I believe Eric is paraphrasing Genesis 3. It's all the serpent's fault.
http://www.ic.unicamp.br/~stolfi/PUB/misc-misc/GenesysParody.html
<http://www.ic.unicamp.br/%7Estolfi/PUB/misc-misc/GenesysParody.html>
On 16/02/2012 02:39, Eric Bennett wrote:
Jacob,
I wish it were that cheery. Do not forget the darker side of history.
The prefix "L-" stands for levorotary. The "levo" comes from the Latin wording for "left side". Left
handedness is also known as sinistrality, from the Latin "sinistra" which also meant the left side, but over time took on the
connotations that we currently associate with the word "sinister". The latter word, of course, is generally associated with dark
and evil. It is therefore erroneous to attribute the L amino acid to the Almighty. The L amino acid is in fact a diabolical corruption of
cellular processes that begin with the D-nucleotide ("D-" meaning rotating to the right, but derived from dexter, meaning
dextrous and skillful). The instrument which causes this perversion of God's perfect righteousness into a sign of evil deserves our
strongest moral condemnation... I am referring, of course, to that devilish piece of cellular machinery known as the ribosome.
The discovery of the ribosome was a significant blow to the success of what Charles
Baudelaire famously called the devil's greatest trick. For years now, his acolytes have
attempted to hide the truth about the ribosome by referring to its work with the neutral,
innocent-sounding phrase "translation". Don't be fooled, but instead pray for
the development of the next generation of ribosome inhibitors, or at least dissolve the
current generation in holy water before ingesting.
-Eric
On Feb 15, 2012, at 7:24 PM, Jacob Keller wrote:
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<wgsc...@ucsc.edu> 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<dj...@cornell.edu> 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<dj...@cornell.edu> 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
--
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
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*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
*******************************************
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Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
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