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

Additional files

Additional file 1:

Table S1. Final configuration for molecular dynamics simulation. Cl- – chloride ions. A – angstrom; wt – wild-type.

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Additional file 2:

Table S2. Available templates with similar structure with TWIST1 sequence. The E47/NeuroD1 complex (accession number 2QL2) used as a template for comparative modeling corresponded to chains C and D, respectively. The capital letters in parentheses correspond to the chain in the crystal. Mm – Mus musculus; Hs – Homo sapiens; NMR – nuclear magnetic resonance; Å – angstrom (10-10 m).

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Additional file 3:

Table S3. Area variation between the wild-type and mutated residues. The TWI_A and TWI_B columns represent homodimer monomers 1 and 2, while the TWI columns correspond to the TWIST1 monomer of the heterodimer. The ratio between the mean and the equilibrated structures is in parentheses. The bolded values decreased throughout the simulation; Å – angstrom (10-10 m).

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Additional file 4:

Figure S1. Radius of gyration for each domain of TWIST1 homo- and heterodimers wt and mutants. Rg analysis was performed for each domain: (A) basic, (B) helix I, (C) loop and (D) helix II. The upper images correspond to the homodimers and the lower images correspond to the heterodimers. Å – angstrom (10-10 m);ns – nanoseconds (10-9 s).

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Additional file 5:

Figure S2. Secondary structure analysis (DSSP) for each dimer in function of time simulation. All eight dimers were assessed for secondary structure over simulation, and the color coding indicates the conformation of the residue sequence. ns – nanoseconds (10-9 s).

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Additional file 6:

Figure S3. Porcupine plots of the four most representative collective motions of all analyzed dimers. The porcupine plots of the four most representative collective motions and the percentage of the motion for each dimer are shown. The homodimers are in blue boxes (TWI_A/TWI_B wt, R118C, S144R and K145E) and the heterodimers are in red boxes (E47/TWI wt, R118C, S144R and K145E). The E47 monomer is represented in pink. The cones point in the direction of atomic movement along the indicated mode of motion, and the amplitude of the motion is represented by the length of the cone.

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Additional file 7:

Table S4. The contribution of the first 10 modes to the total motion of TWIST1 dimers. The percentage of motion is given by the absolute percentage (%) and the cumulative normalized eigenvalues (CNF) are the sum of the eigenvector percentages. The first three eigenvectors were responsible for more than 50% of the motion for all dimers. eigen – eigenvalue; wt – wild-type; CNF – percentage of cumulative normalized eigenvalues.

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