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

Amanda M Maia,João Hm Da Silva,Eliana Abdelhay,Ernesto R Caffarena,André L Mencalha

doi:10.1186/1471-2105-13-184

Amanda M Maia, João Hm Da Silva + Show 3 more

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https://doi.org/10.1186/1471-2105-13-184

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Abstract

BackgroundHuman 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.ResultsThe 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.ConclusionsOur 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.

Highlights

Human TWIST1 is a highly conserved member of the regulatory basic helix-loop-helix transcription factors
Because of the importance of TWIST1 in the regulation of embryonic development, its substantial relationship with Saethre-Chotzen syndrome (SCS) and the lack of an experimentally solved structure for this protein, we performed comparative modeling for the TWIST1 basic helix-loop-helix (bHLH) region for both the homodimer and heterodimer with E47. These are important for DNA binding in the promoter region of target genes, and we evaluated their behavior in aqueous solution using molecular dynamics simulations
Construction of TWIST1 models According to Eukaryotic Linear Motif (ELM), the human TWIST1 sequence deposited in International Protein Index (IPI) (IPI00018907) displayed three regions: the N-terminal region, the bHLH domain and the C-terminal region

Summary

Introduction

Human TWIST1 is a highly conserved member of the regulatory basic helix-loop-helix (bHLH) transcription factors. 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. TWIST1 is a basic helix-loop-helix (bHLH) transcription factor (TF) in which the basic DNA-binding region is. As only the heterodimers of the myogenic bHLH protein with the ubiquitous E2A protein are able to activate muscle-specific gene expression and differentiation, it is very important to ensure that only these heterodimers, and not E2A protein homodimers, bind to the relevant E-box sites. To compete with the E2A protein homodimers, the heterodimers must have a higher affinity for the binding site. In muscle cells and pancreatic cells, they clearly prefer to bind DNA as heterodimers [10,11,12,13]

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