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A collection of programs for one‐dimensional Ising analysis of linear repeat proteins with point substitutions
Author(s) -
Marold Jacob D.,
Sforza Kevin,
GeigerSchuller Kathryn,
Aksel Tural,
Klein Sean,
Petersen Mark,
PoliakovaGeorgantas Ekaterina,
Barrick Doug
Publication year - 2021
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1002/pro.3977
Subject(s) - ising model , folding (dsp implementation) , statistical physics , coupling (piping) , physics , protein folding , point (geometry) , computer science , computational biology , biology , mathematics , materials science , nuclear magnetic resonance , geometry , electrical engineering , metallurgy , engineering
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.