G-d is right-handed, so to speak:
Ex 15:6 "Thy right hand, O LORD, is become glorious in power: thy
right hand, O LORD, hath dashed in pieces the enemy."
Since we are made in His image, and our (chiral) molecules are the
cause of making most of us right-handed, which enantiomer to use was
not a real choice but rather flowed logically from His (right-handed)
Essence. Our chirality is dictated by His, whatever that means!
JPK
On Wed, Feb 15, 2012 at 4:48 PM, William G. Scott <[log in to unmask]> wrote:
> Hi Jacob:
>
> After giving this a great deal of reflection …..
> I realized that you would face the same paradox that
> God had to resolve six thousand years ago at the Dawn of
> Creation, i.e., He needed D-deoxyribose DNA to code for L-amino acid
> proteins, and vice versa. Likewise, you would probably be faced
> with a situation where you need L-deoxyribose DNA to code for D-amino
> acid proteins, so once again, you need a ribozyme self-replicase to
> escape the Irreducible Complexity(™). (The Central Dogma at least is achiral.)
>
> At least it can be done six thousand years, which isn't unreasonable for
> a Ph.D. thesis project (especially when combined with an M.D.), and you,
> unlike Him, have access to a Sigma catalogue.
>
> All the best,
>
> Bill
>
>
> William G. Scott
> Professor
> Department of Chemistry and Biochemistry
> and The Center for the Molecular Biology of RNA
> 228 Sinsheimer Laboratories
> University of California at Santa Cruz
> Santa Cruz, California 95064
> USA
>
>
>
>
>
> On Feb 15, 2012, at 10:28 AM, Jacob Keller wrote:
>
>> So who out there wants to start an all-D microbial culture by total
>> synthesis, a la the bacterium with the synthetic genome a while back?
>> Could it work, I wonder? I guess that would be a certain benchmark for
>> Man's conquest of nature.
>>
>> JPK
>>
>> ps maybe if there is a broadly-acting amino-acid isomerase or set of
>> isomerases of appropriate properties, this could be helpful for
>> getting the culture started--or even for preying on the L world?
>>
>>
>>
>> On Wed, Feb 15, 2012 at 12:17 PM, David Schuller <[log in to unmask]> wrote:
>>> On 02/15/12 12:41, Jacob Keller wrote:
>>>
>>> Are there any all-D proteins out there, of known structure or
>>> otherwise? If so, do enantiomer-specific catalyses become inverted?
>>>
>>> JPK
>>>
>>> What do you mean by "Out There"? If you mean in the PDB, then yes. As of
>>> two weeks ago, there are ~ 14 racemic structures deposited; most in space
>>> group P -1, with one outlier in space group I -4 C 2. This includes RNA,
>>> DNA, and PNA, but 6 entries are actually protein. The longest is over 80
>>> residues.
>>>
>>> Theoretically, enantiomer-specific catalysis ought to be inverted, but most
>>> of the structures solved are not enzymes. kaliotoxin, plectasin, antifreeze
>>> protein, monellin, villin, and a designed peptide.
>>>
>>> On the other hand, if by "out there" you meant in nature outside of
>>> biochemistry and organic chemistry labs; then no, I am not aware of any
>>> all-D proteins. There are a few protein/peptides which include a small
>>> number of D-residues, which is marked up to nonribosomal synthesis.
>>>
>>> The first paper I managed to Google:
>>> http://jb.asm.org/content/185/24/7036.full
>>> Learning from Nature's Drug Factories: Nonribosomal Synthesis of Macrocyclic
>>> Peptides
>>> doi: 10.1128/JB.185.24.7036-7043.2003 J. Bacteriol. December 2003 vol. 185
>>> no. 24 7036-7043
>>>
>>> If racemic crystallization isn't exciting enough for you, look into
>>> quasi-racemic crystallization.
>>>
>>>
>>> On Wed, Feb 15, 2012 at 8:05 AM, David Schuller <[log in to unmask]> wrote:
>>>
>>> Wukovitz & Yeates (1995) Nature Struc. Biol. 2(12): 1062-1067
>>> predicts that the most probable space group for macromolecular
>>> crystallization is P -1 (P 1-bar). All you have to do to try it out is
>>> synthesize the all-D enantiomer of your protein and get it to fold properly.
>>>
>>>
>>> On 02/14/12 18:36, Prem Kaushal wrote:
>>>
>>>
>>> Hi
>>>
>>> We have a protein that crystallized in P21212 space group. We are looking
>>> for some different crystal forms. We tried few things did not work. Now we
>>> are thinking to mutate surface residues. Anybody aware of any software which
>>> can predict the mutations that might help in crystallizing protein in
>>> different space group, please inform me.
>>>
>>> Thanks in advance
>>>
>>> Prem
>>>
>>>
>>> --
>>> =======================================================================
>>> All Things Serve the Beam
>>> =======================================================================
>>> David J. Schuller
>>> modern man in a post-modern world
>>> MacCHESS, Cornell University
>>> [log in to unmask]
>>
>>
>>
>> --
>> *******************************************
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: [log in to unmask]
>> *******************************************
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: [log in to unmask]
*******************************************
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