A collection of programs for one‐dimensional Ising analysis of linear repeat proteins with point substitutions

Marold, Jacob D.; Sforza, Kevin; Geiger-Schuller, Kathryn; Aksel, Tural; Klein, Sean; Petersen, Mark; Poliakova-Georgantas, Ekaterina; Barrick, Doug

doi:10.1002/pro.3977

Cited by 4 publications

(3 citation statements)

References 27 publications

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“…To globally fit unfolding transitions of γDC variants, we generated fitting equations using a one-dimensional Ising model as described previously (39, 55). Python code modified from Marold et.…”

Section: Methodsmentioning

confidence: 99%

“…al. (55) was used to generate and fit partition functions describing the fraction of a given folded state as a function of denaturant using separate equilibrium constants for folding of individual domains and for the interface coupling (Table S3). To fit V132A data, we modified the 1-D Ising partition function to permit coupling between the CTD and the unfolded NTD.…”

Section: Determination Of Global Stability By Intrinsic Tryptophan Fl...mentioning

confidence: 99%

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Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions

Volz,

Malone,

Guseman

et al. 2024

Preprint

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Human γD-crystallin, a monomeric protein abundant in the eye lens nucleus, must remain stably folded for an individual’s entire lifetime to avoid aggregation and protein deposition-associated cataract formation. γD-crystallin contains two homologous domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), which interact via a hydrophobic interface. A number of familial mutations in the gamma crystallin gene are linked to congenital early-onset cataract, most of which result in amino acid changes in the NTD. Several of these, such as V75D and W42R, are known to populate intermediates that, under partially denaturing conditions, possess a natively folded CTD and a completely unfolded NTD, with studies on W42R showing further evidence for a minor population of an intermediate under native conditions. We employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to probe the structural and energetic features of variants of γD-crystallin under both native and partially denaturing conditions. For V75D and W42R, we identify a species under native conditions that retains partial structure in the NTD and is structurally and energetically distinct from the intermediate populated under partially denaturing conditions. Residues at the NTD-CTD interface play crucial roles in stabilizing this intermediate, and disruption of interface contacts either by amino acid substitution or partial denaturation permits direct observation of two intermediates at the same time. The newly identified intermediate exposes hydrophobic amino acids that are buried in both the folded full-length protein and in the protein’s stable isolated domains. Such non-native exposure of a hydrophobic patch may play an important role in cataract formation.Significance StatementHuman γD-crystallin, which plays a structural role in the eye lens, is a long-lived protein that must remain folded for an individual’s entire lifetime to avoid aggregation and protein deposition - associated cataract formation. By using hydrogen-deuterium exchange mass spectrometry, we demonstrate that two cataract-associated variants of γD-crystallin populate an intermediate with partial structure along the interface between its two domains under native conditions. In these intermediates, hydrophobic amino acids that are normally buried in the N-terminal domain’s native folded structure become exposed, possibly leading to aggregation and cataract formation. Our findings illustrate the importance of studying a protein’s energy landscapes under conditions that are close to physiological.

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Section: Methodsmentioning

confidence: 99%

Section: Determination Of Global Stability By Intrinsic Tryptophan Fl...mentioning

confidence: 99%

Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions

Volz,

Malone,

Guseman

et al. 2024

Preprint

View full text Add to dashboard Cite

show abstract

“…Direct measurements of these parameters allow a quantitative assessment of the impacts of a point mutation. Several models have been developed to analyze these perturbations including one dimensional Ising analysis ( Marold et al, 2021 ), positional frustration analysis ( Parra et al, 2015 ; Espada et al, 2017 ), use of energy functions like Rosetta ( Zhu et al, 2016 ), and others ( Hutton et al, 2015 ). Free energy analysis can also be used to define sequence conservation, perhaps more accurately than sequence consensus and co-variation analysis has also been applied to both Ankyrin and TPR proteins ( Mosavi et al, 2002 ; Magliery and Regan, 2004 ) using both real and simulated data to improve the statistical parameters of the analysis ( Travers and Fares, 2007 ).…”

Section: Introductionmentioning

confidence: 99%

The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins

et al. 2021

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Protein repeats are short, highly similar peptide motifs that occur several times within a single protein, for example the TPR and Ankyrin repeats. Understanding the role of mutation in these proteins is complicated by the competing facts that 1) the repeats are much more restricted to a set sequence than non-repeat proteins, so mutations should be harmful much more often because there are more residues that are heavily restricted due to the need of the sequence to repeat and 2) the symmetry of the repeats in allows the distribution of functional contributions over a number of residues so that sometimes no specific site is singularly responsible for function (unlike enzymatic active site catalytic residues). To address this issue, we review the effects of mutations in a number of natural repeat proteins from the tetratricopeptide and Ankyrin repeat families. We find that mutations are context dependent. Some mutations are indeed highly disruptive to the function of the protein repeats while mutations in identical positions in other repeats in the same protein have little to no effect on structure or function.

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Surface residues and nonadditive interactions stabilize a consensus homeodomain protein

Sternke¹,

Tripp²,

Barrick³

2021

Biophysical Journal

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A collection of programs for one‐dimensional Ising analysis of linear repeat proteins with point substitutions

Cited by 4 publications

References 27 publications

Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions

Cataract-prone variants of γD-crystallin populate a conformation with a partially unfolded N-terminal domain under native conditions

The Effect of Mutations in the TPR and Ankyrin Families of Alpha Solenoid Repeat Proteins

Surface residues and nonadditive interactions stabilize a consensus homeodomain protein

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