For the Record

You have full text access to this OnlineOpen article

On the occurrence of linear groups in proteins

  1. Scott A. Hollingsworth,
  2. Donald S. Berkholz,
  3. P. Andrew Karplus*

Article first published online: 16 APR 2009

DOI: 10.1002/pro.133

Issue

Protein Science

Protein Science

Volume 18, Issue 6, pages 1321–1325, June 2009

Additional Information

How to Cite

Hollingsworth, S. A., Berkholz, D. S. and Karplus, P. A. (2009), On the occurrence of linear groups in proteins. Protein Science, 18: 1321–1325. doi: 10.1002/pro.133

Author Information

  1. Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305

*Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331

Publication History

  1. Issue published online: 26 MAY 2009
  2. Article first published online: 16 APR 2009
  3. Accepted manuscript online: 16 APR 2009 12:00AM EST
  4. Manuscript Accepted: 9 APR 2009
  5. Manuscript Revised: 6 APR 2009
  6. Manuscript Received: 19 MAR 2009

Funded by

  • NIH. Grant Number: GM083136
  • Howard Hughes Medical Institute. Grant Number: 52005883

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article with Supporting Information (HTML) Get PDF (316K)

References

  • 1
    Corey R, Donohue J ( 1950) Interatomic distances and bond angles in the polypeptide chain of proteins. Proc Natl Acad Sci USA 72: 2899–2900.
  • 2
    Pauling L, Corey RB, Branson HR ( 1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 37: 205–211.
  • 3
    Pauling L, Corey RB ( 1951) The pleated sheet, a new layer configuration of polypeptide chains. Proc Natl Acad Sci USA 37: 251–256.
  • 4
    Low B, Baybutt R ( 1952) The pi-helix—a hydrogen bonded configuration of the polypeptide chain. J Am Chem Soc 74: 5806–5807.
  • 5
    Donohue J ( 1953) Hydrogen bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci USA 39: 470–478.
  • 6
    Arnott S, Dover SD ( 1968) The structure of poly-L-proline II. Acta Crystallogr B 24: 599–601.
    Direct Link:
  • 7
    Sasisekharan V ( 1959) Structure of poly-L-proline II. Acta Crystallogr 12: 897–903.
    Direct Link:
  • 8
    Ramachandran GN, Ramakrishnan C, Sasisekharan V ( 1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7: 95–99.
  • 9
    IUPAC ( 1970) IUPAC-IUB Commission on biochemical nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains. Biochemistry 9: 3471–3479.
  • 10
    Garrett R, Grisham CM ( 2005) Biochemistry, 3rd ed. Belmont, CA: Thomson Brooks/Cole.
  • 11
    Mathews CK, Van Holde KE, Ahern KG ( 2000) Biochemistry, 3rd ed. San Francisco, California: Benjamin Cummings.
  • 12
    Voet D, Voet JG ( 2004) Biochemistry, 3rd ed. Hoboken, NJ: Wiley.
  • 13
    Lehninger AL, Nelson DL, Cox MM ( 2008) Lehninger principles of biochemistry, 5th ed. New York: W.H. Freeman.
  • 14
    Lesk AM ( 2001) Introduction to protein architecture: the structural biology of proteins. Oxford: Oxford University Press.
  • 15
    Van Holde KE, Johnson WC, Ho PS ( 2006) Principles of physical biochemistry, 2nd ed. Upper Saddle River, NJ: Pearson/Prentice Hall.
  • 16
    Beck DA, Alonso DO, Inoyama D, Daggett V ( 2008) The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins. Proc Natl Acad Sci USA 105: 12259–12264.
  • 17
    Perskie LL, Street TO, Rose GD ( 2008) Structures, basins, and energies: A deconstruction of the protein coil library. Protein Sci 17: 1151–1161.
    Direct Link:
  • 18
    Hobohm U, Sander C ( 1994) Enlarged representative set of protein structures. Protein Sci 3: 522–524.
    Direct Link:
  • 19
    Laskowski RA, Chistyakov VV, Thornton JM ( 2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res 33: D266–D268.
  • 20
    Karplus PA ( 1996) Experimentally observed conformation-dependent geometry and hidden strain in proteins. Protein Sci 5: 1406–1420.
    Direct Link:
  • 21
    Kleywegt GJ, Jones TA ( 1996) Phi/psi-chology: Ramachandran revisited. Structure 4: 1395–1400.
  • 22
    Lovell SC, Davis IW, Arendall WB,III, de Bakker PI, Word JM, Prisant MG, Richardson JS, Richardson DC ( 2003) Structure validation by Cα geometry: phi, psi, and Cβ deviation. Proteins 50: 437–450.
    Direct Link:
  • 23
    Kabsch W, Sander C ( 1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577–2637.
    Direct Link:
  • 24
    Venkatachalam CM ( 1968) Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units. Biopolymers 6: 1425–1436.
    Direct Link:
  • 25
    Street TO, Fitzkee NC, Perskie LL, Rose GD ( 2007) Physical-chemical determinants of turn conformations in globular proteins. Protein Sci 16: 1720–1727.
    Direct Link:
  • 26
    Nagano K ( 1977) Logical analysis of the mechanism of protein folding. IV. Super-secondary structures. J Mol Biol 109: 235–250.
  • 27
    Weaver TM ( 2000) The pi-helix translates structure into function. Protein Sci 9: 201–206.
    Direct Link:
  • 28
    Fodje MN, Al-Karadaghi S ( 2002) Occurrence, conformational features and amino acid propensities for the pi-helix. Protein Eng 15: 353–358.
  • 29
    Richardson JS ( 1981) The anatomy and taxonomy of protein structure. Adv Protein Chem 34: 167–339.
  • 30
    Adzhubei AA, Sternberg MJ ( 1993) Left-handed polyproline II helices commonly occur in globular proteins. J Mol Biol 229: 472–493.
  • 31
    Stapley BJ, Creamer TP ( 1999) A survey of left-handed polyproline II helices. Protein Sci 8: 587–595.
    Direct Link:
  • 32
    Shi Z, Woody RW, Kallenbach NR ( 2002) Is polyproline II a major backbone conformation in unfolded proteins? Adv Protein Chem 62: 163–240.
  • 33
    Creamer TP, Campbell MN ( 2002) Determinants of the polyproline II helix from modeling studies. Adv Protein Chem 62: 263–282.
  • 34
    Whittington SJ, Chellgren BW, Hermann VM, Creamer TP ( 2005) Urea promotes polyproline II helix formation: implications for protein denatured states. Biochemistry 44: 6269–6275.
View Full Article with Supporting Information (HTML) Get PDF (316K)