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Internet Electronic Journal of Molecular Design - IEJMD, ISSN 1538-6414, CODEN IEJMAT
| ABSTRACT - Internet Electron. J. Mol. Des. June 2004, Volume 3, Number 6, 295-307 |
Molecular Modeling of c2h2 Zinc Finger Mutation of Putative Human
Transcription Factor SALL4
Vladimír Frecer, Jan Miertus, Wiktor Borozdin, Jürgen Kohlhase, Antonio Amoroso, and Stanislav Miertus
Internet Electron. J. Mol. Des. 2004, 3, 295-307
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Abstract:
The SALL4 gene, Drosophila's region specific homeotic sal
(spalt)-like gene family member, encodes for a zinc finger (ZF)
transcription factor (TF). Mutations of the SALL4 have been
demonstrated to cause the Okihiro syndrome a combination of
Duane retraction syndrome and radial ray defects. We have
studied a missense point mutation of the SALL4 (nucleotide
substitution 2663A→G, residues substitution
His:888→Arg:888) positioned within the first c2h2 ZF of the
C-terminal double ZF motif in the SALL4 gene identified in an
Italian three-generation family, some members of which
displayed the clinical features of the Okihiro syndrome. We
performed a molecular modeling study on the wild type (wt)
and mutated (mt) ZF domains of the SALL4 TF with the goal
to propose a plausible hypothesis relating the modeled
structural and energetic differences between the wt and mt
forms to the defects connected with the observed mutation.
Sequence alignment, homology protein modeling and
molecular mechanics using CFF91 force field were utilized to
build and refine the ZF models and to estimate their stability
and DNA-binding affinity. We have modeled wt and mt ZF
motifs of the SALL4 TF based on sequence homology with ZF
domains of TFs with known crystal structures co-crystallized
with a B-DNA segment. Secondary structure, zinc ion binding
and DNA binding of the two static ZF models were analyzed in
terms of mutual r.m.s. deviations and intramolecular and
intermolecular interaction energies. The modeled wt and mt
forms of ZF motif of the SALL4 TF did not display significant
structural differences cased by steric strain or charge of the
bulkier Arg:888 and retained similar supersecondary structures
and comparable strength of the zinc ion binding. However,
more significant differences were predicted in their binding
affinities to DNA. Calculated higher DNA binding affinity
(and possibly also changed specificity) of the mt form of the
ZF could be the reason for the altered activator/repressor
function of the mutant form of the SALL4 TF at its natural
target gene or the cause for erroneous targeting of a different
DNA sequence of the same or another gene. We may thus
hypothesize that the pathogenic effects of the mutation could
be related to the altered regulation function by making the
dissociation of the mt SALL4 TF-gene adducts more difficult.
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