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Schafer JW, Chakravarty D, Chen EA, Porter LL. Sequence clustering confounds AlphaFold2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574434. [PMID: 38313252 PMCID: PMC10836070 DOI: 10.1101/2024.01.05.574434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Though typically associated with a single folded state, some globular proteins remodel their secondary and/or tertiary structures in response to cellular stimuli. AlphaFold21 (AF2) readily generates one dominant protein structure for these fold-switching (a.k.a. metamorphic) proteins2, but it often fails to predict their alternative experimentally observed structures3,4. Wayment-Steele, et al. steered AF2 to predict alternative structures of a few metamorphic proteins using a method they call AF-cluster5. However, their Paper lacks some essential controls needed to assess AF-cluster's reliability. We find that these controls show AF-cluster to be a poor predictor of metamorphic proteins. First, closer examination of the Paper's results reveals that random sequence sampling outperforms sequence clustering, challenging the claim that AF-cluster works by "deconvolving conflicting sets of couplings." Further, we observe that AF-cluster mistakes some single-folding KaiB homologs for fold switchers, a critical flaw bound to mislead users. Finally, proper error analysis reveals that AF-cluster predicts many correct structures with low confidence and some experimentally unobserved conformations with confidences similar to experimentally observed ones. For these reasons, we suggest using ColabFold6-based random sequence sampling7-augmented by other predictive approaches-as a more accurate and less computationally intense alternative to AF-cluster.
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Affiliation(s)
- Joseph W. Schafer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Devlina Chakravarty
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Ethan A. Chen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892
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Porter LL. Fluid protein fold space and its implications. Bioessays 2023; 45:e2300057. [PMID: 37431685 PMCID: PMC10529699 DOI: 10.1002/bies.202300057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Fold-switching proteins, which remodel their secondary and tertiary structures in response to cellular stimuli, suggest a new view of protein fold space. For decades, experimental evidence has indicated that protein fold space is discrete: dissimilar folds are encoded by dissimilar amino acid sequences. Challenging this assumption, fold-switching proteins interconnect discrete groups of dissimilar protein folds, making protein fold space fluid. Three recent observations support the concept of fluid fold space: (1) some amino acid sequences interconvert between folds with distinct secondary structures, (2) some naturally occurring sequences have switched folds by stepwise mutation, and (3) fold switching is evolutionarily selected and likely confers advantage. These observations indicate that minor amino acid sequence modifications can transform protein structure and function. Consequently, proteomic structural and functional diversity may be expanded by alternative splicing, small nucleotide polymorphisms, post-translational modifications, and modified translation rates.
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Affiliation(s)
- Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
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Chakravarty D, Schafer JW, Porter LL. Distinguishing features of fold-switching proteins. Protein Sci 2023; 32:e4596. [PMID: 36782353 PMCID: PMC9951197 DOI: 10.1002/pro.4596] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/30/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023]
Abstract
Though many folded proteins assume one stable structure that performs one function, a small-but-increasing number remodel their secondary and tertiary structures and change their functions in response to cellular stimuli. These fold-switching proteins regulate biological processes and are associated with autoimmune dysfunction, severe acute respiratory syndrome coronavirus-2 infection, and more. Despite their biological importance, it is difficult to computationally predict fold switching. With the aim of advancing computational prediction and experimental characterization of fold switchers, this review discusses several features that distinguish fold-switching proteins from their single-fold and intrinsically disordered counterparts. First, the isolated structures of fold switchers are less stable and more heterogeneous than single folders but more stable and less heterogeneous than intrinsically disordered proteins (IDPs). Second, the sequences of single fold, fold switching, and intrinsically disordered proteins can evolve at distinct rates. Third, proteins from these three classes are best predicted using different computational techniques. Finally, late-breaking results suggest that single folders, fold switchers, and IDPs have distinct patterns of residue-residue coevolution. The review closes by discussing high-throughput and medium-throughput experimental approaches that might be used to identify new fold-switching proteins.
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Affiliation(s)
- Devlina Chakravarty
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Joseph W. Schafer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
| | - Lauren L. Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMarylandUSA
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of HealthBethesdaMarylandUSA
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Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein. Comput Struct Biotechnol J 2022; 20:5824-5837. [PMID: 36382197 PMCID: PMC9630627 DOI: 10.1016/j.csbj.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/28/2022] Open
Abstract
Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as their sequences encode two alternative folds, which reversibly interconvert within biologically relevant timescales to trigger different cellular responses. Once considered a rare aberration, metamorphism may be common among proteins that must respond to rapidly changing environments, exemplified by NusG-like proteins, the only transcription factors present in every domain of life. RfaH, a specialized paralog of bacterial NusG, undergoes an all-α to all-β domain switch to activate expression of virulence and conjugation genes in many animal and plant pathogens and is the quintessential example of a metamorphic protein. The dramatic nature of RfaH structural transformation and the richness of its evolutionary history makes for an excellent model for studying how metamorphic proteins switch folds. Here, we summarize the structural and functional evidence that sparked the discovery of RfaH as a metamorphic protein, the experimental and computational approaches that enabled the description of the molecular mechanism and refolding pathways of its structural interconversion, and the ongoing efforts to find signatures and general properties to ultimately describe the protein metamorphome.
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Affiliation(s)
- Irina Artsimovitch
- Department of Microbiology and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - César A. Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
- ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Porter LL, Kim AK, Rimal S, Looger LL, Majumdar A, Mensh BD, Starich MR, Strub MP. Many dissimilar NusG protein domains switch between α-helix and β-sheet folds. Nat Commun 2022; 13:3802. [PMID: 35778397 PMCID: PMC9247905 DOI: 10.1038/s41467-022-31532-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/17/2022] [Indexed: 11/16/2022] Open
Abstract
Folded proteins are assumed to be built upon fixed scaffolds of secondary structure, α-helices and β-sheets. Experimentally determined structures of >58,000 non-redundant proteins support this assumption, though it has recently been challenged by ~100 fold-switching proteins. Though ostensibly rare, these proteins raise the question of how many uncharacterized proteins have shapeshifting-rather than fixed-secondary structures. Here, we use a comparative sequence-based approach to predict fold switching in the universally conserved NusG transcription factor family, one member of which has a 50-residue regulatory subunit experimentally shown to switch between α-helical and β-sheet folds. Our approach predicts that 24% of sequences in this family undergo similar α-helix ⇌ β-sheet transitions. While these predictions cannot be reproduced by other state-of-the-art computational methods, they are confirmed by circular dichroism and nuclear magnetic resonance spectroscopy for 10 out of 10 sequence-diverse variants. This work suggests that fold switching may be a pervasive mechanism of transcriptional regulation in all kingdoms of life.
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Affiliation(s)
- Lauren L Porter
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA.
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Allen K Kim
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Swechha Rimal
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Ananya Majumdar
- The Johns Hopkins University Biomolecular NMR Center, The Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Brett D Mensh
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Mary R Starich
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Marie-Paule Strub
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center, National Institutes of Health, Bethesda, MD, 20892, USA
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Chakravarty D, Porter LL. AlphaFold2
fails to predict protein fold switching. Protein Sci 2022; 31:e4353. [DOI: 10.1002/pro.4353] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 12/15/2022]
Affiliation(s)
- Devlina Chakravarty
- National Library of Medicine, National Center for Biotechnology Information National Institutes of Health Bethesda Maryland USA
| | - Lauren L. Porter
- National Library of Medicine, National Center for Biotechnology Information National Institutes of Health Bethesda Maryland USA
- National Heart, Lung, and Blood Institute, Biochemistry and Biophysics Center National Institutes of Health Bethesda Maryland USA
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Abstract
It has been a long-standing conviction that a protein's native fold is selected from a vast number of conformers by the optimal constellation of enthalpically favorable interactions. In marked contrast, this Perspective introduces a different mechanism, one that emphasizes conformational entropy as the principal organizer in protein folding while proposing that the conventional view is incomplete. This mechanism stems from the realization that hydrogen bond satisfaction is a thermodynamic necessity. In particular, a backbone hydrogen bond may add little to the stability of the native state, but a completely unsatisfied backbone hydrogen bond would be dramatically destabilizing, shifting the U(nfolded) ⇌ N(ative) equilibrium far to the left. If even a single backbone polar group is satisfied by solvent when unfolded but buried and unsatisfied when folded, that energy penalty alone, approximately +5 kcal/mol, would rival almost the entire free energy of protein stabilization, typically between -5 and -15 kcal/mol under physiological conditions. Consequently, upon folding, buried backbone polar groups must form hydrogen bonds, and they do so by assembling scaffolds of α-helices and/or strands of β-sheet, the only conformers in which, with rare exception, hydrogen bond donors and acceptors are exactly balanced. In addition, only a few thousand viable scaffold topologies are possible for a typical protein domain. This thermodynamic imperative winnows the folding population by culling conformers with unsatisfied hydrogen bonds, thereby reducing the entropy cost of folding. Importantly, conformational restrictions imposed by backbone···backbone hydrogen bonding in the scaffold are sequence-independent, enabling mutation─and thus evolution─without sacrificing the structure.
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Affiliation(s)
- George D Rose
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218-2683, United States
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