Computational protocol: Alpha-Helical Destabilization of the Bcl-2-BH4-Domain Peptide Abolishes Its Ability to Inhibit the IP3 Receptor

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Protocol publication

[…] To calculate the change in pseudo-thermodynamic stability induced by the GG substitutions, we used Eris, an automated estimator of free-energy-change variations (ΔΔG), with unbiased force field, side-chain packing and backbone relaxation algorithms []. First, we extrapolated the structure of the Bcl-2-BH4 peptide from the PDB file corresponding to the NMR structure of Bcl-2 protein (PDB: 1G5M []) and submitted it successively to the prediction server. The ΔΔG values reported in this study are indicated in kcal/mol. Additionally, the I-TASSER v 2.1 webserver [] was used to predict the secondary structure of the different BH4 peptides starting from their amino-acid sequence. I-TASSER builds protein models using iterative assembling procedures and multiple threading alignments from template structures libraries. An estimate of accuracy of the predictions is given by the confidence score. In the case of Bcl-2-BH4 peptide, the most accurate I-TASSER model was downloaded as PDB file and imported in PyMOL, a molecular graphics software (http://www.pymol.org). […]

Pipeline specifications

Software tools Eris, I-TASSER, PyMOL
Application Protein structure analysis
Chemicals Glycine, Inositol 1,4,5-Trisphosphate