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
>>
>>
>
|