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Computational Analysis of the Primary and Secondary Structure of Amidases in Relation to their pH Adaptation

[ Vol. 17 , Issue. 2 ]

Author(s):

Neerja Thakur, Nikhil Sharma, Vijay Kumar and Tek Chand Bhalla*   Pages 95 - 106 ( 12 )

Abstract:


Background: Amidases are ubiquitous enzymes and biological functions of these enzymes vary widely. They are considered to be synergistically involved in the synthesis of a wide variety of carboxylic acids, hydroxamic acids and hydrazides, which find applications in commodity chemicals synthesis, pharmaceuticals agrochemicals and wastewater treatments.

Methods: They hydrolyse a wide variety of amides (short-chain aliphatic amides, mid-chain amides, arylamides, α-aminoamides and α-hydroxyamides) and can be grouped on the basis of their catalytic site and preferred substrate. Despite their economic importance, we lack knowledge as to how these amidases withstand elevated pH and temperature whereas others cannot.

Results: The present study focuses on the statistical comparison between the acid-tolerant, alkali tolerant and neutrophilic organisms. In silico analysis of amidases of acid-tolerant, alkali tolerant and neutrophilic organisms revealed some striking trends as to how amino acid composition varies significantly. Statistical analysis of primary and secondary structure revealed amino acid trends in amidases of these three groups of bacteria. The abundance of isoleucine (Ile, I) in acid-tolerant and leucine (Leu, L) in alkali tolerant showed the aliphatic amino acid dominance in extreme conditions of pH in acidtolerant and alkali tolerant amidases.

Conclusion: The present investigation insights physiochemical properties and dominance of some crucial amino acid residues in the primary and secondary structure of some amidases from acid-tolerant, alkali tolerant and neutrophilic microorganisms.

Keywords:

Amidase, acid-tolerant, alkali tolerant, neutrophilic, Tukey test (T-Test), amino acid composition, primary and secondary structure.

Affiliation:

Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, Bioinformatics Centre, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005, Department of Biotechnology, Himachal Pradesh University, Summer Hill, Shimla, Himachal Pradesh 171005



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