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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 >>> [email protected] >> >> >> >> -- >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> email: [email protected] >> ******************************************* > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: [email protected] *******************************************
