Abstract
The high accuracy of X-ray analyses at atomic resolution is now able to display subtle deformations from standard geometry of building blocks in proteins. From the analysis of nine ultra-high resolution protein structures, we derived the first experimental evidence that a significant pyramidalization at the main-chain carbonyl carbon atom occurs in proteins. Our findings also show that this pyramidalization is related to the main-chain psi torsion angle. The carbonyl carbon atoms of residues that adopt alphaR and extended conformations show a clear preference for positive and negative pyramidalization, respectively. The agreement between our data and those previously obtained from small molecule structures demonstrates that carbon pyramidalization is an intrinsic property of the peptide structure. Although small in magnitude, the pyramidalization is well preserved in the complex folded state of a macromolecular structure that results from the interplay of many different forces. In addition, this property of the peptide group may have interesting implications for the enzymatic reactions involving the carbonyl carbon atoms.
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Selected References
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- Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
- Bode W., Huber R. Natural protein proteinase inhibitors and their interaction with proteinases. Eur J Biochem. 1992 Mar 1;204(2):433–451. doi: 10.1111/j.1432-1033.1992.tb16654.x. [DOI] [PubMed] [Google Scholar]
- Dauter Z., Lamzin V. S., Wilson K. S. The benefits of atomic resolution. Curr Opin Struct Biol. 1997 Oct;7(5):681–688. doi: 10.1016/s0959-440x(97)80078-4. [DOI] [PubMed] [Google Scholar]
- Esposito L., Vitagliano L., Sica F., Sorrentino G., Zagari A., Mazzarella L. The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol. 2000 Mar 31;297(3):713–732. doi: 10.1006/jmbi.2000.3597. [DOI] [PubMed] [Google Scholar]
- Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–2637. doi: 10.1002/bip.360221211. [DOI] [PubMed] [Google Scholar]
- Karplus P. A. Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci. 1996 Jul;5(7):1406–1420. doi: 10.1002/pro.5560050719. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lamzin V. S., Morris R. J., Dauter Z., Wilson K. S., Teeter M. M. Experimental observation of bonding electrons in proteins. J Biol Chem. 1999 Jul 23;274(30):20753–20755. doi: 10.1074/jbc.274.30.20753. [DOI] [PubMed] [Google Scholar]
- MacArthur M. W., Thornton J. M. Deviations from planarity of the peptide bond in peptides and proteins. J Mol Biol. 1996 Dec 20;264(5):1180–1195. doi: 10.1006/jmbi.1996.0705. [DOI] [PubMed] [Google Scholar]
- Merritt E. A., Kuhn P., Sarfaty S., Erbe J. L., Holmes R. K., Hol W. G. The 1.25 A resolution refinement of the cholera toxin B-pentamer: evidence of peptide backbone strain at the receptor-binding site. J Mol Biol. 1998 Oct 9;282(5):1043–1059. doi: 10.1006/jmbi.1998.2076. [DOI] [PubMed] [Google Scholar]
- Sevcik J., Dauter Z., Lamzin V. S., Wilson K. S. Ribonuclease from Streptomyces aureofaciens at atomic resolution. Acta Crystallogr D Biol Crystallogr. 1996 Mar 1;52(Pt 2):327–344. doi: 10.1107/S0907444995007669. [DOI] [PubMed] [Google Scholar]