Skip to main content
SpringerLink
Log in

Intramolecular interactions and cis peptidic bonds

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

The cis Gly–Gly peptidic bond observed in dihydrofolate reductase, which takes place between a beta sheet and an alpha helix is chosen as an example to study the various factors which influence this conformation. The peptidic chain of 16 amino acids is studied by a QM/MM scheme (6-31+G* B3LYP—Amber 99). Both electronic and classical contributions to the total energy take part to the stabilization of the cis conformation. A special role is played by the alpha helix when it is bonded to the carbonyl group of the bond of interest.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Rivail J-L, Bouchy A, Loos P-F (2007) J Arg Chem Soc (in press)

  2. Sawaya MR, Kraut J (1997). Biochemistry 36:586

    Article  CAS  Google Scholar 

  3. Jabs A, Weiss MS, Hilgenfeld (1999) J Mol Biol 286:291 (review paper)

  4. E Svensson A-K, O’Neill Jr JC, Matthews CR (2003). J Mol Biol 326:569

    Article  CAS  Google Scholar 

  5. Zimmerman SS, Scheraga HA (1976). Macromolecules 9:408

    Article  CAS  Google Scholar 

  6. Jorgensen WL, Gao J (1988). J Am Chem Soc 110:4212

    Article  CAS  Google Scholar 

  7. Poteau R, Trinquier G (2005). J Am Chem Soc 127:13875

    Article  CAS  Google Scholar 

  8. Enriz RD, Morales ME, Baldoni HA, (2005). J Mol Struct Theochem 731:177

    Article  CAS  Google Scholar 

  9. Assfeld X, Rivail J-L (1996). Chem Phys Lett 263:100

    Article  CAS  Google Scholar 

  10. Ferré N, Assfeld X, Rivail J-L (2002). J Comput Chem 23:610

    Article  CAS  Google Scholar 

  11. Ferré N, Assfeld X (2002). J Chem Phys 117:4119

    Article  CAS  Google Scholar 

  12. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, Revision B.05, Gaussian, Inc., Wallingford

  13. Lee C, Yang W, Parr RG (1988). Phys Rev B 37:785

    Article  CAS  Google Scholar 

  14. Becke AD (1993). J Chem Phys 98:5648

    Article  CAS  Google Scholar 

  15. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM., Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA, (1995). J Am Chem Soc 117:5179

    Article  CAS  Google Scholar 

  16. Wang J, Cieplak P, Kollman PA (2000). J Comput Chem 21:1049

    Article  CAS  Google Scholar 

  17. Li H, Robertson AD, Jensen JH, (2005). Proteins 61:704

    Article  CAS  Google Scholar 

  18. Assfeld X, Ferré N, Rivail J-L (2004). Theor Chem Acc 11:328

    Google Scholar 

  19. Rinaldi D, Bouchy A, Rivail J-L, Dillet V (2004). J Chem Phys 120:2343

    Article  CAS  Google Scholar 

  20. Rinaldi D, Bouchy A, Rivail J-L (2006). Theor Chem Acc 116:664

    Article  CAS  Google Scholar 

  21. Mayer I (1983). Chem Phys Lett 97:270

    Article  CAS  Google Scholar 

  22. Mo Y, Schleyer PvR, Wu W, Lin M, Zhang Q, Gao J (2003). J Phys Chem A 107:10011

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. UMR 7565, Structure et Réactivité des Systèmes Moléculaires Complexes, CNRS-Universté Henri Poincaré, Nancy-Université, 54506, Nancy-Vandoeuvre Cedex, France

    Pierre-François Loos, Xavier Assfeld & Jean-Louis Rivail

Authors
  1. Pierre-François Loos
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xavier Assfeld
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jean-Louis Rivail
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jean-Louis Rivail.

Additional information

Contribution to the Fernando Bernardi Memorial Issue.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Loos, PF., Assfeld, X. & Rivail, JL. Intramolecular interactions and cis peptidic bonds. Theor Chem Account 118, 165–171 (2007). https://doi.org/10.1007/s00214-007-0258-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00214-007-0258-x

Keywords

Search

Navigation