1. A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions
- Author
-
Doug Barrick, Sean Klein, Kevin Sforza, Ekaterina Poliakova-Georgantas, Mark Petersen, Kathryn Geiger-Schuller, Tural Aksel, and Jacob D. Marold
- Subjects
Models, Molecular ,Repetitive Sequences, Amino Acid ,0303 health sciences ,Series (mathematics) ,Tools for Protein Science ,030302 biochemistry & molecular biology ,Proteins ,Folding (DSP implementation) ,Coupling (probability) ,Biochemistry ,03 medical and health sciences ,Amino Acid Substitution ,Sequence Analysis, Protein ,Mutation (genetic algorithm) ,Point Mutation ,Free energies ,Point (geometry) ,Statistical analysis ,Ising model ,Statistical physics ,Molecular Biology ,Software ,030304 developmental biology ,Mathematics - Abstract
A collection of programs is presented to analyze the thermodynamics of folding of linear repeat proteins using a 1D Ising model to determine intrinsic folding and interfacial coupling free energies. Expressions for folding transitions are generated for a series of constructs with different repeat numbers and are globally fitted to transitions for these constructs. These programs are designed to analyze Ising parameters for capped homopolymeric consensus repeat constructs as well as heteropolymeric constructs that contain point substitutions, providing a rigorous framework for analysis of the effects of mutation on intrinsic and directional (i.e., N- vs. C-terminal) interfacial coupling free-energies. A bootstrap analysis is provided to estimate parameter uncertainty as well as correlations among fitted parameters. Rigorous statistical analysis is essential for interpreting fits using the complex models required for Ising analysis of repeat proteins, especially heteropolymeric repeat proteins. Programs described here are available at https://github.com/barricklab-at-jhu/Ising_programs.
- Published
- 2020