SUPPLEMENTARY MATERIAL FOR:
Gain of local structure in an amphipathic
peptide does not require a specific tertiary
framework
Ernesto A. Roman1*, Pablo Rosi1*, Mariano C. González Lebrero1, Rodolfo Wuilloud2,
F. Luis González Flecha1, José M. Delfino1, and Javier Santos1,3 **
Department of Biological Chemistry and Institute of Biochemistry and Biophysics
(IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín
956, C1113AAD, Buenos Aires. Argentina.
1
Department of Biological Chemistry and Institute of Biochemistry and Biophysics
(IQUIFIB), School of Pharmacy and Biochemistry, University of Buenos Aires, Junín
956, C1113AAD, Buenos Aires, Argentina.
2
Laboratory of Environmental Research and Services of Mendoza (LISAMEN)
CCT-CONICET Mendoza. Av. Ruiz Leal S/N Parque General San Martín, M 5502 IRA
Mendoza, Argentina.
3
Department of Science and Technology, University of Quilmes, Roque Sáenz Peña
352, B1876XD, Bernal, Argentina.
Figure S1. Hydrophobic moments of TRX 94-108 and its variants using as a template
the PDB structure for residues 94-108 extracted from the full-length protein (PDB
ID:2TRX). Colored bars represent the hydrophobic moment using different
hydrophobicity scales: Kyte-Doolittle1 (black), Hopp-Woods2 (red), Cornette3 (green),
Eisenberg4 (yellow), Rose5 (blue), Janin6 (violet), Engelman7 (cyan), and Fauchere and
Pliska8 (grey). The brown bar represents the calculated hydrophobic moment using
Fauchere and Pliska scale, but using as a template a canonical -helix instead of the
TRX 94-108 PDB structure.
Figure S2. Ramachandran plots for residues 95 to 106 of TRX94-108. φ (phi) and Ψ
(psi) torsion angles were measured using g_rama Gromacs application along the
simulation at a 3:1 SDS:peptide molar ratio.
Figure S3. Ribbon diagram of E. coli thioredoxin (2TRX), human frataxin (1EKG), and
the soluble actuator domain of A. fulgidus CopA (2HC8). Side-chains corresponding to
each peptide studied in this work are represented as sticks and colored by residue type:
polar (green), basic (blue), acidic (red), and apolar (white).
References
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2.
Hopp TP, Woods KR. Prediction of protein antigenic determinants from amino
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Cornette JL, Cease KB, Margalit H, Spouge JL, Berzofsky JA, DeLisi C.
Hydrophobicity scales and computational techniques for detecting amphipathic
structures in proteins. J Mol Biol 1987;195:659-685.
4.
Eisenberg D, Weiss RM, Terwilliger TC. The helical hydrophobic moment: a
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5.
Rose GD, Geselowitz AR, Lesser GJ, Lee RH, Zehfus MH. Hydrophobicity of
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