Protein & Peptide Letters

Prof. Ben M. Dunn  
Department of Biochemistry and Molecular Biology
University of Florida
College of Medicine
P.O. Box 100245
Gainesville, FL
USA
Email: bdunn@ufl.edu

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Structure and Sequence Based Analysis of Alpha-Amylase Evolution

Author(s): Swati Singh and Lalitha Guruprasad

Affiliation: School of Chemistry, University of Hyderabad, Hyderabad, 500046, India.

Keywords: α-Amylase, calcium ion binding, chloride ion binding, disulfide bond, phylogenetic trees, protein sequence analysis, 3D structure analysis.

Graphical Abstract:


Abstract:

α-Amylases hydrolyze α- 1,4-glycosidic bonds during assimilation of biological macromolecules. The amino acid sequences of these enzymes in thousands of diverse organisms are known and the 3D structures of several proteins have been solved. The 3D structure analysis of these universal enzymes from diverse organisms has been studied by the generation of phylogenetic trees and structure based sequence analysis to generate a metric for the degree of conservation that is responsible for individual speciation. Greater similarities are observed between reference NCBI tree and structure based phylogenetic tree compared to sequence based phylogenetic tree indicating that structures truly represent the functional aspects of proteins than from the sequence information alone. We report differences in the profile specific conserved and insertion/deletion regions, factors responsible for the Ca2+ and Cl- ion binding and the disulfide connectivity pattern that discriminate the enzymes over evolution.

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Article Details

VOLUME: 21
ISSUE: 9
Page: [948 - 956]
Pages: 9
DOI: 10.2174/092986652109140715124139