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Exact correspondence between walk in nucleotide and protein sequence spaces
Dmitry N Ivankov1,2,3
1Laboratory of Evolutionary Genomics, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain.
Plos One
|August 12, 2017
Summary
This study introduces an algorithm to calculate accessible protein sequences from gene mutations. The method reveals a significantly larger number of reachable protein sequences than previously estimated, aiding evolutionary studies.
Area of Science:
- Evolutionary biology
- Bioinformatics
- Computational biology
Background:
- Genes evolve through nucleotide sequence changes, altering protein sequences.
- The precise mapping between nucleotide and protein sequence spaces remains incompletely understood.
- Quantifying reachable protein sequences after a set number of mutations is an open question.
Purpose of the Study:
- To develop an algorithm for calculating the volume of protein sequence space accessible from a given protein sequence.
- To determine the number of protein sequences reachable with a specific number of nucleotide substitutions.
Main Methods:
- Algorithm development utilizing dynamic programming.
- Calculation of accessible protein sequence space volume.
- Application to green fluorescence protein (GFP) as a case study.
Main Results:
- The algorithm efficiently calculates accessible protein sequence space volume on a desktop computer.
- For GFP, the algorithm estimated four times more reachable sequences than prior estimations.
- Despite the increase, previous estimates remain valid as order-of-magnitude approximations.
Conclusions:
- The developed algorithm provides a precise method for quantifying evolutionary trajectories in sequence space.
- This tool has practical applications in understanding protein evolution and sequence space exploration.
- The findings refine our understanding of the relationship between genetic mutations and protein diversity.
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