Journal of Molecular Modeling

, Volume 12, Issue 6, pp 905–914

Molecular modeling of the effects of mutant alleles on chalcone synthase protein structure

  • Christopher D. Dana
  • David R.  Bevan
  • Brenda S. J. Winkel
Original paper

DOI: 10.1007/s00894-005-0071-1

Cite this article as:
Dana, C.D., Bevan, D.R. & Winkel, B.S. J Mol Model (2006) 12: 905. doi:10.1007/s00894-005-0071-1


Chalcone synthase (CHS) catalyzes the first committed step in flavonoid biosynthesis, a major pathway of plant secondary metabolism. An allelic series for the Arabidopsis CHS locus, tt4, was previously characterized at the gene, protein, and end-product levels. In an effort to deduce the molecular basis for the observed phenotypes, homology models were generated for five of the tt4 proteins based on the crystal structure of CHS2 from Medicago. Molecular dynamics simulations provided insights into how even those substitutions that are not in close spatial proximity to key functional residues may still alter the architecture and dynamic movement of the enzyme, with dramatic effects on enzyme function. Simulations carried out at different temperatures pointed to optimized positioning of key residues in the active site or dimerization domain, rather than enhancement of overall structure, as underlying the higher activity of two temperature-sensitive variants at lower temperatures. Extending this type of analysis to account for protein–protein interactions may offer additional insights into the mechanisms by which single amino-acid substitutions can affect diverse aspects of protein function.


Homology modeling Molecular dynamics simulation Allelic series Chalcone synthase transparent testa Arabidopsis thaliana 



Chalcone synthase


Transparent testa


Root mean square deviation

Supplementary material

894_2005_71_MOESM1_ESM.xls (118 kb)
(XLS 120 kb)

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Christopher D. Dana
    • 1
    • 3
  • David R.  Bevan
    • 2
  • Brenda S. J. Winkel
    • 1
  1. 1.Department of Biology and Fralin Biotechnology CenterVirginia TechBlacksburgUSA
  2. 2.Department of BiochemistryVirginia TechBlacksburgUSA
  3. 3.Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingUSA

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