Functional and Regulatory Roles of Fold-Switching Proteins

Kim, Allen K.; Porter, Lauren L.

doi:10.1016/j.str.2020.10.006

Cited by 66 publications

(65 citation statements)

References 79 publications

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“…Nevertheless, increasing evidence suggests that these proteins may be more abundant in nature than previously thought 1 . Fold switching impacts protein function 5 and is associated with a number of diseases 2, 3, 30 . Thus, it would be useful to have a bioinformatic algorithm that identifies more fold switchers from their sequences.…”

Section: Discussionmentioning

confidence: 99%

“…Known instances of these environmentally responsive shapeshifters perform over 30 diverse functions, occur in all domains of life, and are associated with diseases such as cancer 2 , autoimmune disorders 3 , and malaria 4 . Furthermore, increasing evidence suggests that extant fold switchers are central to the regulation of biological processes 5 such as cyanobacterial circadian rhythms 6 and transcription/translation of bacterial virulence genes 7 .…”

Section: Introductionmentioning

confidence: 99%

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A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions

Mishra

Looger

Porter

2021

Preprint

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Extant fold-switching proteins remodel their secondary structures and change their functions in response to cellular stimuli, regulating biological processes and affecting human health. In spite of their biological importance, these proteins remain understudied. Few representative examples of fold switchers are available in the Protein Data Bank, and they are difficult to predict. In fact, all 96 experimentally validated examples of extant fold switchers were stumbled upon by chance. Thus, predictive methods are needed to expedite the process of discovering and characterizing more of these shapeshifting proteins. Previous approaches require a solved structure or all-atom simulations, greatly constraining their use. Here, we propose a high-throughput sequence-based method for predicting extant fold switchers that transition from α-helix in one conformation to β-strand in the other. This method leverages two previous observations: (1) α-helix <-> β-strand prediction discrepancies from JPred4 are a robust predictor of fold switching, and (2) the fold-switching regions (FSRs) of some extant fold switchers have different secondary structure propensities when expressed in isolation (isolated FSRs) than when expressed within the context of their parent protein (contextualized FSRs). Combining these two observations, we ran JPred4 on the sequences of isolated and contextualized FSRs from 14 known extant fold switchers and found α-helix <->β-strand prediction discrepancies in every case. To test the overall robustness of this finding, we randomly selected regions of proteins not expected to switch folds (single-fold proteins) and found significantly fewer α-helix <-> β-strand prediction discrepancies (p < 4.2*10−20, Kolmogorov-Smirnov test). Combining these discrepancies with the overall percentage of predicted secondary structure, we developed a classifier that often robustly identifies extant fold switchers (Matthews Correlation Coefficient of 0.70). Although this classifier had a high false negative rate (6/14), its false positive rate was very low (1/211), suggesting that it can be used to predict a subset of extant fold switchers from billions of available genomic sequences.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions

Mishra

Looger

Porter

2021

Preprint

Self Cite

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“…XCL1 has the additional feature of being metamorphic, i.e., switching between multiple different three-dimensional structures reversibly in solution [ 15 ]. Interest in metamorphic proteins’ biological and therapeutic utility has grown in recent years [ 9 , 10 , 11 , 28 ]. XCL1 can provide unique inspiration for the design of non-toxic, switchable antifungals for which the development of resistance is minimized.…”

Section: Discussionmentioning

confidence: 99%

“…Recent work has shown that these proteins, called metamorphic proteins, may be more common than initially expected [ 8 , 9 ]. Interest in the biological relevance of metamorphic protein folding is growing, and efforts to understand and harness protein metamorphosis for therapeutic benefit are beginning to mount [ 10 , 11 , 12 ].…”

Section: Introductionmentioning

confidence: 99%

Metamorphic Protein Folding Encodes Multiple Anti-Candida Mechanisms in XCL1

Dishman

Volkman

et al. 2021

Pathogens

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Candida species cause serious infections requiring prolonged and sometimes toxic therapy. Antimicrobial proteins, such as chemokines, hold great interest as potential additions to the small number of available antifungal drugs. Metamorphic proteins reversibly switch between multiple different folded structures. XCL1 is a metamorphic, antimicrobial chemokine that interconverts between the conserved chemokine fold (an α–β monomer) and an alternate fold (an all-β dimer). Previous work has shown that human XCL1 kills C. albicans but has not assessed whether one or both XCL1 folds perform this activity. Here, we use structurally locked engineered XCL1 variants and Candida killing assays, adenylate kinase release assays, and propidium iodide uptake assays to demonstrate that both XCL1 folds kill Candida, but they do so via different mechanisms. Our results suggest that the alternate fold kills via membrane disruption, consistent with previous work, and the chemokine fold does not. XCL1 fold-switching thus provides a mechanism to regulate the XCL1 mode of antifungal killing, which could protect surrounding tissue from damage associated with fungal membrane disruption and could allow XCL1 to overcome candidal resistance by switching folds. This work provides inspiration for the future design of switchable, multifunctional antifungal therapeutics.

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“…Their large, sometimes reversible, conformational changes challenge the long-held paradigm that globular proteins have a single fold specified by their amino acid sequences ( 2 ). Fold switchers regulate diverse biological processes ( 3 ) and are associated with human diseases such as cancer ( 4 ), malaria ( 5 ), and COVID-19 ( 6 ).…”

Section: Main Textmentioning

confidence: 99%

Many dissimilar protein domains switch between α-helix and β-sheet folds

Porter

et al. 2021

Preprint

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Fold-switching proteins challenge the one-sequence-one-structure paradigm by adopting multiple stable folds. Nevertheless, it is uncertain whether fold switchers are naturally pervasive or rare exceptions to the well-established rule. To address this question, we developed a predictive method and applied it to the NusG superfamily of >15,000 transcription factors. We predicted that a substantial population (25%) of the proteins in this family switch folds. Circular dichroism and nuclear magnetic resonance spectroscopies of 10 sequence-diverse variants confirmed our predictions. Thus, we leveraged family-wide predictions to determine both conserved contacts and taxonomic distributions of fold-switching proteins. Our results indicate that fold switching is pervasive in the NusG superfamily and that the single-fold paradigm significantly biases structure-prediction strategies.

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Functional and Regulatory Roles of Fold-Switching Proteins

Cited by 66 publications

References 79 publications

A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions

A sequence-based method for predicting extant fold switchers that undergo α-helix <-> β-strand transitions

Metamorphic Protein Folding Encodes Multiple Anti-Candida Mechanisms in XCL1

Many dissimilar protein domains switch between α-helix and β-sheet folds

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