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Nandigrami P, Fiser A. Assessing the functional impact of protein binding site definition. Protein Sci 2024; 33:e5026. [PMID: 38757384 PMCID: PMC11099757 DOI: 10.1002/pro.5026] [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: 10/06/2023] [Revised: 05/01/2024] [Accepted: 05/03/2024] [Indexed: 05/18/2024]
Abstract
Many biomedical applications, such as classification of binding specificities or bioengineering, depend on the accurate definition of protein binding interfaces. Depending on the choice of method used, substantially different sets of residues can be classified as belonging to the interface of a protein. A typical approach used to verify these definitions is to mutate residues and measure the impact of these changes on binding. Besides the lack of exhaustive data, this approach also suffers from the fundamental problem that a mutation introduces an unknown amount of alteration into an interface, which potentially alters the binding characteristics of the interface. In this study we explore the impact of alternative binding site definitions on the ability of a protein to recognize its cognate ligand using a pharmacophore approach, which does not affect the interface. The study also shows that methods for protein binding interface predictions should perform above approximately F-score = 0.7 accuracy level to capture the biological function of a protein.
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Affiliation(s)
- Prithviraj Nandigrami
- Departments of Systems and Computational Biology, and BiochemistryAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Andras Fiser
- Departments of Systems and Computational Biology, and BiochemistryAlbert Einstein College of MedicineBronxNew YorkUSA
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2
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Sendker FL, Lo YK, Heimerl T, Bohn S, Persson LJ, Mais CN, Sadowska W, Paczia N, Nußbaum E, Del Carmen Sánchez Olmos M, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA. Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 2024; 628:894-900. [PMID: 38600380 PMCID: PMC11041685 DOI: 10.1038/s41586-024-07287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 03/08/2024] [Indexed: 04/12/2024]
Abstract
Fractals are patterns that are self-similar across multiple length-scales1. Macroscopic fractals are common in nature2-4; however, so far, molecular assembly into fractals is restricted to synthetic systems5-12. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
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Affiliation(s)
- Franziska L Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Yat Kei Lo
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Thomas Heimerl
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Stefan Bohn
- Cryo-EM Platform and Institute of Structural Biology, Helmholtz Munich, Neuherberg, Germany
| | - Louise J Persson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | - Wiktoria Sadowska
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Nicole Paczia
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Eva Nußbaum
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | | | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Organismic Interactions Department, Cluster of Excellence 'Controlling Microbes to Fight Infections', Tübingen University, Tübingen, Germany
| | - Daniel Schindler
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- MaxGENESYS Biofoundry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford, UK
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Gert Bange
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany
- Max Planck Fellow Group Molecular Physiology of Microbes, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan M Schuller
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany.
- Department of Chemistry, Philipps-University Marburg, Marburg, Germany.
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3
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Oliveira-Filho ER, Voiniciuc C, Hanson AD. Adapting enzymes to improve their functionality in plants: why and how. Biochem Soc Trans 2023; 51:1957-1966. [PMID: 37787016 PMCID: PMC10657173 DOI: 10.1042/bst20230532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023]
Abstract
Synthetic biology creates new metabolic processes and improves existing ones using engineered or natural enzymes. These enzymes are often sourced from cells that differ from those in the target plant organ with respect to, e.g. redox potential, effector levels, or proteostasis machinery. Non-native enzymes may thus need to be adapted to work well in their new plant context ('plantized') even if their specificity and kinetics in vitro are adequate. Hence there are two distinct ways in which an enzyme destined for use in plants can require improvement: In catalytic properties such as substrate and product specificity, kcat, and KM; and in general compatibility with the milieu of cells that express the enzyme. Continuous directed evolution systems can deliver both types of improvement and are so far the most broadly effective way to deliver the second type. Accordingly, in this review we provide a short account of continuous evolution methods, emphasizing the yeast OrthoRep system because of its suitability for plant applications. We then cover the down-to-earth and increasingly urgent issues of which enzymes and enzyme properties can - or cannot - be improved in theory, and which in practice are the best to target for crop improvement, i.e. those that are realistically improvable and important enough to warrant deploying continuous directed evolution. We take horticultural crops as examples because of the opportunities they present and to sharpen the focus.
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Affiliation(s)
| | - Cătălin Voiniciuc
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
| | - Andrew D. Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, U.S.A
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Zdrzałek R, Stone C, De la Concepcion JC, Banfield MJ, Bentham AR. Pathways to engineering plant intracellular NLR immune receptors. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102380. [PMID: 37187111 DOI: 10.1016/j.pbi.2023.102380] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023]
Abstract
Factors including climate change and increased global exchange are set to escalate the prevalence of plant diseases, posing an unprecedented threat to global food security and making it more challenging to meet the demands of an ever-growing population. As such, new methods of pathogen control are essential to help with the growing danger of crop losses to plant diseases. The intracellular immune system of plants utilizes nucleotide-binding leucine-rich repeat (NLR) receptors to recognize and activate defense responses to pathogen virulence proteins (effectors) delivered to the host. Engineering the recognition properties of plant NLRs toward pathogen effectors is a genetic solution to plant diseases with high specificity, and it is more sustainable than several current methods for pathogen control that frequently rely on agrochemicals. Here, we highlight the pioneering approaches toward enhancing effector recognition in plant NLRs and discuss the barriers and solutions in engineering the plant intracellular immune system.
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Affiliation(s)
- Rafał Zdrzałek
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Caroline Stone
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Mark J Banfield
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
| | - Adam R Bentham
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.
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5
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Dishman AF, Volkman BF. Metamorphic protein folding as evolutionary adaptation. Trends Biochem Sci 2023; 48:665-672. [PMID: 37270322 PMCID: PMC10526677 DOI: 10.1016/j.tibs.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/12/2023] [Accepted: 05/04/2023] [Indexed: 06/05/2023]
Abstract
Metamorphic proteins switch reversibly between multiple distinct, stable structures, often with different functions. It was previously hypothesized that metamorphic proteins arose as intermediates in the evolution of a new fold - rare and transient exceptions to the 'one sequence, one fold' paradigm. However, as described herein, mounting evidence suggests that metamorphic folding is an adaptive feature, preserved and optimized over evolutionary time as exemplified by the NusG family and the chemokine XCL1. Analysis of extant protein families and resurrected protein ancestors demonstrates that large regions of sequence space are compatible with metamorphic folding. As a category that enhances biological fitness, metamorphic proteins are likely to employ fold switching to perform important biological functions and may be more common than previously thought.
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Affiliation(s)
- Acacia F Dishman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Medical Scientist Training Program, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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6
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Steube N, Moldenhauer M, Weiland P, Saman D, Kilb A, Ramírez Rojas AA, Garg SG, Schindler D, Graumann PL, Benesch JLP, Bange G, Friedrich T, Hochberg GKA. Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nat Ecol Evol 2023; 7:756-767. [PMID: 37012377 PMCID: PMC10172135 DOI: 10.1038/s41559-023-02018-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/21/2023] [Indexed: 04/05/2023]
Abstract
Highly specific interactions between proteins are a fundamental prerequisite for life, but how they evolve remains an unsolved problem. In particular, interactions between initially unrelated proteins require that they evolve matching surfaces. It is unclear whether such surface compatibilities can only be built by selection in small incremental steps, or whether they can also emerge fortuitously. Here, we used molecular phylogenetics, ancestral sequence reconstruction and biophysical characterization of resurrected proteins to retrace the evolution of an allosteric interaction between two proteins that act in the cyanobacterial photoprotection system. We show that this interaction between the orange carotenoid protein (OCP) and its unrelated regulator, the fluorescence recovery protein (FRP), evolved when a precursor of FRP was horizontally acquired by cyanobacteria. FRP's precursors could already interact with and regulate OCP even before these proteins first encountered each other in an ancestral cyanobacterium. The OCP-FRP interaction exploits an ancient dimer interface in OCP, which also predates the recruitment of FRP into the photoprotection system. Together, our work shows how evolution can fashion complex regulatory systems easily out of pre-existing components.
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Affiliation(s)
- Niklas Steube
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marcus Moldenhauer
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany
| | - Paul Weiland
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Dominik Saman
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Alexandra Kilb
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | | | - Sriram G Garg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Daniel Schindler
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Peter L Graumann
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Justin L P Benesch
- Department of Chemistry, Oxford University, Oxford, UK
- Kavli Institute for Nanoscience Discovery, Oxford University, Oxford, UK
| | - Gert Bange
- Department of Chemistry, University of Marburg, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Thomas Friedrich
- Institute of Chemistry PC14, Technische Universität Berlin, Berlin, Germany.
| | - Georg K A Hochberg
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Chemistry, University of Marburg, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
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7
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Queiroz JPF, Lourenzoni MR, Rocha BAM. Structural evolution of an amphibian-specific globin: A computational evolutionary biochemistry approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 45:101055. [PMID: 36566682 DOI: 10.1016/j.cbd.2022.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
Studies on the globin family are continuously revealing insights into the mechanisms of gene and protein evolution. The rise of a new globin gene type in Pelobatoidea and Neobatrachia (Amphibia:Anura) from an α-globin precursor provides the opportunity to investigate the genetic and physical mechanisms underlying the origin of new protein structural and functional properties. This amphibian-specific globin (globin A/GbA) discovered in the heart of Rana catesbeiana is a monomer. As the ancestral oligomeric state of α-globins is a homodimer, we inferred that the ancestral state was lost somewhere in the GbA lineage. Here, we combined computational molecular evolution with structural bioinformatics to determine the extent to which the loss of the homodimeric state is pervasive in the GbA clade. We also characterized the loci of GbA genes in Bufo bufo. We found two GbA clades in Neobatrachia. One was deleted in Ranidae, but retained and expanded to yield a new globin cluster in Bufonidae species. Loss of the ancestral oligomeric state seems to be pervasive in the GbA clade. However, a taxonomic sampling that includes more Pelobatoidea, as well as early Neobatrachia, lineages would be necessary to determine the oligomeric state of the last common ancestor of all GbA. The evidence presented here points out a possible loss of oligomerization in Pelobatoidea GbA as a result of amino acid substitutions that weaken the homodimeric state. In contrast, the loss of oligomerization in both Neobatrachia GbA clades was linked to independent deletions that disrupted many packing contacts at the homodimer interface.
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Affiliation(s)
- João Pedro Fernandes Queiroz
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
| | - Marcos Roberto Lourenzoni
- Protein Engineering and Health Solutions Group - GEPeSS Fundacao Oswaldo Cruz - Ceara, Eusébio, Ceara, 60175-047, Brazil.
| | - Bruno Anderson Matias Rocha
- Laboratorio de Biocristalografia - LABIC, Departamento de Bioquimica e Biologia Molecular, Universidade Federal do Ceara, Campus do Pici s.n., bloco 907, Av. Mister Hull, Fortaleza, Ceara, 60440-970, Brazil.
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8
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Gianni S, Jemth P. Allostery Frustrates the Experimentalist. J Mol Biol 2023; 435:167934. [PMID: 36586463 DOI: 10.1016/j.jmb.2022.167934] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
Proteins interact with other proteins, with nucleic acids, lipids, carbohydrates and various small molecules in the living cell. These interactions have been quantified and structurally characterized in numerous studies such that we today have a comprehensive picture of protein structure and function. However, proteins are dynamic and even folded proteins are likely more heterogeneous than they appear in most descriptions. One property of proteins that relies on dynamics and heterogeneity is allostery, the ability of a protein to change structure and function upon ligand binding to an allosteric site. Over the last decades the concept of allostery was broadened to embrace all types of long-range interactions across a protein including purely entropic changes without a conformational change in single protein domains. But with this re-definition came a problem: How do we measure allostery? In this opinion, we discuss some caveats arising from the quantitative description of single-domain allostery from an experimental perspective and how the limitations cannot be separated from the definition of allostery per se. Furthermore, we attempt to tie together allostery with the concept of frustration in an effort to investigate the links between these two complex, and yet general, properties of proteins. We arrive at the conclusion that the sensitivity to perturbation of allosteric networks in single protein domains is too large for the networks to be of significant biological relevance.
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Affiliation(s)
- Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, 00185 Rome, Italy.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
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Pillai AS, Hochberg GK, Thornton JW. Simple mechanisms for the evolution of protein complexity. Protein Sci 2022; 31:e4449. [PMID: 36107026 PMCID: PMC9601886 DOI: 10.1002/pro.4449] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/01/2022] [Accepted: 09/10/2022] [Indexed: 01/26/2023]
Abstract
Proteins are tiny models of biological complexity: specific interactions among their many amino acids cause proteins to fold into elaborate structures, assemble with other proteins into higher-order complexes, and change their functions and structures upon binding other molecules. These complex features are classically thought to evolve via long and gradual trajectories driven by persistent natural selection. But a growing body of evidence from biochemistry, protein engineering, and molecular evolution shows that naturally occurring proteins often exist at or near the genetic edge of multimerization, allostery, and even new folds, so just one or a few mutations can trigger acquisition of these properties. These sudden transitions can occur because many of the physical properties that underlie these features are present in simpler proteins as fortuitous by-products of their architecture. Moreover, complex features of proteins can be encoded by huge arrays of sequences, so they are accessible from many different starting points via many possible paths. Because the bridges to these features are both short and numerous, random chance can join selection as a key factor in explaining the evolution of molecular complexity.
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Affiliation(s)
- Arvind S. Pillai
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Institute for Protein DesignUniversity of WashingtonSeattleWAUSA
| | - Georg K.A. Hochberg
- Max Planck Institute for Terrestrial MicrobiologyMarburgGermany
- Department of Chemistry, Center for Synthetic MicrobiologyPhilipps University MarburgMarburgGermany
| | - Joseph W. Thornton
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
- Departments of Human Genetics and Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
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