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BioMed Research International
Volume 2013 (2013), Article ID 326914, 8 pages
http://dx.doi.org/10.1155/2013/326914
Research Article

Interplay between Peptide Bond Geometrical Parameters in Nonglobular Structural Contexts

1Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Napoli, Italy
2Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
3Division of Molecular Biosciences, Imperial College South Kensington Campus, London SW7 2AZ, UK

Received 10 September 2013; Accepted 29 November 2013

Academic Editor: Kei Yura

Copyright © 2013 Luciana Esposito et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. S. Richardson, “The anatomy and taxonomy of protein structure,” Advances in Protein Chemistry, vol. 34, pp. 167–339, 1981. View at Publisher · View at Google Scholar · View at Scopus
  2. P. A. Karplus, “Experimentally observed conformation-dependent geometry and hidden strain in proteins,” Protein Science, vol. 5, no. 7, pp. 1406–1420, 1996. View at Scopus
  3. L. Esposito, L. Vitagliano, F. Sica, G. Sorrentino, A. Zagari, and L. Mazzarella, “The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis,” Journal of Molecular Biology, vol. 297, no. 3, pp. 713–732, 2000. View at Publisher · View at Google Scholar · View at Scopus
  4. L. Esposito, L. Vitagliano, A. Zagari, and L. Mazzarella, “Experimental evidence for the correlation of bond distances in peptide groups detected in ultrahigh-resolution protein structures,” Protein Engineering, vol. 13, no. 12, pp. 825–828, 2000. View at Scopus
  5. L. Esposito, A. de Simone, A. Zagari, and L. Vitagliano, “Correlation between ω and ψ dihedral angles in protein structures,” Journal of Molecular Biology, vol. 347, no. 3, pp. 483–487, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. L. Esposito, L. Vitagliano, and L. Mazzarella, “Recent advances in atomic resolution protein crystallography,” Protein and Peptide Letters, vol. 9, no. 2, pp. 95–105, 2002. View at Scopus
  7. R. Improta, L. Vitagliano, and L. Esposito, “Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures,” PLoS ONE, vol. 6, no. 9, Article ID e24533, 2011. View at Publisher · View at Google Scholar · View at Scopus
  8. P. A. Karplus, M. V. Shapovalov, R. L. Dunbrack Jr., and D. S. Berkholz, “A forward-looking suggestion for resolving the stereochemical restraints debate: ideal geometry functions,” Acta Crystallographica D, vol. 64, no. 3, pp. 335–336, 2008. View at Publisher · View at Google Scholar · View at Scopus
  9. D. S. Berkholz, P. B. Krenesky, J. R. Davidson, and P. A. Karplus, “Protein geometry database: a flexible engine to explore backbone conformations and their relationships to covalent geometry,” Nucleic Acids Research, vol. 38, no. 1, pp. D320–D325, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. D. S. Berkholz, M. V. Shapovalov, R. L. Dunbrack Jr., and P. A. Karplus, “Conformation dependence of backbone geometry in proteins,” Structure, vol. 17, no. 10, pp. 1316–1325, 2009. View at Publisher · View at Google Scholar · View at Scopus
  11. D. S. Berkholz, C. M. Driggers, M. V. Shapovalov, R. L. Dunbrack Jr., and P. A. Karplus, “Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 2, pp. 449–453, 2012. View at Publisher · View at Google Scholar · View at Scopus
  12. M. Jaskolski, M. Gilski, Z. Dauter, and A. Wlodawer, “Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?” Acta Crystallographica D, vol. 63, no. 5, Article ID wd5076, pp. 611–620, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. M. Jaskolski, M. Gilski, Z. Dauter, and A. Wlodawer, “Numerology versus reality: a voice in a recent dispute,” Acta Crystallographica D, vol. 63, no. 12, pp. 1282–1283, 2007. View at Publisher · View at Google Scholar · View at Scopus
  14. B. Stec, “Comment on stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them? By Jaskolski, Gilski, Dauter & Wlodawer (2007),” Acta Crystallographica D, vol. 63, no. 10, pp. 1113–1114, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. I. J. Tickle, “Experimental determination of optimal root-mean-square deviations of macromolecular bond lengths and angles from their restrained ideal values,” Acta Crystallographica D, vol. 63, no. 12, pp. 1274–1281, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. Z. Dauter and A. Wlodawer, “Proteins do not have strong spines after all,” Structure, vol. 17, no. 10, pp. 1278–1279, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. R. Improta, V. Barone, K. N. Kudin, and G. E. Scuseria, “Structure and conformational behavior of biopolymers by density functional calculations employing periodic boundary conditions. I. The case of polyglycine, polyalanine, and poly-α-aminoisobutyric acid in vacuo,” Journal of the American Chemical Society, vol. 123, no. 14, pp. 3311–3322, 2001. View at Publisher · View at Google Scholar · View at Scopus
  18. W. G. Touw and G. Vriend, “On the complexity of Engh and Huber refinement restraints: the angle τ as example,” Acta Crystallographica D, vol. 66, no. 12, pp. 1341–1350, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. L. Esposito, L. Vitagliano, A. Zagari, and L. Mazzarella, “Pyramidalization of backbone carbonyl carbon atoms in proteins,” Protein Science, vol. 9, no. 10, pp. 2038–2042, 2000. View at Scopus
  20. R. Berisio, A. de Simone, A. Ruggiero, R. Improta, and L. Vitagliano, “Role of side chains in collagen triple helix stabilization and partner recognition,” Journal of Peptide Science, vol. 15, no. 3, pp. 131–140, 2009. View at Publisher · View at Google Scholar · View at Scopus
  21. M. D. Shoulders and R. T. Raines, “Collagen structure and stability,” Annual Review of Biochemistry, vol. 78, pp. 929–958, 2009. View at Publisher · View at Google Scholar · View at Scopus
  22. K. Okuyama, “Revisiting the molecular structure of collagen,” Connective Tissue Research, vol. 49, no. 5, pp. 299–310, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. R. Nelson, M. R. Sawaya, M. Balbirnie et al., “Structure of the cross-β spine of amyloid-like fibrils,” Nature, vol. 435, no. 7043, pp. 773–778, 2005. View at Publisher · View at Google Scholar · View at Scopus
  24. M. R. Sawaya, S. Sambashivan, R. Nelson et al., “Atomic structures of amyloid cross-β spines reveal varied steric zippers,” Nature, vol. 447, no. 7143, pp. 453–457, 2007. View at Publisher · View at Google Scholar · View at Scopus
  25. B. Brodsky and A. V. Persikov, “Molecular structure of the collagen triple helix,” Advances in Protein Chemistry, vol. 70, pp. 301–339, 2005. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Ahram, Z. I. Litou, R. Fang, and G. Al-Tawallbeh, “Estimation of membrane proteins in the human proteome,” In Silico Biology, vol. 6, no. 5, pp. 379–386, 2006. View at Scopus
  27. L. Goldschmidt, P. K. Teng, R. Riek, and D. Eisenberg, “Identifying the amylome, proteins capable of forming amyloid-like fibrils,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 8, pp. 3487–3492, 2010. View at Publisher · View at Google Scholar · View at Scopus
  28. H. Berman, K. Henrick, H. Nakamura, and J. L. Markley, “The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data,” Nucleic Acids Research, vol. 35, no. 1, pp. D301–D303, 2007. View at Publisher · View at Google Scholar · View at Scopus
  29. D. Kozma, I. Simon, and G. E. Tusnady, “PDBTM: protein data bank of transmembrane proteins after 8 years,” Nucleic Acids Research, vol. 41, pp. D524–D529, 2013.
  30. W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983. View at Scopus
  31. K. Okuyama, T. Kawaguchi, M. Shimura, K. Noguchi, K. Mizuno, and H. P. Bachinger, “Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 A resolution,” Biopolymers, vol. 99, pp. 436–447, 2013.
  32. K. Okuyama, K. Miyama, T. Morimoto, K. Masakiyo, K. Mizuno, and H. P. Bächinger, “Stabilization of triple-helical structures of collagen peptides containing a Hyp-Thr-Gly, Hyp-Val-Gly, or Hyp-Ser-Gly sequence,” Biopolymers, vol. 95, no. 9, pp. 628–640, 2011. View at Publisher · View at Google Scholar · View at Scopus
  33. K. Okuyama, X. Xu, M. Iguchi, and K. Noguchi, “Revision of collagen molecular structure,” Biopolymers, vol. 84, no. 2, pp. 181–191, 2006. View at Publisher · View at Google Scholar · View at Scopus
  34. R. Berisio and L. Vitagliano, “Polyproline and triple helix motifs in host-pathogen recognition,” Current Protein & Peptide Science, vol. 13, pp. 855–865, 2012.
  35. D. E. Tronrud and P. A. Karplus, “A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution,” Acta Crystallographica D, vol. 67, no. 8, pp. 699–706, 2011. View at Publisher · View at Google Scholar · View at Scopus