ArticleMethods in enzymology2009
Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models.
Article in Methods in enzymology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Unraveling the Mechanics of a Repeat-Protein Nanospring: From Folding of Individual Repeats to Fluctuations of the Superhelix.ACS nano · 2022Article
- Analysis of Tandem Repeat Protein Folding Using Nearest-Neighbor Models.Annual review of biophysics · 2021Review
- Testing the length limit of loop grafting in a helical repeat protein.Current research in structural biology · 2021Article
- A collection of programs for one-dimensional Ising analysis of linear repeat proteins with point substitutions.Protein science : a publication of the Protein Society · 2021Article
- A modified Ising model of Barabási-Albert network with gene-type spins.Journal of mathematical biology · 2020Article
- The Anti-Aggregation Holdase Hsp33 Promotes the Formation of Folded Protein Structures.Biophysical journal · 2020Article
- Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold.Scientific reports · 2019Article
- Functional instability allows access to DNA in longer transcription Activator-Like effector (TALE) arrays.eLife · 2019Article
- Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins.Biophysical journal · 2018Article
- Removal of a consensus proline is not sufficient to allow tetratricopeptide repeat oligomerization.Protein science : a publication of the Protein Society · 2017Article
- Broken TALEs: Transcription Activator-like Effectors Populate Partly Folded States.Biophysical journal · 2016Article
- GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins.Protein engineering, design & selection : PEDS · 2016Article
- Article
- Ising Model Reprogramming of a Repeat Protein's Equilibrium Unfolding Pathway.Journal of molecular biology · 2016Article
- A Naturally Occurring Repeat Protein with High Internal Sequence Identity Defines a New Class of TPR-like Proteins.Structure (London, England : 1993) · 2015Article
- Capturing coevolutionary signals inrepeat proteins.BMC bioinformatics · 2015Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- General mechanism of two-state protein folding kinetics.Journal of the American Chemical Society · 2014Article
- Direct observation of parallel folding pathways revealed using a symmetric repeat protein system.Biophysical journal · 2014Article
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2 authors.
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Abstract
The linear "Ising" model, which has been around for nearly a century, treats the behavior of linear arrays of repetitive, interacting subunits. Linear "repeat-proteins" have only been described in the last decade or so, and their folding energies have only been characterized very recently. Owing to their repetitive structures, linear repeat-proteins are particularly well suited for analysis by the nearest-neighbor Ising formalism. After briefly describing the historical origins and applications of the Ising model to biopolymers, and introducing repeat protein structure, this chapter will focus on the application of the linear Ising model to repeat proteins. When applied to homopolymers, the model can be represented and applied in a fairly simplified form. When applied to heteropolymers, where differences in energies among individual subunits (i.e. repeats) must be included, some (but not all) of this simplicity is lost. Derivations of the linear Ising model for both homopolymer and heteropolymer repeat-proteins will be presented. With the increased complexity required for analysis of heteropolymeric repeat proteins, the ability to resolve different energy terms from experimental data can be compromised. Thus, a simple matrix approach will be developed to help inform on the degree to which different thermodynamic parameters can be extracted from a particular set of unfolding curves. Finally, we will describe the application of these models to analyze repeat-protein folding equilibria, focusing on simplified repeat proteins based on "consensus" sequence information.
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