Journal of Protein Chemistry

, Volume 11, Issue 6, pp 653–656 | Cite as

Method for calculating 3-D coordinates from molecular stereograms

  • Juan GuevaraJr.
  • Roger D. Knapp
  • John Spurlino
  • B. V. Venkataram Prasad
  • Joel D. Morrisett
Article
  • 21 Downloads

Abstract

The three-dimensional coordinates for the α-carbon atoms of crambin and basic pancreatic trypsin inhibitor (BPTI) were determined from the respective α-carbon trace stereograms using an improved Simplex algorithm. This algorithm was used in a two-step process to estimate thez-coordinate values. In one approach, an average interatomic distance value, an approximate viewing angle, and a table of digitized values forxleft,yleft andxright,yright are provided in the first step. In the second step, thez-coordinate values are derived by varyingz to minimize the bond distance error (Rossmann and Argos, 1980). In another approach, only a reference bond distance table is provided along with the table ofxleft,yleft andxright,yright digitized values. In the first step, the viewing angle (φ), a combined scale and viewing distance parameter (q), a rotational angular distortion from digitizing and/or photocopying (z), and translational distortion factors (xerr andyerr) are calculated. In the second step, thez-coordinate values are varied to minimize the bond distance error. RMS difference values of less than 1.5 Å were obtained for both crambin and BPTI α-carbon atoms.

Keywords

Trypsin Bioorganic Chemistry Bond Distance Interatomic Distance Argos 

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References

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Copyright information

© Plenum Publishing Corporation 1993

Authors and Affiliations

  • Juan GuevaraJr.
    • 1
  • Roger D. Knapp
    • 1
  • John Spurlino
    • 2
  • B. V. Venkataram Prasad
    • 2
  • Joel D. Morrisett
    • 1
    • 2
  1. 1.Department of MedicineBaylor College of MedicineHouston
  2. 2.Department of Biochemistry, Howard Hughes Medical InstituteBaylor College of MedicineHouston

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