PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins

Lowe, Alan R.; Perez-Riba, Albert; Itzhaki, Laura S.; Main, Ewan R. G.

doi:10.1016/j.bpj.2017.11.3779

Cited by 7 publications

(11 citation statements)

References 47 publications

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“…0.5 s; 20 accumulations), and the values at 222 nm were plotted. Denaturation curves were fitted using a two‐state transition model to determine the apparent denaturation temperature (Python) using the equation (Clarke & Fersht, 1993; Lowe et al , 2018):

F = e^{m (x - d 50) / RT} / (1 + e^{m (x - d 50) / RT})

…”

Section: Methodsmentioning

confidence: 99%

Evolutionary adaptation of the protein folding pathway for secretability

et al. 2022

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Secretory preproteins of the Sec pathway are targeted posttranslationally and cross cellular membranes through translocases. During cytoplasmic transit, mature domains remain non-folded for translocase recognition/translocation. After translocation and signal peptide cleavage, mature domains fold to native states in the bacterial periplasm or traffic further. We sought the structural basis for delayed mature domain folding and how signal peptides regulate it. We compared how evolution diversified a periplasmic peptidyl-prolyl isomerase PpiA mature domain from its structural cytoplasmic PpiB twin. Global and local hydrogen-deuterium exchange mass spectrometry showed that PpiA is a slower folder. We defined at near-residue resolution hierarchical folding initiated by similar foldons in the twins, at different order and rates. PpiA folding is delayed by less hydrophobic native contacts, frustrated residues and a β-turn in the earliest foldon and by signal peptidemediated disruption of foldon hierarchy. When selected PpiA residues and/or its signal peptide were grafted onto PpiB, they converted it into a slow folder with enhanced in vivo secretion. These structural adaptations in a secretory protein facilitate trafficking.

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F = e^{m (x - d 50) / RT} / (1 + e^{m (x - d 50) / RT})

…”

Section: Methodsmentioning

confidence: 99%

Evolutionary adaptation of the protein folding pathway for secretability

et al. 2022

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“…After normalization, the series of curves were globally fitted to either a homozipper or heteropolymer Ising model using the PyFolding package 27 . Both the homozipper and heteropolymer Ising models were constructed as previously described 28,30 .…”

Section: Methodsmentioning

confidence: 99%

Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold

Perez-Riba

Komives

Main

et al. 2019

Sci Rep

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The simple topology and modular architecture of tandem-repeat proteins such as tetratricopeptide repeats (TPRs) and ankyrin repeats makes them straightforward to dissect and redesign. Repeat-protein stability can be manipulated in a predictable way using site-specific mutations. Here we explore a different type of modification - loop insertion - that will enable a simple route to functionalisation of this versatile scaffold. We previously showed that a single loop insertion has a dramatically different effect on stability depending on its location in the repeat array. Here we dissect this effect by a combination of multiple and alternated loop insertions to understand the origins of the context-dependent loss in stability. We find that the scaffold is remarkably robust in that its overall structure is maintained. However, adjacent repeats are now only weakly coupled, and consequently the increase in solvent protection, and thus stability, with increasing repeat number that defines the tandem-repeat protein class is lost. Our results also provide us with a rulebook with which we can apply these principles to the design of artificial repeat proteins with precisely tuned folding landscapes and functional capabilities, thereby paving the way for their exploitation as a versatile and truly modular platform in synthetic biology.

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“…After normalization, all of the curves were globally fitted to a heteropolymer Ising model using the PyFolding package (38). We constructed the 1D heteropolymer Ising model using a matrix formulation as previously described (12).…”

Section: Methodsmentioning

confidence: 99%

Context-Dependent Energetics of Loop Extensions in a Family of Tandem-Repeat Proteins

Perez-Riba

Lowe

Main

et al. 2018

Biophysical Journal

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Consensus-designed tetratricopeptide repeat proteins are highly stable, modular proteins that are strikingly amenable to rational engineering. They therefore have tremendous potential as building blocks for biomaterials and biomedicine. Here, we explore the possibility of extending the loops between repeats to enable further diversification, and we investigate how this modification affects stability and folding cooperativity. We find that extending a single loop by up to 25 residues does not disrupt the overall protein structure, but, strikingly, the effect on stability is highly context-dependent: in a two-repeat array, destabilization is relatively small and can be accounted for purely in entropic terms, whereas extending a loop in the middle of a large array is much more costly because of weakening of the interaction between the repeats. Our findings provide important and, to our knowledge, new insights that increase our understanding of the structure, folding, and function of natural repeat proteins and the design of artificial repeat proteins in biotechnology.

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PyFolding: Open-Source Graphing, Simulation, and Analysis of the Biophysical Properties of Proteins

Cited by 7 publications

References 47 publications

Evolutionary adaptation of the protein folding pathway for secretability

Evolutionary adaptation of the protein folding pathway for secretability

Decoupling a tandem-repeat protein: Impact of multiple loop insertions on a modular scaffold

Context-Dependent Energetics of Loop Extensions in a Family of Tandem-Repeat Proteins

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