Whoops, sorry of course that is right. But 3 amino acids would be
8000, etc.
-Greg
On Sep 7, 2010, at 12:46 AM, Murray, James W wrote:
>
>> So, let's say instead these adaptors recognize 2 amino acids at a
>> time
>> (still probably not robust enough). Then, one would need 2^20
>> adaptors, already a far greater number of gene products than that
>> present in any genome than I know of...
>
> Surely only 20^2, which is 400? A lot, but managable.
>
> James
>
> --
> Dr. James W. Murray
> David Phillips Research Fellow
> Division on Molecular Biosciences
> Imperial College, LONDON
> Tel: +44 (0)20 759 48895
> ________________________________________
> From: CCP4 bulletin board [[log in to unmask]] On Behalf Of Greg
> Alushin [[log in to unmask]]
> Sent: Tuesday, September 07, 2010 3:19 AM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Reverse Translatase
>
> Hi Jacob-
>
> What an intriguing proposition. I can think of multiple reasons why
> such a system would not exist, but there is a mechanistic one which is
> most fundamental, having to do with the nature of the genetic code.
>
> Say that there is a cellular machine which would unfold a protein and
> expose it to some sort of reading system (already a hard problem).
> There is now the issue of transforming the amino acid information into
> nucleic acid information. For simplicity let's assume that this
> system only uses one codon per amino acid, bypassing the degeneracy
> problem.
>
> How would the cell then read off the amino acid sequence? It seems
> the simplest solution would be analogous to translation, i.e. having
> adaptor molecules analogues to tRNAs which would guide an enzyme that
> synthesized the nucleic acid. Otherwise, one would have to invoke the
> idea of a single enzyme recognizing every amino acid, which seems
> impossible to me.
>
> As we know, the problem of protein-protein recognition is relatively
> complex. At a minimum, one would need 20 adaptor proteins to
> recognize the 20 canonical amino acids: however, it seems unlikely
> that recognition of a single amino acid would be robust enough to
> select for the correct adaptor molecule.
>
> So, let's say instead these adaptors recognize 2 amino acids at a time
> (still probably not robust enough). Then, one would need 2^20
> adaptors, already a far greater number of gene products than that
> present in any genome than I know of...
>
> It might be tempting to draw an analogy between this system and the
> immune system, where an incredible diversity is generated from a small
> number of genes. However, diverse immune proteins all take the same
> input sequence (say antigen recognition) and lead to a single
> response, whereas this system has a 1 to 1 correspondence between
> inputs (protein sequence) and outputs (nucleic acid sequences), and
> thus there is no way that a randomization system could generate the
> required diversity.
>
> Cheers,
> -Greg Alushin
> Nogales lab
> UC Berkeley
>
> On Sep 6, 2010, at 7:12 PM, Michael Thompson wrote:
>
>> Jacob,
>>
>> The idea is enticing, but don't forget that there are multiple
>> degenerate codons for a given amino acid. Once the protein is
>> synthesized, the specific codon information is lost.
>>
>> I think that's a fundamental problem.
>>
>> Keep the ideas coming,
>>
>> Mike Thompson
>>
>>
>>
>>
>> ----- Original Message -----
>> From: "Jacob Keller" <[log in to unmask]>
>> To: [log in to unmask]
>> Sent: Monday, September 6, 2010 6:36:14 PM GMT -08:00 US/Canada
>> Pacific
>> Subject: [ccp4bb] Reverse Translatase
>>
>> Dear Crystallographers,
>>
>> does anyone know of any conceptual reason why a reverse translatase
>> enzyme
>> (protein-->nucleic acid) could not exist? I can think of so many
>> things for
>> which such an enzyme would be helpful, both to cells and to
>> scientists...!
>> Unless there is something I am missing, it would seem to me
>> conceptually
>> almost impossible that it *not* exist.
>>
>> Best Regards,
>>
>> Jacob Keller
>>
>>
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> Dallos Laboratory
>> F. Searle 1-240
>> 2240 Campus Drive
>> Evanston IL 60208
>> lab: 847.491.2438
>> cel: 773.608.9185
>> email: [log in to unmask]
>> *******************************************
>>
>> --
>> Michael C. Thompson
>>
>> Graduate Student
>>
>> Biochemistry & Molecular Biology Division
>>
>> Department of Chemistry & Biochemistry
>>
>> University of California, Los Angeles
>>
>> [log in to unmask]
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