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Porter LL, Artsimovitch I, Ramírez-Sarmiento CA. Metamorphic proteins and how to find them. Curr Opin Struct Biol 2024; 86:102807. [PMID: 38537533 DOI: 10.1016/j.sbi.2024.102807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
In the last two decades, our existing notion that most foldable proteins have a unique native state has been challenged by the discovery of metamorphic proteins, which reversibly interconvert between multiple, sometimes highly dissimilar, native states. As the number of known metamorphic proteins increases, several computational and experimental strategies have emerged for gaining insights about their refolding processes and identifying unknown metamorphic proteins amongst the known proteome. In this review, we describe the current advances in biophysically and functionally ascertaining the structural interconversions of metamorphic proteins and how coevolution can be harnessed to identify novel metamorphic proteins from sequence information. We also discuss the challenges and ongoing efforts in using artificial intelligence-based protein structure prediction methods to discover metamorphic proteins and predict their corresponding three-dimensional structures.
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Affiliation(s)
- Lauren L Porter
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Irina Artsimovitch
- Department of Microbiology and Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA.
| | - César A Ramírez-Sarmiento
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; ANID, Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago 833150, Chile.
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2
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Shibata M, Lin X, Onuchic JN, Yura K, Cheng RR. Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies. Biophys J 2024; 123:681-692. [PMID: 38291753 PMCID: PMC10995415 DOI: 10.1016/j.bpj.2024.01.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/31/2023] [Accepted: 01/24/2024] [Indexed: 02/01/2024] Open
Abstract
DNA-binding response regulators (DBRRs) are a broad class of proteins that operate in tandem with their partner kinase proteins to form two-component signal transduction systems in bacteria. Typical DBRRs are composed of two domains where the conserved N-terminal domain accepts transduced signals and the evolutionarily diverse C-terminal domain binds to DNA. These domains are assumed to be functionally independent, and hence recombination of the two domains should yield novel DBRRs of arbitrary input/output response, which can be used as biosensors. This idea has been proved to be successful in some cases; yet, the error rate is not trivial. Improvement of the success rate of this technique requires a deeper understanding of the linker-domain and inter-domain residue interactions, which have not yet been thoroughly examined. Here, we studied residue coevolution of DBRRs of the two main subfamilies (OmpR and NarL) using large collections of bacterial amino acid sequences to extensively investigate the evolutionary signatures of linker-domain and inter-domain residue interactions. Coevolutionary analysis uncovered evolutionarily selected linker-domain and inter-domain residue interactions of known experimental structures, as well as previously unknown inter-domain residue interactions. We examined the possibility of these inter-domain residue interactions as contacts that stabilize an inactive conformation of the DBRR where DNA binding is inhibited for both subfamilies. The newly gained insights on linker-domain/inter-domain residue interactions and shared inactivation mechanisms improve the understanding of the functional mechanism of DBRRs, providing clues to efficiently create functional DBRR-based biosensors. Additionally, we show the feasibility of applying coevolutionary landscape models to predict the functionality of domain-swapped DBRR proteins. The presented result demonstrates that sequence information can be used to filter out bioengineered DBRR proteins that are predicted to be nonfunctional due to a high negative predictive value.
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Affiliation(s)
- Mayu Shibata
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, Japan; Center for Theoretical Biological Physics, Rice University, Houston Texas
| | - Xingcheng Lin
- Department of Physics, North Carolina State University, Raleigh, North Carolina; Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston Texas; Department of Physics and Astronomy, Chemistry, and Biosciences, Rice University, Houston, Texas
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, Bunkyo, Tokyo, Japan; Center for Interdisciplinary AI and Data Science, Ochanomizu University, Bunkyo, Tokyo, Japan; Graduate School of Advanced Science and Engineering, Waseda University, Shinjuku, Tokyo, Japan
| | - Ryan R Cheng
- Department of Chemistry, University of Kentucky, Lexington, Kentucky.
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Wayment-Steele HK, Ojoawo A, Otten R, Apitz JM, Pitsawong W, Hömberger M, Ovchinnikov S, Colwell L, Kern D. Predicting multiple conformations via sequence clustering and AlphaFold2. Nature 2024; 625:832-839. [PMID: 37956700 PMCID: PMC10808063 DOI: 10.1038/s41586-023-06832-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023]
Abstract
AlphaFold2 (ref. 1) has revolutionized structural biology by accurately predicting single structures of proteins. However, a protein's biological function often depends on multiple conformational substates2, and disease-causing point mutations often cause population changes within these substates3,4. We demonstrate that clustering a multiple-sequence alignment by sequence similarity enables AlphaFold2 to sample alternative states of known metamorphic proteins with high confidence. Using this method, named AF-Cluster, we investigated the evolutionary distribution of predicted structures for the metamorphic protein KaiB5 and found that predictions of both conformations were distributed in clusters across the KaiB family. We used nuclear magnetic resonance spectroscopy to confirm an AF-Cluster prediction: a cyanobacteria KaiB variant is stabilized in the opposite state compared with the more widely studied variant. To test AF-Cluster's sensitivity to point mutations, we designed and experimentally verified a set of three mutations predicted to flip KaiB from Rhodobacter sphaeroides from the ground to the fold-switched state. Finally, screening for alternative states in protein families without known fold switching identified a putative alternative state for the oxidoreductase Mpt53 in Mycobacterium tuberculosis. Further development of such bioinformatic methods in tandem with experiments will probably have a considerable impact on predicting protein energy landscapes, essential for illuminating biological function.
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Affiliation(s)
- Hannah K Wayment-Steele
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Adedolapo Ojoawo
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Renee Otten
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | - Julia M Apitz
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
| | - Warintra Pitsawong
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Biomolecular Discovery, Relay Therapeutics, Cambridge, MA, USA
| | - Marc Hömberger
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA
- Treeline Biosciences, Watertown, MA, USA
| | | | - Lucy Colwell
- Google Research, Cambridge, MA, USA
- Cambridge University, Cambridge, UK
| | - Dorothee Kern
- Department of Biochemistry, Brandeis University and Howard Hughes Medical Institute, Waltham, MA, USA.
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Abstract
Although most globular proteins fold into a single stable structure, an increasing number have been shown to remodel their secondary and tertiary structures in response to cellular stimuli. State-of-the-art algorithms predict that these fold-switching proteins adopt only one stable structure, missing their functionally critical alternative folds. Why these algorithms predict a single fold is unclear, but all of them infer protein structure from coevolved amino acid pairs. Here, we hypothesize that coevolutionary signatures are being missed. Suspecting that single-fold variants could be masking these signatures, we developed an approach, called Alternative Contact Enhancement (ACE), to search both highly diverse protein superfamilies-composed of single-fold and fold-switching variants-and protein subfamilies with more fold-switching variants. ACE successfully revealed coevolution of amino acid pairs uniquely corresponding to both conformations of 56/56 fold-switching proteins from distinct families. Then, we used ACE-derived contacts to (1) predict two experimentally consistent conformations of a candidate protein with unsolved structure and (2) develop a blind prediction pipeline for fold-switching proteins. The discovery of widespread dual-fold coevolution indicates that fold-switching sequences have been preserved by natural selection, implying that their functionalities provide evolutionary advantage and paving the way for predictions of diverse protein structures from single sequences.
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Affiliation(s)
- Joseph W Schafer
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, 20894, USA
| | - 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.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Krishnamohan A, Hamilton GL, Goutam R, Sanabria H, Morcos F. Coevolution and smFRET Enhances Conformation Sampling and FRET Experimental Design in Tandem PDZ1-2 Proteins. J Phys Chem B 2023; 127:884-898. [PMID: 36693159 PMCID: PMC9900596 DOI: 10.1021/acs.jpcb.2c06720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The structural flexibility of proteins is crucial for their functions. Many experimental and computational approaches can probe protein dynamics across a range of time and length-scales. Integrative approaches synthesize the complementary outputs of these techniques and provide a comprehensive view of the dynamic conformational space of proteins, including the functionally relevant limiting conformational states and transition pathways between them. Here, we introduce an integrative paradigm to model the conformational states of multidomain proteins. As a model system, we use the first two tandem PDZ domains of postsynaptic density protein 95. First, we utilize available sequence information collected from genomic databases to identify potential amino acid interactions in the PDZ1-2 tandem that underlie modeling of the functionally relevant conformations maintained through evolution. This was accomplished through combination of coarse-grained structural modeling with outputs from direct coupling analysis measuring amino acid coevolution, a hybrid approach called SBM+DCA. We recapitulated five distinct, experimentally derived PDZ1-2 tandem conformations. In addition, SBM+DCA unveiled an unidentified, twisted conformation of the PDZ1-2 tandem. Finally, we implemented an integrative framework for the design of single-molecule Förster resonance energy transfer (smFRET) experiments incorporating the outputs of SBM+DCA with simulated FRET observables. This resulting FRET network is designed to mutually resolve the predicted limiting state conformations through global analysis. Using simulated FRET observables, we demonstrate that structural modeling with the newly designed FRET network is expected to outperform a previously used empirical FRET network at resolving all states simultaneously. Integrative approaches to experimental design have the potential to provide a new level of detail in characterizing the evolutionarily conserved conformational landscapes of proteins, and thus new insights into functional relevance of protein dynamics in biological function.
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Affiliation(s)
- Aishwarya Krishnamohan
- Departments of Biological Sciences and Bioengineering, University of Texas at Dallas, Richardson, Texas75080, United States
| | - George L Hamilton
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Rajen Goutam
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Hugo Sanabria
- Department of Physics and Astronomy, Clemson University, Clemson, South Carolina29634, United States
| | - Faruck Morcos
- Departments of Biological Sciences and Bioengineering, University of Texas at Dallas, Richardson, Texas75080, United States.,Center for Systems Biology, University of Texas at Dallas, Richardson, Texas75080, United States
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Abstract
Although most globular proteins fold into a single stable structure 1 , an increasing number have been shown to remodel their secondary and tertiary structures in response to cellular stimuli 2 . State-of-the-art algorithms 3-5 predict that these fold-switching proteins assume only one stable structure 6,7 , missing their functionally critical alternative folds. Why these algorithms predict a single fold is unclear, but all of them infer protein structure from coevolved amino acid pairs. Here, we hypothesize that coevolutionary signatures are being missed. Suspecting that over-represented single-fold sequences may be masking these signatures, we developed an approach to search both highly diverse protein superfamilies-composed of single-fold and fold-switching variants-and protein subfamilies with more fold-switching variants. This approach successfully revealed coevolution of amino acid pairs uniquely corresponding to both conformations of 56/58 fold-switching proteins from distinct families. Then, using a set of coevolved amino acid pairs predicted by our approach, we successfully biased AlphaFold2 5 to predict two experimentally consistent conformations of a candidate protein with unsolved structure. The discovery of widespread dual-fold coevolution indicates that fold-switching sequences have been preserved by natural selection, implying that their functionalities provide evolutionary advantage and paving the way for predictions of diverse protein structures from single sequences.
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Affiliation(s)
- Joseph W. Schafer
- National Library of Medicine, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894, USA
| | - 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
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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