Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets
In molecular biology, protein synthesis is an essential biological process of generating specific proteins in living systems. Many mathematical models are designed to characterize the process of the flow of genetic information from deoxyribonucleic acid (DNA) to protein; however, most of them cannot...
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| Format: | Article |
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IEEE
2018-01-01
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| Series: | IEEE Access |
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| Online Access: | https://ieeexplore.ieee.org/document/8335264/ |
| _version_ | 1818927801245368320 |
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| author | Jinliang Yang Haitao Pu Jian Lian Jason Gu Mingqu Fan |
| author_facet | Jinliang Yang Haitao Pu Jian Lian Jason Gu Mingqu Fan |
| author_sort | Jinliang Yang |
| collection | DOAJ |
| description | In molecular biology, protein synthesis is an essential biological process of generating specific proteins in living systems. Many mathematical models are designed to characterize the process of the flow of genetic information from deoxyribonucleic acid (DNA) to protein; however, most of them cannot provide detailed and observed steps to describe and analyze this fundamental biological process. Colored Petri Net (CPN), as a mathematical method widely applied in the process analysis of discrete event dynamic systems, has increasingly become an innovative and efficient theoretical approach for exploring the biological processes. Aiming at describing the entire process of protein synthesis, a CPN-based model has been designed that successfully and intuitively represents the flow of genetic information involving transcription and translation. DNA mutations are permanent alterations in the nucleotide sequence of the DNA strand, while different types of mutations have various effects on the synthesized proteins. Based on the proposed protein synthesis model, we put forward a new CPN model to identify the type of mutation, which is beneficial for analyzing whether the mutation has impacts on the structure or function of the produced protein. The mutation position and bases mutated rate are obtained by contrasting the nucleobases on DNA sequences, while the mutation type is determined via the alignment of the amino acids in the polypeptide chain. The model's effectiveness and accuracy are illustrated by biological mutation examples, indicating this method offers great superiority in modeling and analyzing the complex biological processes. |
| first_indexed | 2024-12-20T03:18:47Z |
| format | Article |
| id | doaj.art-55c5cc7b03b74c78a0e819ae6ea4ace6 |
| institution | Directory Open Access Journal |
| issn | 2169-3536 |
| language | English |
| last_indexed | 2024-12-20T03:18:47Z |
| publishDate | 2018-01-01 |
| publisher | IEEE |
| record_format | Article |
| series | IEEE Access |
| spelling | doaj.art-55c5cc7b03b74c78a0e819ae6ea4ace62022-12-21T19:55:16ZengIEEEIEEE Access2169-35362018-01-016223862240010.1109/ACCESS.2018.28257828335264Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri NetsJinliang Yang0https://orcid.org/0000-0002-3647-1950Haitao Pu1Jian Lian2https://orcid.org/0000-0003-0305-8454Jason Gu3https://orcid.org/0000-0002-7626-1077Mingqu Fan4Department of Electrical Engineering and Information Technology, Shandong University of Science and Technology, Jinan, ChinaDepartment of Electrical Engineering and Information Technology, Shandong University of Science and Technology, Jinan, ChinaDepartment of Electrical Engineering and Information Technology, Shandong University of Science and Technology, Jinan, ChinaDepartment of Electrical and Computer Engineering, Dalhousie University, Halifax, NS, CanadaDepartment of Electrical Engineering and Information Technology, Shandong University of Science and Technology, Jinan, ChinaIn molecular biology, protein synthesis is an essential biological process of generating specific proteins in living systems. Many mathematical models are designed to characterize the process of the flow of genetic information from deoxyribonucleic acid (DNA) to protein; however, most of them cannot provide detailed and observed steps to describe and analyze this fundamental biological process. Colored Petri Net (CPN), as a mathematical method widely applied in the process analysis of discrete event dynamic systems, has increasingly become an innovative and efficient theoretical approach for exploring the biological processes. Aiming at describing the entire process of protein synthesis, a CPN-based model has been designed that successfully and intuitively represents the flow of genetic information involving transcription and translation. DNA mutations are permanent alterations in the nucleotide sequence of the DNA strand, while different types of mutations have various effects on the synthesized proteins. Based on the proposed protein synthesis model, we put forward a new CPN model to identify the type of mutation, which is beneficial for analyzing whether the mutation has impacts on the structure or function of the produced protein. The mutation position and bases mutated rate are obtained by contrasting the nucleobases on DNA sequences, while the mutation type is determined via the alignment of the amino acids in the polypeptide chain. The model's effectiveness and accuracy are illustrated by biological mutation examples, indicating this method offers great superiority in modeling and analyzing the complex biological processes.https://ieeexplore.ieee.org/document/8335264/Protein synthesismodelingdeoxyribonucleic acid (DNA) mutationtype determinationcolored Petri Net |
| spellingShingle | Jinliang Yang Haitao Pu Jian Lian Jason Gu Mingqu Fan Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets IEEE Access Protein synthesis modeling deoxyribonucleic acid (DNA) mutation type determination colored Petri Net |
| title | Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets |
| title_full | Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets |
| title_fullStr | Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets |
| title_full_unstemmed | Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets |
| title_short | Modeling and Analysis of Protein Synthesis and DNA Mutation Using Colored Petri Nets |
| title_sort | modeling and analysis of protein synthesis and dna mutation using colored petri nets |
| topic | Protein synthesis modeling deoxyribonucleic acid (DNA) mutation type determination colored Petri Net |
| url | https://ieeexplore.ieee.org/document/8335264/ |
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