Open Access Research article

Computational modeling of the bHLH domain of the transcription factor TWIST1 and R118C, S144R and K145E mutants

Amanda M Maia1, João HM da Silva2, André L Mencalha1, Ernesto R Caffarena2* and Eliana Abdelhay1

Author Affiliations

1 Laboratório de Célula-tronco – CEMO/INCA, Praça da Cruz Vermelha 23 6 andar, Centro, Rio de Janeiro/RJ, Brasil

2 Laboratório de Biofísica Computacional e Modelagem Molecular – PROCC/ FIOCRUZ, Av Brasil, 4365, Manguinhos, Rio de Janeiro/RJ, Brasil

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BMC Bioinformatics 2012, 13:184  doi:10.1186/1471-2105-13-184

Published: 28 July 2012

Abstract

Background

Human TWIST1 is a highly conserved member of the regulatory basic helix-loop-helix (bHLH) transcription factors. TWIST1 forms homo- or heterodimers with E-box proteins, such as E2A (isoforms E12 and E47), MYOD and HAND2. Haploinsufficiency germ-line mutations of the twist1 gene in humans are the main cause of Saethre-Chotzen syndrome (SCS), which is characterized by limb abnormalities and premature fusion of cranial sutures. Because of the importance of TWIST1 in the regulation of embryonic development and its relationship with SCS, along with the lack of an experimentally solved 3D structure, we performed comparative modeling for the TWIST1 bHLH region arranged into wild-type homodimers and heterodimers with E47. In addition, three mutations that promote DNA binding failure (R118C, S144R and K145E) were studied on the TWIST1 monomer. We also explored the behavior of the mutant forms in aqueous solution using molecular dynamics (MD) simulations, focusing on the structural changes of the wild-type versus mutant dimers.

Results

The solvent-accessible surface area of the homodimers was smaller on wild-type dimers, which indicates that the cleft between the monomers remained more open on the mutant homodimers. RMSD and RMSF analyses indicated that mutated dimers presented values that were higher than those for the wild-type dimers. For a more careful investigation, the monomer was subdivided into four regions: basic, helix I, loop and helix II. The basic domain presented a higher flexibility in all of the parameters that were analyzed, and the mutant dimer basic domains presented values that were higher than the wild-type dimers. The essential dynamic analysis also indicated a higher collective motion for the basic domain.

Conclusions

Our results suggest the mutations studied turned the dimers into more unstable structures with a wider cleft, which may be a reason for the loss of DNA binding capacity observed for in vitro circumstances.

Keywords:
Twist1; Transcription factor; bHLH; Comparative modeling; Molecular dynamics simulation; Collective motions