1
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Zhang N, Sood D, Guo SC, Chen N, Antoszewski A, Marianchuk T, Chavan A, Dey S, Xiao Y, Hong L, Peng X, Baxa M, Partch C, Wang LP, Sosnick TR, Dinner AR, LiWang A. Temperature-Dependent Fold-Switching Mechanism of the Circadian Clock Protein KaiB. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.594594. [PMID: 38826295 PMCID: PMC11142059 DOI: 10.1101/2024.05.21.594594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The oscillator of the cyanobacterial circadian clock relies on the ability of the KaiB protein to switch reversibly between a stable ground-state fold (gsKaiB) and an unstable fold-switched fold (fsKaiB). Rare fold-switching events by KaiB provide a critical delay in the negative feedback loop of this post-translational oscillator. In this study, we experimentally and computationally investigate the temperature dependence of fold switching and its mechanism. We demonstrate that the stability of gsKaiB increases with temperature compared to fsKaiB and that the Q10 value for the gsKaiB → fsKaiB transition is nearly three times smaller than that for the reverse transition. Simulations and native-state hydrogen-deuterium exchange NMR experiments suggest that fold switching can involve both subglobally and near-globally unfolded intermediates. The simulations predict that the transition state for fold switching coincides with isomerization of conserved prolines in the most rapidly exchanging region, and we confirm experimentally that proline isomerization is a rate-limiting step for fold switching. We explore the implications of our results for temperature compensation, a hallmark of circadian clocks, through a kinetic model.
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2
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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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3
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Zaman AB, Inan TT, De Jong K, Shehu A. Adaptive Stochastic Optimization to Improve Protein Conformation Sampling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:2759-2771. [PMID: 34882562 DOI: 10.1109/tcbb.2021.3134103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We have long known that characterizing protein structures structure is key to understanding protein function. Computational approaches have largely addressed a narrow formulation of the problem, seeking to compute one native structure from an amino-acid sequence. Now AlphaFold2 is shown to be able to reveal a high-quality native structure for many proteins. However, researchers over the years have argued for broadening our view to account for the multiplicity of native structures. We now know that many protein molecules switch between different structures to regulate interactions with molecular partners in the cell. Elucidating such structures de novo is exceptionally difficult, as it requires exploration of possibly a very large structure space in search of competing, near-optimal structures. Here we report on a novel stochastic optimization method capable of revealing very different structures for a given protein from knowledge of its amino-acid sequence. The method leverages evolutionary search techniques and adapts its exploration of the search space to balance between exploration and exploitation in the presence of a computational budget. In addition to demonstrating the utility of this method for identifying multiple native structures, we additionally provide a benchmark dataset for researchers to continue work on this problem.
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4
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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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5
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Ruan B, He Y, Chen Y, Choi EJ, Chen Y, Motabar D, Solomon T, Simmerman R, Kauffman T, Gallagher DT, Orban J, Bryan PN. Design and characterization of a protein fold switching network. Nat Commun 2023; 14:431. [PMID: 36702827 PMCID: PMC9879998 DOI: 10.1038/s41467-023-36065-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/13/2023] [Indexed: 01/27/2023] Open
Abstract
To better understand how amino acid sequence encodes protein structure, we engineered mutational pathways that connect three common folds (3α, β-grasp, and α/β-plait). The structures of proteins at high sequence-identity intersections in the pathways (nodes) were determined using NMR spectroscopy and analyzed for stability and function. To generate nodes, the amino acid sequence encoding a smaller fold is embedded in the structure of an ~50% larger fold and a new sequence compatible with two sets of native interactions is designed. This generates protein pairs with a 3α or β-grasp fold in the smaller form but an α/β-plait fold in the larger form. Further, embedding smaller antagonistic folds creates critical states in the larger folds such that single amino acid substitutions can switch both their fold and function. The results help explain the underlying ambiguity in the protein folding code and show that new protein structures can evolve via abrupt fold switching.
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Affiliation(s)
- Biao Ruan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yanan He
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Yingwei Chen
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Eun Jung Choi
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Yihong Chen
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - Dana Motabar
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
- Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Tsega Solomon
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Richard Simmerman
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA
| | - Thomas Kauffman
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - D Travis Gallagher
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
- National Institute of Standards and Technology and the University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
| | - John Orban
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA.
| | - Philip N Bryan
- Potomac Affinity Proteins, 11305 Dunleith Pl, North Potomac, MD, 20878, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD, 20850, USA.
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6
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Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022; 299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein phase separation is thought to be a primary driving force for the formation of membrane-less organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. Among phase-separating (PS) proteins, many have intrinsically disordered regions (IDRs) that are needed for phase separation to occur. Accurate identification of IDRs that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and PS ID sequences. We then used these sequence sets to examine how broadly existing amino acid property scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving protein phase separation. Collectively, our findings provide further insight into the classification of IDRs and the elements involved in protein phase separation.
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Affiliation(s)
- Ayyam Y. Ibrahim
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | | | - John J. Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Loren E. Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA,For correspondence: Steven T. Whitten; Loren E. Hough
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA,For correspondence: Steven T. Whitten; Loren E. Hough
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7
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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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8
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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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9
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Wang Y, Zhao L, Zhou X, Zhang J, Jiang J, Dong H. Global Fold Switching of the RafH Protein: Diverse Structures with a Conserved Pathway. J Phys Chem B 2022; 126:2979-2989. [PMID: 35438983 DOI: 10.1021/acs.jpcb.1c10965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
It is generally believed that a protein's sequence uniquely determines its structure, the basis for a protein to perform biological functions. However, as a representative metamorphic protein, RfaH can be encoded by a single amino acid sequence into two distinct native state structures. Its C-terminal domain (CTD) either takes an all-α-helical configuration to pack tightly with its N-terminal domain (NTD), or the CTD disassociates from the NTD, transforms into an all-β-barrel fold, and further attaches to the ribosome, leaving the NTD exposed to bind RNA polymerases. Therefore, the RfaH protein couples transcription and translation processes. Although previous studies have provided a preliminary understanding of its function, the full course of the conformational change of RfaH-CTD at the atomic level is elusive. We used teDA2, a feature space-based enhanced sampling protocol, to explore the transformation of RfaH-CTD. We found that it undergoes a large-scale structural rearrangement, with characteristic spectra as the fingerprint, and a global unfolding transition with a tighter and energetically moderate molten globule-like nucleus formed in between. The formation of this nucleus limits the possible intermediate conformations, facilitates the formation of secondary and tertiary structures, and thus ensures the efficiency of transformation. The key features along the transition path disclosed from this work are likely associated with the evolution of RfaH, such that encoding a single sequence into multiple folds with distinct biological functions is energetically unhindered.
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Affiliation(s)
- Yiqiao Wang
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China.,School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Luyuan Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Xuejie Zhou
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China
| | - Jian Zhang
- School of Physics, National Laboratory of Solid State Microstructure, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China.,Institute for Brain Sciences, Nanjing University, Nanjing 210023, China
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, Collaborative Innovation Center of Chemistry for Energy Materials, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, Anhui, China
| | - Hao Dong
- Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China.,Institute for Brain Sciences, Nanjing University, Nanjing 210023, China.,State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210023, China.,Engineering Research Center of Protein and Peptide Medicine of Ministry of Education, Nanjing University, Nanjing 210023, China
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10
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Affiliation(s)
- Andy LiWang
- University of California, Merced, California, USA
| | - Lauren L Porter
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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11
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Das M, Chen N, LiWang A, Wang LP. Identification and characterization of metamorphic proteins: Current and future perspectives. Biopolymers 2021; 112:e23473. [PMID: 34528703 DOI: 10.1002/bip.23473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/06/2022]
Abstract
Proteins that can reversibly alternate between distinctly different folds under native conditions are described as being metamorphic. The "metamorphome" is the collection of all metamorphic proteins in the proteome, but it remains unknown the extent to which the proteome is populated by this class of proteins. We propose that uncovering the metamorphome will require a synergy of computational screening of protein sequences to identify potential metamorphic behavior and validation through experimental techniques. This perspective discusses computational and experimental approaches that are currently used to predict and characterize metamorphic proteins as well as the need for developing improved methodologies. Since metamorphic proteins act as molecular switches, understanding their properties and behavior could lead to novel applications of these proteins as sensors in biological or environmental contexts.
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Affiliation(s)
- Madhurima Das
- School of Natural Sciences, University of California, Merced, California, USA
| | - Nanhao Chen
- Department of Chemistry, University of California, Davis, California, USA
| | - Andy LiWang
- School of Natural Sciences, University of California, Merced, California, USA.,Department of Chemistry and Biochemistry, University of California, Merced, California, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, California, USA.,Health Sciences Research Institute, University of California, Merced, California, USA.,Center for Circadian Biology, University of California, San Diego, California, USA
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California, USA
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12
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Mishra S, Looger LL, Porter LL. A sequence-based method for predicting extant fold switchers that undergo α-helix ↔ β-strand transitions. Biopolymers 2021; 112:e23471. [PMID: 34498740 PMCID: PMC8545793 DOI: 10.1002/bip.23471] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 12/21/2022]
Abstract
Extant fold‐switching proteins remodel their secondary structures and change their functions in response to cellular stimuli, regulating biological processes and affecting human health. Despite their biological importance, these proteins remain understudied. Predictive methods are needed to expedite the process of discovering and characterizing more of these shapeshifting proteins. Most 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: (a) α‐helix ↔ β‐strand prediction discrepancies from JPred4 are a robust predictor of fold switching, and (b) the fold‐switching regions (FSRs) of some extant fold switchers have different secondary structure propensities when expressed by themselves (isolated FSRs) than when expressed within the context of their parent protein (contextualized FSRs). Combining these two observations, we ran JPred4 on 99‐fold‐switching proteins and found strong correspondence between predicted and experimentally observed α‐helix ↔ β‐strand discrepancies. 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 predicted α‐helix ↔ β‐strand discrepancies. Combining these discrepancies with the overall percentage of predicted secondary structure, we developed a classifier to identify extant fold switchers (Matthews correlation coefficient of .71). Although this classifier had a high false‐negative rate (7/17), its false‐positive rate was very low (2/136), suggesting that it can be used to predict a subset of extant fold switchers from a multitude of available genomic sequences.
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Affiliation(s)
- Soumya Mishra
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.,Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA
| | - Lauren L Porter
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.,National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
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13
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Madhurima K, Nandi B, Sekhar A. Metamorphic proteins: the Janus proteins of structural biology. Open Biol 2021; 11:210012. [PMID: 33878950 PMCID: PMC8059507 DOI: 10.1098/rsob.210012] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The structural paradigm that the sequence of a protein encodes for a unique three-dimensional native fold does not acknowledge the intrinsic plasticity encapsulated in conformational free energy landscapes. Metamorphic proteins are a recently discovered class of biomolecules that illustrate this plasticity by folding into at least two distinct native state structures of comparable stability in the absence of ligands or cofactors to facilitate fold-switching. The expanding list of metamorphic proteins clearly shows that these proteins are not mere aberrations in protein evolution, but may have actually been a consequence of distinctive patterns in selection pressure such as those found in virus–host co-evolution. In this review, we describe the structure–function relationships observed in well-studied metamorphic protein systems, with specific focus on how functional residues are sequestered or exposed in the two folds of the protein. We also discuss the implications of metamorphosis for protein evolution and the efforts that are underway to predict metamorphic systems from sequence properties alone.
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Affiliation(s)
- Kulkarni Madhurima
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Bodhisatwa Nandi
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Ashok Sekhar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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14
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LiWang PJ, Wang LP, LiWang A. Resurrected Ancestors Reveal Origins of Metamorphism in XCL1. Trends Biochem Sci 2021; 46:433-434. [PMID: 33752957 DOI: 10.1016/j.tibs.2021.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
In a recent study, Dishman et al. resurrected ancestors of the metamorphic chemokine, XCL1, inferred through phylogenetics, and found that metamorphism arose in the XCL1 lineage ~150 million years ago. A zigzagging evolutionary path suggests that the metamorphic properties are adaptive and reveals three design principles that could be used for technological applications.
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Affiliation(s)
- Patricia J LiWang
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA.
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | - Andy LiWang
- Department of Chemistry and Biochemistry, University of California, Merced, CA 95343, USA.
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15
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Seifi B, Aina A, Wallin S. Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH. Proteins 2020; 89:289-300. [PMID: 32996201 DOI: 10.1002/prot.26014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 08/31/2020] [Indexed: 01/08/2023]
Abstract
RfaH is a compact two-domain bacterial transcription factor that functions both as a regulator of transcription and an enhancer of translation. Underpinning the dual functional roles of RfaH is a partial but dramatic fold switch, which completely transforms the ~50-amino acid C-terminal domain (CTD) from an all-α state to an all-β state. The fold switch of the CTD occurs when RfaH binds to RNA polymerase (RNAP), however, the details of how this structural transformation is triggered is not well understood. Here we use all-atom Monte Carlo simulations to characterize structural fluctuations and mechanical stability properties of the full-length RfaH and the CTD as an isolated fragment. In agreement with experiments, we find that interdomain contacts are crucial for maintaining a stable, all-α CTD in free RfaH. To probe mechanical properties, we use pulling simulations to measure the work required to inflict local deformations at different positions along the chain. The resulting mechanical stability profile reveals that free RfaH can be divided into a "rigid" part and a "soft" part, with a boundary that nearly coincides with the boundary between the two domains. We discuss the potential role of this feature for how fold switching may be triggered by interaction with RNAP.
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Affiliation(s)
- Bahman Seifi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Adekunle Aina
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
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