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The structure of an all D-amino acid version of the HIV-1 protease was solved in 1992 (see Milton, Milton, and Kent, 1992, Science, 256:1445-1448). The D-enzyme was seen to have a structure that is the mirror image of the L-enzyme, and showed specificity for the enantiomeric form of the chiral substrate. ________________________________________ P. Shing Ho, PhD Professor & Chair Department of Biochemistry & Molecular Biology Colorado State University Fort Collins, CO 80524-1870 ________________________________________ On 2/15/12 11:28 AM, "Jacob Keller" <[log in to unmask]> 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] >*******************************************