Ribosomal computing: implementation of the computational method

• Published in: BMC bioinformatics Vol. 25; no. 1; pp. 321 - 27
• Main Authors: Chatterjee, Pratima, Ghosal, Prasun, Shit, Sahadeb, Biswas, Arindam, Mallik, Saurav, Allabun, Sarah, Othman, Manal, Ali, Almubarak Hassan, Elshiekh, E, Soufiene, Ben Othman
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03.10.2024; BioMed Central; BMC
• Subjects: Algorithms; Amino acid sequence; Analysis; Automation; Biological computing; Biological effects; Biological models (mathematics); Biological properties; Chemical synthesis; Computational biology; Computational Biology - methods; Computational model; Computer applications; Computer Simulation; DNA sequencing; Gene mutations; Gene sequencing; Health aspects; Mathematical functions; Mathematical model; Mathematical models; Mutation; Peptides; Point mutation; Protein Biosynthesis; Protein structure; Protein synthesis; Proteins; Ribonucleic acid; Ribosomal computing; Ribosome; Ribosomes - metabolism; RNA; Stalling; Saudi Arabia; Ribosome; Gene sequence; Protein synthesis; Mutation; Computational model; Mathematical model; Simulator; Stalling; Protein; Ribosomal computing
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-024-05945-w

Several computational and mathematical models of protein synthesis have been explored to accomplish the quantitative analysis of protein synthesis components and polysome structure. The effect of gene sequence (coding and non-coding region) in protein synthesis, mutation in gene sequence, and functional model of ribosome needs to be explored to investigate the relationship among protein synthesis components further. Ribosomal computing is implemented by imitating the functional property of protein synthesis. In the proposed work, a general framework of ribosomal computing is demonstrated by developing a computational model to present the relationship between biological details of protein synthesis and computing principles. Here, mathematical abstractions are chosen carefully without probing into intricate chemical details of the micro-operations of protein synthesis for ease of understanding. This model demonstrates the cause and effect of ribosome stalling during protein synthesis and the relationship between functional protein and gene sequence. Moreover, it also reveals the computing nature of ribosome molecules and other protein synthesis components. The effect of gene mutation on protein synthesis is also explored in this model. The computational model for ribosomal computing is implemented in this work. The proposed model demonstrates the relationship among gene sequences and protein synthesis components. This model also helps to implement a simulation environment (a simulator) for generating protein chains from gene sequences and can spot the problem during protein synthesis. Thus, this simulator can identify a disease that can happen due to a protein synthesis problem and suggest precautions for it.