Journal of Protein Chemistry

, Volume 15, Issue 1, pp 11–16 | Cite as

Prediction of the three-dimensional structure of the rap-1A protein from its homology to theras-gene-encoded p21 protein

  • James M. Chen
  • Rosalyn Grad
  • Regina Monaco
  • Matthew R. Pincus
Article

Abstract

rap-1A, an anti-oncogene-encoded protein, is aras-p21-like protein whose sequence is over 80% homologous to p21 and which interacts with the same intracellular target proteins and is activated by the same mechanisms as p21, e.g., by binding GTP in place of GDP. Both interact with effector proteins in the same region, involving residues 32–47. However, activated rap-1A blocks the mitogenic signal transducing effects of p21. Optimal sequence alignment of p21 and rap-1A shows two insertions of rap-1A atras positions 120 and 138. We have constructed the three-dimensional structure of rap-1A bound to GTP by using the energy-minimized three-dimensional structure ofras-p21 as the basis for the modeling using a stepwise procedure in which identical and homologous amino acid residues in rap-1A are assumed to adopt the same conformation as the corresponding residues in p21. Side-chain conformations for homologous and nonhomologous residues are generated in conformations that are as close as possible to those of the corresponding side chains in p21. The entire structure has been subjected to a nested series of energy minimizations. The final predicted structure has an overall backbone deviation of 0.7 å from that ofras-p21. The effector binding domains from residues 32–47 are identical in both proteins (except for different side chains of different residues at position 45). A major difference occurs in the insertion region at residue 120. This region is in the middle of another effector loop of the p21 protein involving residues 115–126. Differences in sequence and structure in this region may contribute to the differences in cellular functions of these two proteins.

Key words

rap-1A ras-p21 protein homologous sequence energy minimization 

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Copyright information

© Plenum Publishing Corporation 1996

Authors and Affiliations

  • James M. Chen
    • 1
  • Rosalyn Grad
    • 2
  • Regina Monaco
    • 3
    • 4
    • 5
  • Matthew R. Pincus
    • 3
    • 4
  1. 1.Dupont Agricultural ProductsStein-Haskell Research CenterNewark
  2. 2.Department of BiologyNew York UniversityNew York
  3. 3.Department of Pathology and Laboratory MedicineVeterans Affairs Medical CenterBrooklyn
  4. 4.Department of PathologySUNY Health Science Center at BrooklynBrooklyn
  5. 5.Department of ChemistryNew York UniversityNew York

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