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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Protein sequence comparison based on representation on a finite dimensional unit hypercube

Soumen Ghosh^1,2, Jayanta Pal³, Carlo Cattani⁴

¹Electronics & Communication Engineering, National Institute of Technology, Durgapur, West Bengal, India.

Journal of Biomolecular Structure & Dynamics

|October 14, 2023

Abstract

None:

Numerous techniques are used to compare protein sequences based on the values of the physiochemical properties of amino acids. In this work, a single physical/chemical property value based non-binary representation of protein sequences is obtained on a 20 × 20-dimensional unit hypercube. The represented vector expressed in the matrix form is taken as the descriptor. The generalized NTV metric, which is an extension of the NTV metric used for polynucleotide space is taken as a distance measure. Based on this distance measure, a distance matrix is obtained for protein sequence comparison. Using this distance matrix, phylogenetic trees are drawn by using Molecular Evolutionary Genetics Analysis 11 (MEGA11) software applying the neighbor-joining method. Data sets used in this current work are 9-ND4, 9-ND5, 9-ND6, 24 TF-LF proteins, 27 different viruses and 127 proteins from the protein kinase C (PKC) family. Two sets of phylogenetic trees are obtained - one based on property value of polarity and the other based on property value of molecular weight. They are found to be exactly the same. Similar results also hold for other single property value based representation. The present trees are individually tested for efficiency based on the criterion of rationalized perception and computational time. The results of the present method are compared with those obtained earlier by other methods on the same protein sequences using assessment criteria of Symmetric distance (SD), Correlation coefficient, and Rationalized perception. In all the cases, the present results are found to be better than the results of other methods under comparison.Communicated by Ramaswamy H. Sarma.

Keywords:

ClustalW Single property descriptor (SPD)generalized NTV metric physiochemical property rank correlation coefficient rationalized perception symmetric distance

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