/096
Wei Chen, Yihui Ren, Ai Kagawa, Matthew R. Carbone, Samuel Yen-Chi Chen, Xiaohui Qu, Shinjae Yoo, Austin Clyde, Arvind Ramanathan, Rick L. Stevens, Hubertus J. J. van Dam, and Deyu Liu Transferable Graph Neural Fingerprint Models for Quick Response to Future Bio-Threats
Jonas Berx, Alireza Mashaghi. Decoding chirality in circuit topology of a self entangled chain through braiding. Soft Matter, 2023, Advance Article DOI: https://doi.org/10.1039/D3SM00390F
Hai Lan, Xian Wei. Simplicial Message Passing for Chemical Property Prediction.
Published
How to Cite
Issue
Section
License
Copyright (c) 2023 Jonathan Toledo-Toledo, Dalia Elizabeth García Sánchez , Nancy Márquez Lázaro , Adrián López Antonio

This work is licensed under a Creative Commons Attribution 4.0 International License.
