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Proceedings Paper

Zn-metalloprotease sequences in extremophiles
Author(s): T. Holden; S. Dehipawala; U. Golebiewska; E. Cheung; G. Tremberger Jr.; E. Williams; P. Schneider; N. Gadura; D. Lieberman; T. Cheung
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Paper Abstract

The Zn-metalloprotease family contains conserved amino acid structures such that the nucleotide fluctuation at the DNA level would exhibit correlated randomness as described by fractal dimension. A nucleotide sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. The structure's vibration modes can also be studied using a Gaussian Network Model. The vibration measure and fractal dimension values form a two-dimensional plot with a standard vector metric that can be used for comparison of structures. The preference for amino acid usage in extremophiles may suppress nucleotide fluctuations that could be analyzed in terms of fractal dimension and Shannon entropy. A protein level cold adaptation study of the thermolysin Zn-metalloprotease family using molecular dynamics simulation was reported recently and our results show that the associated nucleotide fluctuation suppression is consistent with a regression pattern generated from the sequences's fractal dimension and entropy values (R-square ~ 0.98, N =5). It was observed that cold adaptation selected for high entropy and low fractal dimension values. Extension to the Archaemetzincin M54 family in extremophiles reveals a similar regression pattern (R-square = 0.98, N = 6). It was observed that the metalloprotease sequences of extremely halophilic organisms possess high fractal dimension and low entropy values as compared with non-halophiles. The zinc atom is usually bonded to the histidine residue, which shows limited levels of vibration in the Gaussian Network Model. The variability of the fractal dimension and entropy for a given protein structure suggests that extremophiles would have evolved after mesophiles, consistent with the bias usage of non-prebiotic amino acids by extremophiles. It may be argued that extremophiles have the capacity to offer extinction protection during drastic changes in astrobiological environments.

Paper Details

Date Published: 7 September 2010
PDF: 9 pages
Proc. SPIE 7819, Instruments, Methods, and Missions for Astrobiology XIII, 78190V (7 September 2010); doi: 10.1117/12.860091
Show Author Affiliations
T. Holden, Queensborough Community College (United States)
S. Dehipawala, Queensborough Community College (United States)
U. Golebiewska, Queensborough Community College (United States)
E. Cheung, Queensborough Community College (United States)
G. Tremberger Jr., Queensborough Community College (United States)
E. Williams, Queensborough Community College (United States)
P. Schneider, Queensborough Community College (United States)
N. Gadura, Queensborough Community College (United States)
D. Lieberman, Queensborough Community College (United States)
T. Cheung, Queensborough Community College (United States)

Published in SPIE Proceedings Vol. 7819:
Instruments, Methods, and Missions for Astrobiology XIII
Richard B. Hoover; Gilbert V. Levin; Alexei Yu. Rozanov; Paul C. W. Davies, Editor(s)

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