Analysis of Elongation Factor-Tu (EF-Tu) DNA Sequences Using Free Energy & Shannon Entropy

A paleo-experimental evolution report on elongation factor EF-Tu structural stability results using the ancestral protein sequence reconstruction modeling has been used in teaching community college pre-engineering students to do research. A project analyzing free energy and Shannon entropy of the engineered DNA sequences would benefit students interested in protein engineering. The studying of EF-Tu DNA sequences obtained from such an ancestral protein sequence reconstruction model shows a clustering pattern in the graph of Shannon entropy versus free energy calculated from the NUPACK software, posted on the internet by Caltech. The inclusion of HB8 and E. coli EF-Tu sequences for comparison suggests that a local area on the graph in the unit of bits-kcal/mol would serve as a marker for ancestral protein sequence reconstruction modeling constraints, while the separation distance between two such areas would represent selection pressure differential between organisms. Extension to transcription elongation factor retained the clustering pattern. The inclusion of Pandoravirus supports a regression trend of entropy versus free energy for the studied transcription elongation factor sequences with adjusted R-sq 0.984 (N =4). Keywords— Shannon entropy; NUPACK; EF-Tu; transcription