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Bui TYH, De Zitter E, Moeyaert B, Pecqueur L, Srinivasu BY, Economou A, Fontecave M, Van Meervelt L, Dedecker P, Pedre B. Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry. Int J Biol Macromol 2023; 239:124179. [PMID: 36972828 DOI: 10.1016/j.ijbiomac.2023.124179] [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: 12/12/2022] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Reversibly switchable monomeric Cherry (rsCherry) is a photoswitchable variant of the red fluorescent protein mCherry. We report that this protein gradually and irreversibly loses its red fluorescence in the dark over a period of months at 4 °C and a few days at 37 °C. We also find that its ancestor, mCherry, undergoes a similar fluorescence loss but at a slower rate. X-ray crystallography and mass spectrometry reveal that this is caused by the cleavage of the p-hydroxyphenyl ring from the chromophore and the formation of two novel types of cyclic structures at the remaining chromophore moiety. Overall, our work sheds light on a new process occurring within fluorescent proteins, further adding to the chemical diversity and versatility of these molecules.
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Affiliation(s)
- Thi Yen Hang Bui
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Elke De Zitter
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Benjamien Moeyaert
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, UMR 8229 CNRS, Sorbonne Université, PSL University, Paris, France
| | - Bindu Y Srinivasu
- Laboratory of Molecular Bacteriology, Rega Institute, KU, Leuven, Belgium
| | | | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, UMR 8229 CNRS, Sorbonne Université, PSL University, Paris, France
| | - Luc Van Meervelt
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Peter Dedecker
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium.
| | - Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium.
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2
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Lansky S, Salama R, Biarnés X, Shwartstein O, Schneidman-Duhovny D, Planas A, Shoham Y, Shoham G. Integrative structure determination reveals functional global flexibility for an ultra-multimodular arabinanase. Commun Biol 2022; 5:465. [PMID: 35577850 PMCID: PMC9110388 DOI: 10.1038/s42003-022-03054-z] [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: 12/27/2019] [Accepted: 07/15/2021] [Indexed: 11/08/2022] Open
Abstract
AbnA is an extracellular GH43 α-L-arabinanase from Geobacillus stearothermophilus, a key bacterial enzyme in the degradation and utilization of arabinan. We present herein its full-length crystal structure, revealing the only ultra-multimodular architecture and the largest structure to be reported so far within the GH43 family. Additionally, the structure of AbnA appears to contain two domains belonging to new uncharacterized carbohydrate-binding module (CBM) families. Three crystallographic conformational states are determined for AbnA, and this conformational flexibility is thoroughly investigated further using the "integrative structure determination" approach, integrating molecular dynamics, metadynamics, normal mode analysis, small angle X-ray scattering, dynamic light scattering, cross-linking, and kinetic experiments to reveal large functional conformational changes for AbnA, involving up to ~100 Å movement in the relative positions of its domains. The integrative structure determination approach demonstrated here may apply also to the conformational study of other ultra-multimodular proteins of diverse functions and structures.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel
| | - Xevi Biarnés
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Omer Shwartstein
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, 08017, Spain
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion, Haifa, 3200, Israel.
| | - Gil Shoham
- Institute of Chemistry, the Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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Schieferstein JM, Pawate AS, Varel MJ, Guha S, Astrauskaite I, Gennis RB, Kenis PJA. X-ray transparent microfluidic platforms for membrane protein crystallization with microseeds. LAB ON A CHIP 2018; 18:944-954. [PMID: 29469138 PMCID: PMC5849577 DOI: 10.1039/c7lc01141e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Crystallization of membrane proteins is a critical step for uncovering atomic resolution 3-D structures and elucidating structure-function relationships. Microseeding, the process of transferring sub-microscopic crystal nuclei from initial screens into new crystallization experiments, is an effective, yet underutilized approach to grow crystals suitable for X-ray crystallography. Here, we report simplified methods for crystallization of membrane proteins that utilize microseeding in X-ray transparent microfluidic chips. First, a microfluidic method for introduction of microseed dilutions into metastable crystallization experiments is demonstrated for photoactive yellow protein and cytochrome bo3 oxidase. As microseed concentration decreased, the number of crystals decreased while the average size increased. Second, we demonstrate a microfluidic chip for microseed screening, where many crystallization conditions were formulated on-chip prior to mixing with microseeds. Crystallization composition, crystal size, and diffraction data were collected and mapped on phase diagrams, which revealed that crystals of similar diffraction quality and size typically grow in distinct regions of the phase diagram.
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Affiliation(s)
- Jeremy M Schieferstein
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S Mathews Ave, Urbana, IL, USA.
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Zhou RB, Cao HL, Zhang CY, Yin DC. A review on recent advances for nucleants and nucleation in protein crystallization. CrystEngComm 2017. [DOI: 10.1039/c6ce02562e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation. Biol Chem 2009; 390:1163-70. [DOI: 10.1515/bc.2009.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractThe periplasmic ligand-binding protein ChoX is part of the ABC transport system ChoVWX that imports choline as a nutrient into the soil bacteriumSinorhizobium meliloti. We have recently reported the crystal structures of ChoX in complex with its ligands choline and acetylcholine and the structure of a fully closed but substrate-free state of ChoX. This latter structure revealed an architecture of the ligand-binding site that is superimposable to the closed, ligand-bound form of ChoX. We report here the crystal structure of ChoX in an unusual, ligand-free conformation that represents a semi-closed form of ChoX. The analysis revealed a subdomain movement in the N-lobe of ChoX. Comparison with the two well-characterized substrate binding proteins, MBP and HisJ, suggests the presence of a similar subdomain in these proteins.
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Oswald C, Smits SHJ, Höing M, Sohn-Bösser L, Dupont L, Le Rudulier D, Schmitt L, Bremer E. Crystal structures of the choline/acetylcholine substrate-binding protein ChoX from Sinorhizobium meliloti in the liganded and unliganded-closed states. J Biol Chem 2008; 283:32848-59. [PMID: 18779321 DOI: 10.1074/jbc.m806021200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ATP-binding cassette transporter ChoVWX is one of several choline import systems operating in Sinorhizobium meliloti. Here fluorescence-based ligand binding assays were used to quantitate substrate binding by the periplasmic ligand-binding protein ChoX. These data confirmed that ChoX recognizes choline and acetylcholine with high and medium affinity, respectively. We also report the crystal structures of ChoX in complex with either choline or acetylcholine. These structural investigations revealed an architecture of the ChoX binding pocket and mode of substrate binding similar to that reported previously for several compatible solute-binding proteins. Additionally the ChoX-acetylcholine complex permitted a detailed structural comparison with the carbamylcholine-binding site of the acetylcholine-binding protein from the mollusc Lymnaea stagnalis. In addition to the two liganded structures of ChoX, we were also able to solve the crystal structure of ChoX in a closed, substrate-free conformation that revealed an architecture of the ligand-binding site that is superimposable to the closed, ligand-bound form of ChoX. This structure is only the second of its kind and raises the important question of how ATP-binding cassette transporters are capable of distinguishing liganded and unliganded-closed states of the binding protein.
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Affiliation(s)
- Christine Oswald
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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