Formulation of the protein synthesis rate with sequence information
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
AIMS Press
2018-03-01
|
| Series: | Mathematical Biosciences and Engineering |
| Subjects: | |
| Online Access: | https://www.aimspress.com/article/doi/10.3934/mbe.2018023 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832590085248253952 |
|---|---|
| author | Wenjun Xia Jinzhi Lei |
| author_facet | Wenjun Xia Jinzhi Lei |
| author_sort | Wenjun Xia |
| collection | DOAJ |
| description | Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the tRNA pool and biochemical reactions involved in the translation elongation. The results show that the translation efficiency is mainly limited by the available ribosome number, translation initiation and the translation elongation time. The elongation time is a log-normal distribution, with the mean and variance determined by the codon saturation and the process of aa-tRNA selection at each codon binding site. Moreover, our simulations show that the translation accuracy exponentially decreases with the sequence length. These results suggest that aa-tRNA competition is crucial for both translation elongation, translation efficiency and the accuracy, which in turn determined the effective protein production rate of correct proteins. Our results improve the dynamical equation of protein production with a delay differential equation that is dependent on sequence information through both the effective production rate and the distribution of elongation time. |
| format | Article |
| id | doaj-art-e1bc8e686cbd43b0981d4f982b6b9005 |
| institution | Kabale University |
| issn | 1551-0018 |
| language | English |
| publishDate | 2018-03-01 |
| publisher | AIMS Press |
| record_format | Article |
| series | Mathematical Biosciences and Engineering |
| spelling | doaj-art-e1bc8e686cbd43b0981d4f982b6b90052025-01-24T02:40:44ZengAIMS PressMathematical Biosciences and Engineering1551-00182018-03-0115250752210.3934/mbe.2018023Formulation of the protein synthesis rate with sequence informationWenjun Xia0Jinzhi Lei1Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013, ChinaZhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing 100084, ChinaTranslation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the tRNA pool and biochemical reactions involved in the translation elongation. The results show that the translation efficiency is mainly limited by the available ribosome number, translation initiation and the translation elongation time. The elongation time is a log-normal distribution, with the mean and variance determined by the codon saturation and the process of aa-tRNA selection at each codon binding site. Moreover, our simulations show that the translation accuracy exponentially decreases with the sequence length. These results suggest that aa-tRNA competition is crucial for both translation elongation, translation efficiency and the accuracy, which in turn determined the effective protein production rate of correct proteins. Our results improve the dynamical equation of protein production with a delay differential equation that is dependent on sequence information through both the effective production rate and the distribution of elongation time.https://www.aimspress.com/article/doi/10.3934/mbe.2018023rna translationefficiencydelay differential equationnoncoding rna |
| spellingShingle | Wenjun Xia Jinzhi Lei Formulation of the protein synthesis rate with sequence information Mathematical Biosciences and Engineering rna translation efficiency delay differential equation noncoding rna |
| title | Formulation of the protein synthesis rate with sequence information |
| title_full | Formulation of the protein synthesis rate with sequence information |
| title_fullStr | Formulation of the protein synthesis rate with sequence information |
| title_full_unstemmed | Formulation of the protein synthesis rate with sequence information |
| title_short | Formulation of the protein synthesis rate with sequence information |
| title_sort | formulation of the protein synthesis rate with sequence information |
| topic | rna translation efficiency delay differential equation noncoding rna |
| url | https://www.aimspress.com/article/doi/10.3934/mbe.2018023 |
| work_keys_str_mv | AT wenjunxia formulationoftheproteinsynthesisratewithsequenceinformation AT jinzhilei formulationoftheproteinsynthesisratewithsequenceinformation |