Re: [DIYbio] Re: On protein expression in eukaryotes

As far as N-terminal amino rule, yes; it differs by kingdom, sometimes
even at lower branches in the tree. There are scripts online that
calculate relative stability but they all require you to select your target!

> Expression signals, ribosome ramp, codon usage, stability... All
> enhanced if you choose the right protein...

There might be cleaner ways to do ribosome ramp and codon usage.
PySplicer does both, DNA2.0's app does at least codon usage properly,
may also do Ribosome Ramp by now.

As far as more cryptic expression signals, not sure of any tools right
now, so in difficult cases the hacky way of stealing some N-term from
another protein may still be useful.

This does make me think that PySplicer needs a patch to treat the first
codon specially, to try and enhance the RBS without changing the codons,
if possible. Would require additional info for each species' codon
table, but I could always implement it as "if there's RBS info in the
species table, use that, otherwise skip this optimisation".

On 13/03/14 11:40, Mega [Andreas Stuermer] wrote:
> What is always helpful: adding the N-terminus of a native protein to
> the N-terminus of your intended protein...
>>
>>
> Expression signals, ribosome ramp, codon usage, stability... All
> enhanced if you choose the right protein...
>
> Like add the first (7-15) amino acids of (Rubisco is a bad example
> because it has to be stable in the chloroplast rather than in the
> cytosolic environment) ... a very stable protein in the cytosol to
> your protein...
>

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