The number of tRNA varies among different cells, which I think might cause a different speed of translation. I'm curious as to whether the speed will possibly have an impact on the configuration of a translated protein? Are there any other factors that may contribute to the change of configuration?
Yes, it does and many other factors influence protein structure. I would recommend reading the review I have attached, as well as this paper I found performing a brief search on this topic: PMID: 20043920.
Hopefully these answer some of your questions, can can lead you to other references as well.
Good luck,
~Adam
Yes, it does and many other factors influence protein structure. I would recommend reading the review I have attached, as well as this paper I found performing a brief search on this topic: PMID: 20043920.
Hopefully these answer some of your questions, can can lead you to other references as well.
Good luck,
~Adam
Hi Adam, thx~ But something wrong with the attached pdf, I couldn't open it. Maybe you can just tell me the title of the review?
This group at the FDA has done some interesting work on this subject in order to determine whether codon optimization (synonymous substitutions of amino acids) affects protein structure and function. PMID: 21878961
You must mean conformation not configuration. Configuration would not be affected, all proteinogenic amino acids are still L- . As far as conformation/folding is concerned, speed of translation can certainly affect these. One of the reasons people cool down temperature of induction to 30 - 16 oC to reduce inclusion body formation.
I am not sure why the speed of translation will determine the protein conformation. Perhaps if the synthesis rate is very fast, one can understand that the protein is extruded from the machine faster than the take up spool can handle. Under normal cases, it would not.
And for special cases, special considerations apply.
Under normal conditions, the rate of protein synthesis will be "mostly" governed by the tRNA supply. Some amino acids are consumed faster and these tRNA must be regenerated faster. Under normal conditions, these are the rate limiting processes and the protein chain dangling from the riobosome continuously and dynamically undergoes the folding process.
Synonymous mutation can be related to misfolding and dysfunction of the protein.
I recently proposed that translational rate is modulated by pairs of consecutive codons or bicodons [1]. By a statistical analysis of coding sequences, we compute a rate translational measure of all bicodons. We found that bicodons associated with sequences encoding low abundant proteins are involved in translational rate attenuation. Furthermore, we observe that the misfolding in many protein, such MDR1 gene [2], is better explained by a big change in the translational rate due to the synonymous bicodon variant, rather than by a relatively small change in the codon usage.
1.- Coding translational rates: the hidden genetic code
http://biorxiv.org/content/early/2016/07/08/062935
2.- Kimchi-Sarfaty, et al. A silent polymorphism in the MDR1 gene changes substrate specificity.
Science 315, 525–528 (2007).
more about translational rate and codon pairs: Bicodon bias can determine the role of synonymous SNPs in human diseases (DOI: 10.1186/s12864-017-3609-6)
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