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Structural chemometrics of ABP1 – auxin interaction

Ferreira M. M. C. and Kiralj R.

Universidade Estadual de Campinas - Campinas SP

Resumo [Abstract]

Auxin binding protein 1  (ABP1)  has  been  recently  structurally characterized as uncomplexed  and  complexed  with  an
auxin [1]. Auxins,  primarily indole-3-acetic acid (IAA)  and its  derivatives,  are important plant growh hormones.  Before
reporting the  3D  structure of ABP1, there  was no clear picture  of  auxin  binding mode  in  the   binding  site  of  ABP1.
Functional ABP1  is  a dimmer that binds two auxin molecules.  Each  of  the two zinc ions is  hexacoordinated,  with  two
Zn – O bonds established with the carboxyl group of auxin molecule. To understand ABP1- auxin binding and to  correlate
it with quantitative structure-activity studies [2],  two structural chemometric analyses  were  performed.  In  one study,  a
systematic search for IAA, its analogues and derivatives  was carried out using t he Cambridge Structural Database  (CSD)
[3] and the Protein Data Bank (PDB). Interatomic distances and torsion angles which define the position of the acetic acid
side chain with respect to the  (hetero)aromatic  ring were measured  in retrieved structures  of organic compounds,  metal
complexes and proteins complexed with IAA-like ligands.  The structural parameters were analyzed by means of  Principal
Component Analysis  (PCA)  and  Hierarchical Cluster Analysis (HCA).  Both analyses showed  clustering  of  samples  in
accordance with their structural types.  These findings were interpreted  in terms of molecular graphics of modeled  ABP1-
auxin complexes, quantitative structure-activity  study  and  ab initio calculations of  isolated auxins  in ground state.  In the
Zn ion.  Distances,  angles  and  torsion angles  and  absolute torsion angles  based  on bound and non-bound atoms of  the
carboxylate – Zn ring and carboxylate chain, were measured in all structures.  Correlation analysis, HCA and PCA  applied
its binding mode to the Zn ion.  Clustering of samples with respect  to their structural types has been also observed.  These
findings gave more insight into bioactive conformational properties of auxins in the  ABP1  binding site.  In  both structural
chemometric analyses,  attention was paid  to  the space group,  number of asymmetric units  and  the existence of  special
positions in every sample. In some cases,  crystal structures provided two or more samples with torsion angles different  in
absolute value and/or sign.

Agradecimentos [Acknowledgement]

FAPESP

Referências [References]

1. E. J. Woo et al., EMBO J. 2, 2877 (2002)
2. R. Kiralj, M. M. C. Ferreira, Chemometr. Intell. Lab. Syst., submitted
3. F. H. Allen, Acta Cryst. B58, 380 (2002)
 
 
 
 

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