Accurate Prediction of Cellular Co-Translational Folding Indicates Proteins can Switch from Post- to Co-Translational Folding

Nissley, Daniel A.

doi:10.1016/j.bpj.2016.11.259

Cited by 7 publications

(10 citation statements)

References 45 publications

(88 reference statements)

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“…For example, it was suggested that translation elongation is lower downstream of the protein domain boundaries probably to improve the fidelity of co-translational domain-wise protein folding (57,66). Similar ideas related to elongation and co-translational folding have been suggested based on additional techniques including the tAI and TASEP based models (98,169). …”

Section: Introductionmentioning

confidence: 80%

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

2016

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mRNA translation is the fundamental process of decoding the information encoded in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this process in various biomedical disciplines such as cell biology, evolution and biotechnology, encouraged the development of dozens of mathematical and computational models of translation in recent years. These models aimed at capturing various biophysical aspects of the process. The objective of this review is to survey these models, focusing on those based and/or validated on real large-scale genomic data. We consider aspects such as the complexity of the models, the biophysical aspects they regard and the predictions they may provide. Furthermore, we survey the central systems biology discoveries reported on their basis. This review demonstrates the fundamental advantages of employing computational biophysical translation models in general, and discusses the relative advantages of the different approaches and the challenges in the field.

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Section: Introductionmentioning

confidence: 80%

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

2016

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“…In some cases, these changes are associated with diseases . Synonymous mutations that change elongation rates can even switch folding of some protein domains from post‐translational to cotranslational . Alterations in codon context caused by synonymous mutations may also induce the mis‐incorporation of amino acids, leading to protein misfolding …”

Section: Elongation Processivity and Protein Foldingmentioning

confidence: 99%

The ribosome in action: Tuning of translational efficiency and protein folding

2016

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The cellular proteome is shaped by the combined activities of the gene expression and quality control machineries. While transcription plays an undoubtedly important role, in recent years also translation emerged as a key step that defines the composition and quality of the proteome and the functional activity of proteins in the cell. Among the different post-transcriptional control mechanisms, translation initiation and elongation provide multiple checkpoints that can affect translational efficiency. A multitude of specific signals in mRNAs can determine the frequency of translation initiation, choice of the open reading frame, global and local elongation velocities, and the folding of the emerging protein. In addition to specific signatures in the mRNAs, also variations in the global pools of translation components, including ribosomes, tRNAs, mRNAs, and translation factors can alter translational efficiencies. The cellular outcomes of phenomena such as mRNA codon bias are sometimes difficult to understand due to the staggering complexity of covariates that affect codon usage, translation, and protein folding. Here we summarize the experimental evidence on how the ribosome-together with the other components of the translational machinery-can alter translational efficiencies of mRNA at the initiation and elongation stages and how translation velocity affects protein folding. We seek to explain these findings in the context of mechanistic work on the ribosome. The results argue in favour of a new understanding of translation control as a hub that links mRNA homeostasis to production and quality control of proteins in the cell.

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“…There is evidence of computational analysis that fast translation speed can increase the probability of cotranslational protein folding. [75][76][77] It is now important to consider the coding sequence while performing protein folding in silico. In this regard, the recently developed CSandS database is worth to consider while designing protein three-dimensional structure.…”

Section: Translation Kinetics Guides Cotranslational Protein Foldingmentioning

confidence: 99%

Synonymous codons influencing gene expression in organisms

Mitra¹,

Ray²,

Banerjee³

2016

RRBC

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Nowadays, it is beyond doubt that synonymous codons are not the same with respect to expression of a gene. In favor of this, ribosome profiling experiments in vivo and in vitro have suggested that ribosome occupancy time is not the same for different synonymous codons. Therefore, synonymous codons influence differently the speed of translation elongation, which guides further cotranslational folding kinetics of a protein. It is now realized that the position of each codon in a coding sequence is important. The effect of synonymous codons on protein structure is an exciting field of research nowadays. This review discusses the recent developments in this field.

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Accurate Prediction of Cellular Co-Translational Folding Indicates Proteins can Switch from Post- to Co-Translational Folding

Cited by 7 publications

References 45 publications

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

The ribosome in action: Tuning of translational efficiency and protein folding

Synonymous codons influencing gene expression in organisms

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