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Proceedings Paper

Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction
Author(s): Sunil Dehipawala; A. Nguyen; G. Tremberger; E. Cheung; P. Schneider; D. Lieberman; T. Holden; T. Cheung
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Paper Abstract

A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson’s disease.

Paper Details

Date Published: 26 September 2013
PDF: 15 pages
Proc. SPIE 8865, Instruments, Methods, and Missions for Astrobiology XVI, 88650G (26 September 2013); doi: 10.1117/12.2024627
Show Author Affiliations
Sunil Dehipawala, Queensborough Community College (United States)
A. Nguyen, Queensborough Community College (United States)
G. Tremberger, Queensborough Community College (United States)
E. Cheung, Queensborough Community College (United States)
P. Schneider, Queensborough Community College (United States)
D. Lieberman, Queensborough Community College (United States)
T. Holden, Queensborough Community College (United States)
T. Cheung, Queensborough Community College (United States)


Published in SPIE Proceedings Vol. 8865:
Instruments, Methods, and Missions for Astrobiology XVI
Richard B. Hoover; Gilbert V. Levin; Alexei Yu. Rozanov; Nalin C. Wickramasinghe, Editor(s)

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