Zn-metalloprotease sequences in extremophiles

T. Holden; S. Dehipawala; U. Golebiewska; E. Cheung; G. Tremberger Jr.; E. Williams; P. Schneider; N. Gadura; D. Lieberman; T. Cheung

doi:10.1117/12.860091

7 September 2010 Zn-metalloprotease sequences in extremophiles

T. Holden, S. Dehipawala, U. Golebiewska, E. Cheung, G. Tremberger Jr., E. Williams, P. Schneider, N. Gadura, D. Lieberman, T. Cheung

Author Affiliations +

Proceedings Volume 7819, Instruments, Methods, and Missions for Astrobiology XIII; 78190V (2010) https://doi.org/10.1117/12.860091
Event: SPIE Optical Engineering + Applications, 2010, San Diego, California, United States

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.

Citation Download Citation

T. Holden, S. Dehipawala, U. Golebiewska, E. Cheung, G. Tremberger Jr., E. Williams, P. Schneider, N. Gadura, D. Lieberman, and T. Cheung "Zn-metalloprotease sequences in extremophiles", Proc. SPIE 7819, Instruments, Methods, and Missions for Astrobiology XIII, 78190V (7 September 2010); https://doi.org/10.1117/12.860091

ACCESS THE FULL ARTICLE

INSTITUTIONAL
Select your institution to access the SPIE Digital Library.

SELECT YOUR INSTITUTION

PERSONAL
Sign in with your SPIE account to access your personal subscriptions or to use specific features such as save to my library, sign up for alerts, save searches, etc.

PERSONAL SIGN IN

No SPIE Account? Create one

PURCHASE THIS CONTENT

SUBSCRIBE TO DIGITAL LIBRARY

50 downloads per 1-year subscription

Members: $195

Non-members: $335 ADD TO CART

25 downloads per 1 - year subscription

Members: $145

Non-members: $250 ADD TO CART

PURCHASE SINGLE ARTICLE

Includes PDF, HTML & Video, when available