Computational protocol: Polymorphisms in the Mitochondrial Ribosome Recycling Factor EF-G2mt/MEF2 Compromise Cell Respiratory Function and Increase Atorvastatin Toxicity

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Protocol publication

[…] The protein model of the human EF-G2mt protein was based on the crystal structure of the Thermus thermophilus EF-G protein (Protein Data Bank 2bm0) . This shares 39% residue identity. Selection of the T. thermophilus template and homology modelling was carried out using the SWISS-MODEL server in ‘project mode’ to enable alignment inspection prior to modelling . The completed model was then submitted to the SWISS-MODEL suite of quality check programs which tests for model quality and stereochemistry using algorithms such as ANOLEA and PROCHECK . The model was visualised using the Visual Molecular Dynamics program (VMD), version 1.8.7 (University of Illinois) and this software was also used for the assignment of protein secondary structure and the assessment of electrostatic potential. [...] All sequences, both yeast and human, were obtained from the Ensembl database. There are three known human EF-G2mt protein isoforms but isoform I (AAH15712.1) was used throughout this study. Human EF-G2mt SNPs were identified using the dbSNP database available on the National Center for Biotechnology Information (NCBI) website (www.ncbi.nlm.nih.gov/SNP/index.html). The Lalign program available on the Swiss EMBnet server (www.ch.embnet.org/software/lalign_form.html) was used to generate global alignments of protein sequences, based on the BLOSUM50 matrix . Graphical representations were constructed using the BioEdit version 7.0.5 sequence alignment editor. […]

Pipeline specifications

Software tools PROCHECK, LALIGN, BioEdit
Databases dbSNP
Applications Protein structure analysis, Nucleotide sequence alignment
Organisms Saccharomyces cerevisiae, Homo sapiens
Diseases Hypercholesterolemia, Drug-Related Side Effects and Adverse Reactions
Chemicals Galactose