Zn-metalloprotease sequences in extremophiles
2010
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.
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