• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Sep 1993; 2(9): 1511–1519.
PMCID: PMC2142462

Verification of protein structures: patterns of nonbonded atomic interactions.

Abstract

A novel method for differentiating between correctly and incorrectly determined regions of protein structures based on characteristic atomic interaction is described. Different types of atoms are distributed nonrandomly with respect to each other in proteins. Errors in model building lead to more randomized distributions of the different atom types, which can be distinguished from correct distributions by statistical methods. Atoms are classified in one of three categories: carbon (C), nitrogen (N), and oxygen (O). This leads to six different combinations of pairwise noncovalently bonded interactions (CC, CN, CO, NN, NO, and OO). A quadratic error function is used to characterize the set of pairwise interactions from nine-residue sliding windows in a database of 96 reliable protein structures. Regions of candidate protein structures that are mistraced or misregistered can then be identified by analysis of the pattern of nonbonded interactions from each window.

Full Text

The Full Text of this article is available as a PDF (709K).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Baker EN, Hubbard RE. Hydrogen bonding in globular proteins. Prog Biophys Mol Biol. 1984;44(2):97–179. [PubMed]
  • Baumann G, Frömmel C, Sander C. Polarity as a criterion in protein design. Protein Eng. 1989 Jan;2(5):329–334. [PubMed]
  • Bernstein FC, Koetzle TF, Williams GJ, Meyer EF, Jr, Brice MD, Rodgers JR, 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. [PubMed]
  • Boberg J, Salakoski T, Vihinen M. Selection of a representative set of structures from Brookhaven Protein Data Bank. Proteins. 1992 Oct;14(2):265–276. [PubMed]
  • Chapman MS, Suh SW, Curmi PM, Cascio D, Smith WW, Eisenberg DS. Tertiary structure of plant RuBisCO: domains and their contacts. Science. 1988 Jul 1;241(4861):71–74. [PubMed]
  • Curmi PM, Cascio D, Sweet RM, Eisenberg D, Schreuder H. Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution. J Biol Chem. 1992 Aug 25;267(24):16980–16989. [PubMed]
  • de Vos AM, Tong L, Milburn MV, Matias PM, Jancarik J, Noguchi S, Nishimura S, Miura K, Ohtsuka E, Kim SH. Three-dimensional structure of an oncogene protein: catalytic domain of human c-H-ras p21. Science. 1988 Feb 19;239(4842):888–893. [PubMed]
  • Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature. 1986 Jan 16;319(6050):199–203. [PubMed]
  • Fitzgerald PM, McKeever BM, VanMiddlesworth JF, Springer JP, Heimbach JC, Leu CT, Herber WK, Dixon RA, Darke PL. Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution. J Biol Chem. 1990 Aug 25;265(24):14209–14219. [PubMed]
  • Ghosh D, O'Donnell S, Furey W, Jr, Robbins AH, Stout CD. Iron-sulfur clusters and protein structure of Azotobacter ferredoxin at 2.0 A resolution. J Mol Biol. 1982 Jun 15;158(1):73–109. [PubMed]
  • Hendlich M, Lackner P, Weitckus S, Floeckner H, Froschauer R, Gottsbacher K, Casari G, Sippl MJ. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J Mol Biol. 1990 Nov 5;216(1):167–180. [PubMed]
  • Jones TA, Zou JY, Cowan SW, Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A. 1991 Mar 1;47(Pt 2):110–119. [PubMed]
  • Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM. Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science. 1990 Sep 14;249(4974):1307–1309. [PubMed]
  • Lüthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992 Mar 5;356(6364):83–85. [PubMed]
  • McClarin JA, Frederick CA, Wang BC, Greene P, Boyer HW, Grable J, Rosenberg JM. Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution. Science. 1986 Dec 19;234(4783):1526–1541. [PubMed]
  • Navia MA, Fitzgerald PM, McKeever BM, Leu CT, Heimbach JC, Herber WK, Sigal IS, Darke PL, Springer JP. Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1. Nature. 1989 Feb 16;337(6208):615–620. [PubMed]
  • Novotný J, Bruccoleri R, Karplus M. An analysis of incorrectly folded protein models. Implications for structure predictions. J Mol Biol. 1984 Aug 25;177(4):787–818. [PubMed]
  • Novotný J, Rashin AA, Bruccoleri RE. Criteria that discriminate between native proteins and incorrectly folded models. Proteins. 1988;4(1):19–30. [PubMed]
  • Priestle JP, Grütter MG, White JL, Vincent MG, Kania M, Wilson E, Jardetzky TS, Kirschner K, Jansonius JN. Three-dimensional structure of the bifunctional enzyme N-(5'-phosphoribosyl)anthranilate isomerase-indole-3-glycerol-phosphate synthase from Escherichia coli. Proc Natl Acad Sci U S A. 1987 Aug;84(16):5690–5694. [PMC free article] [PubMed]
  • Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem. 1968;23:283–438. [PubMed]
  • Stickle DF, Presta LG, Dill KA, Rose GD. Hydrogen bonding in globular proteins. J Mol Biol. 1992 Aug 20;226(4):1143–1159. [PubMed]
  • Tanaka S, Scheraga HA. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules. 1976 Nov-Dec;9(6):945–950. [PubMed]
  • Wlodawer A, Miller M, Jaskólski M, Sathyanarayana BK, Baldwin E, Weber IT, Selk LM, Clawson L, Schneider J, Kent SB. Conserved folding in retroviral proteases: crystal structure of a synthetic HIV-1 protease. Science. 1989 Aug 11;245(4918):616–621. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Compound
    Compound
    PubChem Compound links
  • PubMed
    PubMed
    PubMed citations for these articles
  • Substance
    Substance
    PubChem Substance links