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Hupfeld E, Schlee S, Wurm JP, Rajendran C, Yehorova D, Vos E, Ravindra Raju D, Kamerlin SCL, Sprangers R, Sterner R. Conformational Modulation of a Mobile Loop Controls Catalysis in the (βα) 8-Barrel Enzyme of Histidine Biosynthesis HisF. JACS AU 2024; 4:3258-3276. [PMID: 39211614 PMCID: PMC11350729 DOI: 10.1021/jacsau.4c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/04/2024]
Abstract
The overall significance of loop motions for enzymatic activity is generally accepted. However, it has largely remained unclear whether and how such motions can control different steps of catalysis. We have studied this problem on the example of the mobile active site β1α1-loop (loop1) of the (βα)8-barrel enzyme HisF, which is the cyclase subunit of imidazole glycerol phosphate synthase. Loop1 variants containing single mutations of conserved amino acids showed drastically reduced rates for the turnover of the substrates N'-[(5'-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) and ammonia to the products imidazole glycerol phosphate (ImGP) and 5-aminoimidazole-4-carboxamide-ribotide (AICAR). A comprehensive mechanistic analysis including stopped-flow kinetics, X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations detected three conformations of loop1 (open, detached, closed) whose populations differed between wild-type HisF and functionally affected loop1 variants. Transient stopped-flow kinetic experiments demonstrated that wt-HisF binds PrFAR by an induced-fit mechanism whereas catalytically impaired loop1 variants bind PrFAR by a simple two-state mechanism. Our findings suggest that PrFAR-induced formation of the closed conformation of loop1 brings active site residues in a productive orientation for chemical turnover, which we show to be the rate-limiting step of HisF catalysis. After the cyclase reaction, the closed loop conformation is destabilized, which favors the formation of detached and open conformations and hence facilitates the release of the products ImGP and AICAR. Our data demonstrate how different conformations of active site loops contribute to different catalytic steps, a finding that is presumably of broad relevance for the reaction mechanisms of (βα)8-barrel enzymes and beyond.
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Affiliation(s)
- Enrico Hupfeld
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Sandra Schlee
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Chitra Rajendran
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Dariia Yehorova
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Eva Vos
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Dinesh Ravindra Raju
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Shina Caroline Lynn Kamerlin
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30318, United States
| | - Remco Sprangers
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Reinhard Sterner
- Institute
of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
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Davies AM, Beavil RL, Barbolov M, Sandhar BS, Gould HJ, Beavil AJ, Sutton BJ, McDonnell JM. Crystal structures of the human IgD Fab reveal insights into C H1 domain diversity. Mol Immunol 2023; 159:28-37. [PMID: 37267832 DOI: 10.1016/j.molimm.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/17/2023] [Accepted: 05/20/2023] [Indexed: 06/04/2023]
Abstract
Antibodies of the IgD isotype remain the least well characterized of the mammalian immunoglobulin isotypes. Here we report three-dimensional structures for the Fab region of IgD, based on four different crystal structures, at resolutions of 1.45-2.75 Å. These IgD Fab crystals provide the first high-resolution views of the unique Cδ1 domain. Structural comparisons identify regions of conformational diversity within the Cδ1 domain, as well as among the homologous domains of Cα1, Cγ1 and Cμ1. The IgD Fab structure also possesses a unique conformation of the upper hinge region, which may contribute to the overall disposition of the very long linker sequence between the Fab and Fc regions found in human IgD. Structural similarities observed between IgD and IgG, and differences with IgA and IgM, are consistent with predicted evolutionary relationships for the mammalian antibody isotypes.
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Affiliation(s)
- Anna M Davies
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Rebecca L Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Momchil Barbolov
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Balraj S Sandhar
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Hannah J Gould
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Andrew J Beavil
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - Brian J Sutton
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom
| | - James M McDonnell
- King's College London, Randall Centre for Cell and Molecular Biophysics, New Hunt's House, London SE1 1UL, United Kingdom.
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Krueger TD, Tang L, Fang C. Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing. BIOSENSORS 2023; 13:bios13020218. [PMID: 36831983 PMCID: PMC9954042 DOI: 10.3390/bios13020218] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 05/14/2023]
Abstract
Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca2+) concentrations in vivo with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca2+-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca2+-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities.
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Krueger TD, Tang L, Chen C, Zhu L, Breen IL, Wachter RM, Fang C. To twist or not to twist: From chromophore structure to dynamics inside engineered photoconvertible and photoswitchable fluorescent proteins. Protein Sci 2023; 32:e4517. [PMID: 36403093 PMCID: PMC9793981 DOI: 10.1002/pro.4517] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/31/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
Green-to-red photoconvertible fluorescent proteins (FPs) are vital biomimetic tools for powerful techniques such as super-resolution imaging. A unique Kaede-type FP named the least evolved ancestor (LEA) enables delineation of the evolutionary step to acquire photoconversion capability from the ancestral green fluorescent protein (GFP). A key residue, Ala69, was identified through several steady-state and time-resolved spectroscopic techniques that allows LEA to effectively photoswitch and enhance the green-to-red photoconversion. However, the inner workings of this functional protein have remained elusive due to practical challenges of capturing the photoexcited chromophore motions in real time. Here, we implemented femtosecond stimulated Raman spectroscopy and transient absorption on LEA-A69T, aided by relevant crystal structures and control FPs, revealing that Thr69 promotes a stronger π-π stacking interaction between the chromophore phenolate (P-)ring and His193 in FP mutants that cannot photoconvert or photoswitch. Characteristic time constants of ~60-67 ps are attributed to P-ring twist as the onset for photoswitching in LEA (major) and LEA-A69T (minor) with photoconversion capability, different from ~16/29 ps in correlation with the Gln62/His62 side-chain twist in ALL-GFP/ALL-Q62H, indicative of the light-induced conformational relaxation preferences in various local environments. A minor subpopulation of LEA-A69T capable of positive photoswitching was revealed by time-resolved electronic spectroscopies with targeted light irradiation wavelengths. The unveiled chromophore structure and dynamics inside engineered FPs in an aqueous buffer solution can be generalized to improve other green-to-red photoconvertible FPs from the bottom up for deeper biophysics with molecular biology insights and powerful bioimaging advances.
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Affiliation(s)
| | - Longteng Tang
- Department of ChemistryOregon State UniversityCorvallisOregonUSA
| | - Cheng Chen
- Department of ChemistryOregon State UniversityCorvallisOregonUSA
| | - Liangdong Zhu
- Department of ChemistryOregon State UniversityCorvallisOregonUSA
| | - Isabella L. Breen
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural DiscoveryArizona State UniversityTempeArizonaUSA
| | - Rebekka M. Wachter
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural DiscoveryArizona State UniversityTempeArizonaUSA
| | - Chong Fang
- Department of ChemistryOregon State UniversityCorvallisOregonUSA
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Gutiérrez-Fernández J, Javaid F, De Rossi G, Chudasama V, Greenwood J, Moss SE, Luecke H. Structural basis of human LRG1 recognition by Magacizumab, a humanized monoclonal antibody with therapeutic potential. Acta Crystallogr D Struct Biol 2022; 78:725-734. [PMID: 35647920 PMCID: PMC9159282 DOI: 10.1107/s2059798322004132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/19/2022] [Indexed: 11/10/2022] Open
Abstract
The formation of new dysfunctional blood vessels is a crucial stage in the development of various conditions such as macular degeneration, diabetes, cardiovascular disease, neurological disease and inflammatory disorders, as well as during tumor growth, eventually contributing to metastasis. An important factor involved in pathogenic angiogenesis is leucine-rich α-2-glycoprotein 1 (LRG1), the antibody blockade of which has been shown to lead to a reduction in both choroidal neovascularization and tumor growth in mouse models. In this work, the structural interactions between the LRG1 epitope and the Fab fragment of Magacizumab, a humanized function-blocking IgG4 against LRG1, are analysed, determining its specific binding mode and the key residues involved in LRG1 recognition. Based on these structural findings, a series of mutations are suggested that could be introduced into Magacizumab to increase its affinity for LRG1, as well as a model of the entire Fab-LRG1 complex that could enlighten new strategies to enhance affinity, consequently leading towards an even more efficient therapeutic.
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Affiliation(s)
- Javier Gutiérrez-Fernández
- Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Faiza Javaid
- Institute of Ophthalmology, University College London, London, United Kingdom
- Department of Chemistry, University College London, London, United Kingdom
| | - Giulia De Rossi
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Vijay Chudasama
- Department of Chemistry, University College London, London, United Kingdom
| | - John Greenwood
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Stephen E. Moss
- Institute of Ophthalmology, University College London, London, United Kingdom
| | - Hartmut Luecke
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
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Structural basis for blocked excited state proton transfer in a fluorescent, photoacidic non-canonical amino acid-containing antibody fragment. J Mol Biol 2022; 434:167455. [PMID: 35033559 PMCID: PMC9018508 DOI: 10.1016/j.jmb.2022.167455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/05/2022] [Accepted: 01/09/2022] [Indexed: 11/20/2022]
Abstract
The fluorescent non-canonical amino acid (fNCAA) L-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) contains a photoacidic 7-hydroxycoumarin (7-HC) side chain whose fluorescence properties can be tuned by its environment. In proteins, many alterations to 7-HCAA's fluorescence spectra have been reported including increases and decreases in intensity and red- and blue-shifted emission maxima. The ability to rationally design protein environments that alter 7-HCAA's fluorescence properties in predictable ways could lead to novel protein-based sensors of biological function. However, these efforts are likely limited by a lack of structural characterization of 7-HCAA-containing proteins. Here, we report the steady-state spectroscopic and x-ray crystallographic characterization of a 7-HCAA-containing antibody fragment (in the apo and antigen-bound forms) in which a substantially blue-shifted 7-HCAA emission maximum (∼70 nm) is observed relative to the free amino acid. Our structural characterization of these proteins provides evidence that the blue shift is a consequence of the fact that excited state proton transfer (ESPT) from the 7-HC phenol has been almost completely blocked by interactions with the protein backbone. Furthermore, a direct interaction between a residue in the antigen and the fluorophore served to further block proton transfer relative to the apoprotein. The structural basis of the unprecedented blue shift in 7-HCAA emission reported here provides a framework for the development of new fluorescent protein-based sensors.
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Gleason PR, Kolbaba-Kartchner B, Henderson JN, Stahl EP, Simmons CR, Mills JH. Structural Origins of Altered Spectroscopic Properties upon Ligand Binding in Proteins Containing a Fluorescent Noncanonical Amino Acid. Biochemistry 2021; 60:2577-2585. [PMID: 34415744 DOI: 10.1021/acs.biochem.1c00291] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescent noncanonical amino acids (fNCAAs) could serve as starting points for the rational design of protein-based fluorescent sensors of biological activity. However, efforts toward this goal are likely hampered by a lack of atomic-level characterization of fNCAAs within proteins. Here, we describe the spectroscopic and structural characterization of five streptavidin mutants that contain the fNCAA l-(7-hydroxycoumarin-4-yl)ethylglycine (7-HCAA) at sites proximal to the binding site of its substrate, biotin. Many of the mutants exhibited altered fluorescence spectra in response to biotin binding, which included both increases and decreases in fluorescence intensity as well as red- or blue-shifted emission maxima. Structural data were also obtained for three of the five mutants. The crystal structures shed light on interactions between 7-HCAA and functional groups, contributed either by the protein or by the substrate, that may be responsible for the observed changes in the 7-HCAA spectra. These data could be used in future studies aimed at the rational design of fluorescent, protein-based sensors of small molecule binding or dissociation.
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