To add to my rather spotty coverage of the literature on this subject:
- M. S. Weiss, H. J. Metzner & R. Hilgenfeld (1998). Two non-proline cis
peptide bonds may be important for factor XIII function. FEBS Lett. 423, 291-296.
- M. S. Weiss, A. Jabs & R. Hilgenfeld (1998). Peptide bonds revisited. Nature
Struct. Biol. 5, 676.
- A. Jabs, M. S. Weiss & R. Hilgenfeld (1999). Non-proline cis peptide bonds in
proteins. J. Mol. Biol. 286, 291-304.
- M. S. Weiss & R. Hilgenfeld (1999). A method to detect non-proline cis
peptide bonds in proteins. Biopolymers 50, 536-544.
And maybe:
- Malcolm W. MacArthur, Janet M. Thornton (1991) Influence of proline residues
on protein conformationJournal of Molecular Biology 218; 397–412
- J.S. Richardson, D.C. Richardson, Amino acid preferences for specific
locations at
the ends of alpha helices, Science 240 (1988) 1648–1652.
Stewart, D. E., Sarkar, A., and Wampler, J. E. (1990) J. Mol. Biol. 214, 253–260
D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their
conformations, interactions and locations, J. Mol. Biol. 294 (1999) 271–288.
(and I'm sure that is far from complete)
On 02/16/2015 12:30 PM, Edward A. Berry wrote:
However it is important to note that there are real non-proline cis peptides in
high-resolution structures, and to not throw out these babies with the
bathwater! In fact I think they are probably under-represented because people
are hesitant to build a non-pro cis peptide even when the density favors it,
unless it is absolutely clear!
Examples:
2BS2 1.78 Asp A398 trans, should be cis.
http://sb20.lbl.gov/SQR/cis-asp398.gif
3cx5 1.8 Ser C223 trans, should be cis, corrected in 4PD4
1NEK 2.6 Ser-A393 trans, should be cis, corrected in 2WDQ
Stewart, D. E., Sarkar, A., and Wampler, J. E. (1990) J. Mol. Biol. 214, 253–260
D. Pal, P. Chakrabarti, Cis peptide bonds in proteins: residues involved, their
conformations, interactions and locations, J. Mol. Biol. 294 (1999) 271–288.
eab
On 02/16/2015 04:58 AM, Tristan Croll wrote:
Dear all,
My apologies for the spam-like nature of my post, but I would like to draw your
attention to an important issue (outlined in an upcoming short communication to
/Acta D/, which will appear at **doi:10.1107/S1399004715000826 once it's online).
At present, neither the structural quality checks in commonly-used crystallography
packages nor those run on deposition of a structure to the PDB are flagging the
presence of non-proline /cis /peptide bonds. This has led to the presence of many
erroneous /cis /bonds creeping into the PDB - primarily in low-resolution
structures as one would expect, but I have identified clearly erroneous examples
in structures with resolutions as high as 1.3 Angstroms. From my analysis, I
estimate that a few thousand structures have been affected to some extent, with
the worst cases having as high as 3% of their peptide bonds in /cis/. Particularly
if you have published anything >2.5 Angstroms in the past few years, may I
gently suggest that you make a
quick double-check of your deposited structures? This can be done quickly and
simply in Coot (Extensions-Modelling-Residues with Cis peptide bonds).
Best regards,
Tristan
