Consensus Finder web tool to predict stabilizing substitutions in proteins
Bryan J Jones1, Chi Nok Enoch Kan1, Christine Luo1
1Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Saint Paul, MN, United States.
Abstract:
The consensus sequence approach to predicting stabilizing substitutions in proteins rests on the notion that conserved amino acids are more likely to contribute to the stability of a protein fold than non-conserved amino acids. To implement a prediction for a target protein sequence, one finds homologous sequences and aligns them in a multiple sequence alignment. The sequence of the most frequently occurring amino acid at each position is the consensus sequence. Replacement of a rarely occurring amino acid in the target with a frequently occurring amino acid from the consensus sequence is predicted to be stabilizing. Consensus Finder is an open-source web tool that automates this prediction. This chapter reviews the rationale for the consensus sequence approach and explains the options for fine-tuning this approach using Staphylococcus nuclease A as an example.
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