Exploring the Peptide Bond

  • Tim Skern
Part of the Learning Materials in Biosciences book series (LMB)


In this chapter, we will learn to examine the arrangements of the atoms that make up the backbone of a protein and how the arrangements derive from the properties of the peptide bond. Using the modest but biochemically famous protein RNase A, you will discover how to measure the bond lengths and angles in the main chain and how to decide whether a proline residue is in the cis or trans configuration. Finally, two internet algorithms are introduced that allow you to generate a Ramachandran plot from any protein structure in the PDB.


  1. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223–230CrossRefPubMedGoogle Scholar
  2. Chen VB, Arendall WB 3rd, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12–21. CrossRefPubMedGoogle Scholar
  3. Edison AS (2001) Linus Pauling and the planar peptide bond. Nat Struct Biol 8(3):201–202. CrossRefPubMedGoogle Scholar
  4. Kamphuis IG, Kalk KH, Swarte MB, Drenth J (1984) Structure of papain refined at 1.65 A resolution. J Mol Biol 179(2):233–256CrossRefPubMedGoogle Scholar
  5. Kleywegt GJ, Jones TA (1996) Phi/psi-chology: Ramachandran revisited. Structure 4(12):1395–1400CrossRefPubMedGoogle Scholar
  6. Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29(1):221–222CrossRefPubMedPubMedCentralGoogle Scholar
  7. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993a) Procheck – a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291. CrossRefGoogle Scholar
  8. Laskowski RA, Moss DS, Thornton JM (1993b) Main-chain bond lengths and bond angles in protein structures. J Mol Biol 231(4):1049–1067. CrossRefPubMedGoogle Scholar
  9. Laskowski RA, Jablonska J, Pravda L, Varekova RS, Thornton JM (2017) PDBsum: structural summaries of PDB entries. Protein Sci.
  10. Neurath H, Walsh KA (1976) Role of proteolytic enzymes in biological regulation (a review). Proc Natl Acad Sci U S A 73(11):3825–3832CrossRefPubMedPubMedCentralGoogle Scholar
  11. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7(1):95–99CrossRefPubMedGoogle Scholar
  12. Tong LA, de Vos AM, Milburn MV, Kim SH (1991) Crystal structures at 2.2 Å resolution of the catalytic domains of normal ras protein and an oncogenic mutant complexed with GDP. J Mol Biol 217(3):503–516CrossRefPubMedGoogle Scholar
  13. Wedemeyer WJ, Welker E, Scheraga HA (2002) Proline cis-trans isomerization and protein folding. Biochemistry 41(50):14637–14644CrossRefPubMedGoogle Scholar
  14. Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC (2017) MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci.
  15. Wlodawer A, Svensson LA, Sjolin L, Gilliland GL (1988) Structure of phosphate-free ribonuclease A refined at 1.26 A. Biochemistry 27(8):2705–2717CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Tim Skern
    • 1
  1. 1.Max F. Perutz LaboratoriesMedical University of ViennaViennaAustria

Personalised recommendations