Abstract
Background: Single nucleotide substitutions (SNS) in genetic codon are of prime importance due to their ability to alter an amino acid sequence as a result. Given the nature of genetic code, any SNS is expected to change the protein sequence randomly into any of the 64 possible codons. In this paper, we present a theoretical analysis of how single nucleotide substitutions in genetic codon may affect resulting amino acid residue and what is the most likely amino acid that will get selected as a result. Methods: A probability matrix was developed showing possible changes and routes likely being followed as a result of base substitution mutation causing changes at the translational level for the amino acid being encoded. Results: We observe that in event of single base pair substitution in a given amino acid; a chosen set of amino acids is theoretically more probable to be resulted suggesting a directional rather than a random change. This study also indicates that for a given amino acid coded by a number of synonymous codons, all synonymous codons will result into same list of amino acids in case of all possible SNS at three positions. Conclusion: The present work has resulted into development of a theoretical probability matrix which can be used to predict changes in amino acid residues in a protein sequence caused by single base substitutions.
Highlights
Single nucleotide substitutions (SNS) in genetic codon are of prime importance due to their ability to alter an amino acid sequence as a result
It is observed that mutations lead to a wide range of amino acid changes in a protein sequence, but single base substitutions in genetic codons, in most cases result in no significant change at the amino acid level due to more or less equal probability of synonymous substitution or no change at all (Tables 2 - 3)
From the perspective of synonymous and non-synonymous substitutions due to single base substitutions, our finding suggests that whenever such a mutation occurs in a codon, an amino acid may get replaced but only into a more similar amino acids or in other words, synonymous substitutions are more favored over nonsynonymous substitutions
Summary
Single nucleotide substitutions (SNS) in genetic codon are of prime importance due to their ability to alter an amino acid sequence as a result. Given the nature of genetic code, any SNS is expected to change the protein sequence randomly into any of the 64 possible codons. We present a theoretical analysis of how single nucleotide substitutions in genetic codon may affect resulting amino acid residue and what is the most likely amino acid that will get selected as a result. Methods: A probability matrix was developed showing possible changes and routes likely being followed as a result of base substitution mutation causing changes at the translational level for the amino acid being encoded. Conclusion: The present work has resulted into development of a theoretical probability matrix which can be used to predict changes in amino acid residues in a protein sequence caused by single base substitutions. With an assumption that the net outcome would be random according to the nature of the code we attempt to envisage the possible amino acid substitutions occurring when single base
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