1
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Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [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: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
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Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
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2
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Gruhl T, Weinert T, Rodrigues MJ, Milne CJ, Ortolani G, Nass K, Nango E, Sen S, Johnson PJM, Cirelli C, Furrer A, Mous S, Skopintsev P, James D, Dworkowski F, Båth P, Kekilli D, Ozerov D, Tanaka R, Glover H, Bacellar C, Brünle S, Casadei CM, Diethelm AD, Gashi D, Gotthard G, Guixà-González R, Joti Y, Kabanova V, Knopp G, Lesca E, Ma P, Martiel I, Mühle J, Owada S, Pamula F, Sarabi D, Tejero O, Tsai CJ, Varma N, Wach A, Boutet S, Tono K, Nogly P, Deupi X, Iwata S, Neutze R, Standfuss J, Schertler G, Panneels V. Ultrafast structural changes direct the first molecular events of vision. Nature 2023; 615:939-944. [PMID: 36949205 PMCID: PMC10060157 DOI: 10.1038/s41586-023-05863-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [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: 04/02/2022] [Accepted: 02/17/2023] [Indexed: 03/24/2023]
Abstract
Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
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Affiliation(s)
- Thomas Gruhl
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Matthew J Rodrigues
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Christopher J Milne
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- European XFEL, Schenefeld, Germany
| | - Giorgia Ortolani
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Karol Nass
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Eriko Nango
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
- RIKEN SPring-8 Center, Hyogo, Japan
| | - Saumik Sen
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Philip J M Johnson
- Photon Science Division, Laboratory for Nonlinear Optics, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Claudio Cirelli
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sandra Mous
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Petr Skopintsev
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA
| | - Daniel James
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Physics, Utah Valley University, Orem, UT, USA
| | - Florian Dworkowski
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Petra Båth
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Demet Kekilli
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dmitry Ozerov
- Division Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hannah Glover
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Camila Bacellar
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Steffen Brünle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
| | | | - Azeglio D Diethelm
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Dardan Gashi
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Guillaume Gotthard
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ramon Guixà-González
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Victoria Kabanova
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
- Laboratory for Ultrafast X-ray Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gregor Knopp
- Photon Science Division, Laboratory for Femtochemistry, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Elena Lesca
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Pikyee Ma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Isabelle Martiel
- Photon Science Division, Laboratory for Macromolecules and Bioimaging, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Jonas Mühle
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Filip Pamula
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Daniel Sarabi
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Oliver Tejero
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Ching-Ju Tsai
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Niranjan Varma
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Anna Wach
- Institute of Nuclear Physics Polish Academy of Sciences, Kraców, Poland
- Operando X-ray Spectroscopy, Energy and Environment Division, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Przemyslaw Nogly
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, Zurich, Switzerland
- Dioscuri Center For Structural Dynamics of Receptors, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Kraków, Kraków, Poland
| | - Xavier Deupi
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
- Condensed Matter Theory Group, Laboratory for Theoretical and Computational Physics, Division of Scientific Computing, Theory and Data, Paul Scherrer Institute, Villigen PSI, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland
| | - Gebhard Schertler
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Valerie Panneels
- Division of Biology and Chemistry, Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen PSI, Switzerland.
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3
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Zhao F, Zhai X, Liu X, Lian M, Liang G, Cui J, Dong H, Wang W. Effects of High-Intensity Ultrasound Pretreatment on Structure, Properties, and Enzymolysis of Walnut Protein Isolate. Molecules 2021; 27:molecules27010208. [PMID: 35011440 PMCID: PMC8746484 DOI: 10.3390/molecules27010208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
Abstract
The purpose of this paper was to investigate the effect of high-intensity ultrasonication (HIU) pretreatment before enzymolysis on structural conformations of walnut protein isolate (WPI) and antioxidant activity of its hydrolysates. Aqueous WPI suspensions were subjected to ultrasonic processing at different power levels (600-2000 W) and times (5-30 min), and then changes in the particle size, zeta (ζ) potential, and structure of WPI were investigated, and antioxidant activity of its hydrolysates was determined. The particle size of the particles of aqueous WPI suspensions was decreased after ultrasound, indicating that sonication destroyed protein aggregates. The ζ-potential values of a protein solution significantly changed after sonication, demonstrating that the original dense structure of the protein was destroyed. Fourier transform infrared spectroscopy indicated a change in the secondary structure of WPI after sonication, with a decrease in β-turn and an increase in α-helix, β-sheet, and random coil content. Two absorption peaks of WPI were generated, and the fluorescence emission intensity of the proteins decreased after ultrasonic treatment, indicating that the changes in protein tertiary structure occurred. Moreover, the degree of hydrolysis and the antioxidant activity of the WPI hydrolysates increased after sonication. These results suggest that HIU pretreatment is a potential tool for improving the functional properties of walnut proteins.
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Affiliation(s)
- Fei Zhao
- College of Agronomy and Environment, Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Weifang 262700, China; (M.L.); (G.L.); (J.C.)
- Correspondence: (F.Z.); (W.W.); Tel.: +86-538-824-2850 (W.W.)
| | - Xiaosong Zhai
- College of Food Science and Engineering, Engineering and Technology Center for Grain Processing of Shandong Province, Shandong Agricultural University, Taian 271018, China; (X.Z.); (H.D.)
| | - Xuemei Liu
- Jinan Fruit Research Institute, All-China Federation of Supply and Marketing Co-Operatives, Jinan 250014, China;
| | - Meng Lian
- College of Agronomy and Environment, Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Weifang 262700, China; (M.L.); (G.L.); (J.C.)
| | - Guoting Liang
- College of Agronomy and Environment, Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Weifang 262700, China; (M.L.); (G.L.); (J.C.)
| | - Jingxiang Cui
- College of Agronomy and Environment, Shandong Facility Horticulture Bioengineering Research Center, Weifang University of Science and Technology, Weifang 262700, China; (M.L.); (G.L.); (J.C.)
| | - Haizhou Dong
- College of Food Science and Engineering, Engineering and Technology Center for Grain Processing of Shandong Province, Shandong Agricultural University, Taian 271018, China; (X.Z.); (H.D.)
| | - Wentao Wang
- College of Food Science and Engineering, Engineering and Technology Center for Grain Processing of Shandong Province, Shandong Agricultural University, Taian 271018, China; (X.Z.); (H.D.)
- Correspondence: (F.Z.); (W.W.); Tel.: +86-538-824-2850 (W.W.)
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Macias LA, Sipe SN, Santos IC, Bashyal A, Mehaffey MR, Brodbelt JS. Influence of Primary Structure on Fragmentation of Native-Like Proteins by Ultraviolet Photodissociation. J Am Soc Mass Spectrom 2021; 32:2860-2873. [PMID: 34714071 PMCID: PMC8639798 DOI: 10.1021/jasms.1c00269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Analysis of native-like protein structures in the gas phase via native mass spectrometry and auxiliary techniques has become a powerful tool for structural biology applications. In combination with ultraviolet photodissociation (UVPD), native top-down mass spectrometry informs backbone flexibility, topology, hydrogen bonding networks, and conformational changes in protein structure. Although it is known that the primary structure affects dissociation of peptides and proteins in the gas phase, its effect on the types and locations of backbone cleavages promoted by UVPD and concomitant influence on structural characterization of native-like proteins is not well understood. Here, trends in the fragmentation of native-like proteins were evaluated by tracking the propensity of 10 fragment types (a, a+1, b, c, x, x+1, y, y-1, Y, and z) in relation to primary structure in a native-top down UVPD data set encompassing >9600 fragment ions. Differing fragmentation trends are reported for the production of distinct fragment types, attributed to a combination of both direct dissociation pathways from excited electronic states and those surmised to involve intramolecular vibrational energy redistribution after internal conversion. The latter pathways were systematically evaluated to evince the role of proton mobility in the generation of "CID-like" fragments through UVPD, providing pertinent insight into the characterization of native-like proteins. Fragmentation trends presented here are envisioned to enhance analysis of the protein higher-order structure or augment scoring algorithms in the high-throughput analysis of intact proteins.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Sarah N Sipe
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês C Santos
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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5
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Takaki K, Takahashi K, Guionet A, Ohshima T. Pulsed Power Applications for Protein Conformational Change and the Permeabilization of Agricultural Products. Molecules 2021; 26:molecules26206288. [PMID: 34684869 PMCID: PMC8537387 DOI: 10.3390/molecules26206288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
Pulsed electric fields (PEFs), which are generated by pulsed power technologies, are being tested for their applicability in food processing through protein conformational change and the poration of cell membranes. In this article, enzyme activity change and the permeabilization of agricultural products using pulsed power technologies are reviewed as novel, nonthermal food processes. Compact pulsed power systems have been developed with repetitive operation and moderate output power for application in food processing. Firstly, the compact pulsed power systems for the enzyme activity change and permeabilization are outlined. Exposure to electric fields affects hydrogen bonds in the secondary and tertiary structures of proteins; as a result, the protein conformation is induced to be changed. The conformational change induces an activity change in enzymes such as α-amylase and peroxidase. Secondly, the conformational change in proteins and the induced protein functional change are reviewed. The permeabilization of agricultural products is caused through the poration of cell membranes by applying PEFs produced by pulsed discharges. The permeabilization of cell membranes can be used for the extraction of nutrients and health-promoting agents such as polyphenols and vitamins. The electrical poration can also be used as a pre-treatment for food drying and blanching processes. Finally, the permeabilization of cell membranes and its applications in food processing are reviewed.
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Affiliation(s)
- Koichi Takaki
- Faculty of Science and Engineering, Iwate University, Morioka 020-8551, Japan;
- Agri-Innovation Center, Iwate University, Morioka 020-8550, Japan;
- Correspondence: ; Tel./Fax: +81-19-621-6941
| | - Katsuyuki Takahashi
- Faculty of Science and Engineering, Iwate University, Morioka 020-8551, Japan;
- Agri-Innovation Center, Iwate University, Morioka 020-8550, Japan;
| | - Alexis Guionet
- Agri-Innovation Center, Iwate University, Morioka 020-8550, Japan;
| | - Takayuki Ohshima
- Faculty of Science and Engineering, Gunma University, Kiryu 376-8515, Japan;
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Olagunju MO, Liu Y, Frenkel AI, Knecht MR. Atomically Resolved Characterization of Optically Driven Ligand Reconfiguration on Nanoparticle Catalyst Surfaces. ACS Appl Mater Interfaces 2021; 13:44302-44311. [PMID: 34499467 DOI: 10.1021/acsami.1c11256] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Dynamic ligand layers on nanoparticle surfaces could prove to be critically important to enhance the functionality of individual materials. Such capabilities could complement the properties of the inorganic component to provide multifunctionality or the ability to be remotely actuated. Peptide-based ligands have demonstrated the ability to be remotely responsive to structural changes when adsorbed to nanoparticle surfaces via incorporation of photoswitches into their molecular structure. In this contribution, direct spectroscopic evidence of the remote actuation of a photoswitchable peptide adsorbed onto Au nanoparticles is demonstrated using X-ray absorption fine structure spectroscopic methods. From this analysis, Au-X (X = C or N) coordination numbers confirm the changes before and after photoswitching in the surface ligand conformation, which was correlated directly to variations in the catalytic application of the materials for nitrophenol reduction processes. In addition, the catalytic application of the materials was demonstrated to be significantly sensitive to the structure of the nitrophenol substrate used in the reaction, suggesting that changes in the reactivity are likely based upon the peptide conformation and substrate structure. Such results confirm that surface ligands can be remotely reconfigured on nanoparticle surfaces, providing pathways to apply such capabilities to a variety of applications beyond catalysis ranging from drug delivery to sensing.
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Affiliation(s)
- Mary O Olagunju
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Yang Liu
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
| | - Anatoly I Frenkel
- Department of Materials Science and Chemical Engineering, Stony Brook University, Stony Brook, New York 11794, United States
- Chemistry Division, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Marc R Knecht
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, UM Life Science Technology Building, 1951 NW 7th Avenue, Suite 475, Miami, Florida 33136, United States
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Zhao Z, Engholm-Keller K, Poojary MM, Boelt SG, Rogowska-Wrzesinska A, Skibsted LH, Davies MJ, Lund MN. Generation of Aggregates of α-Lactalbumin by UV-B Light Exposure. J Agric Food Chem 2020; 68:6701-6714. [PMID: 32396720 DOI: 10.1021/acs.jafc.0c00757] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Whey proteins are widely used as ingredients in the form of aggregates to obtain certain functionalities in food applications. The aim of this study was to understand how UV illumination generates aggregates of α-lactalbumin (α-LA) as an alternative to heat treatments traditionally used for industrial production of protein aggregates. Absorption of UV light by α-LA caused cleavage of disulfide bonds and release of thiol groups, which resulted in primarily disulfide-mediated aggregation. This process mediated efficient aggregation with up to 98% monomer conversion into aggregates through formation of intermolecular disulfide bonds, while only minor levels of nonreducible cross-links were observed. SDS-PAGE analysis revealed that illumination led to formation of dimeric, trimeric, and oligomeric forms of α-LA. LC-MS/MS analysis showed that all of the four native disulfide bonds in α-LA were cleaved by UV illumination but to different extents, and the extent of cleavage was found to be higher in the absence of calcium. Seventeen different non-native disulfides were formed after 24 h of UV illumination. Two dityrosine bonds were identified (Tyr103-Tyr103 and Tyr36-Tyr103) alongside ditryptophan (Trp118-Trp118) and tyrosine-tryptophan (Tyr50-Trp60) cross-links. In addition, Trp60, Trp118, Cys73, Cys91, Cys120, Phe80, Met90, His68, and His107 were found to be oxidized up to 12% as compared to a nonilluminated control. Our work illustrates that light exposure can be used for generation of α-LA aggregates, but optimization of the illumination conditions is required to reduce oxidative damage to Trp, Cys, Phe, Met, and His residues.
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Affiliation(s)
- Zichen Zhao
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Kasper Engholm-Keller
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Mahesha M Poojary
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Sanne G Boelt
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | | | - Leif H Skibsted
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Michael J Davies
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Marianne N Lund
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
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8
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Leopold AV, Pletnev S, Verkhusha VV. Bacterial Phytochrome as a Scaffold for Engineering of Receptor Tyrosine Kinases Controlled with Near-Infrared Light. J Mol Biol 2020; 432:3749-3760. [PMID: 32302608 PMCID: PMC7306426 DOI: 10.1016/j.jmb.2020.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 11/13/2019] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 01/18/2023]
Abstract
Optically controlled receptor tyrosine kinases (opto-RTKs) allow regulation of RTK signaling using light. Until recently, the majority of opto-RTKs were activated with blue-green light. Fusing a photosensory core module of Deinococcus radiodurans bacterial phytochrome (DrBphP-PCM) to the kinase domains of neurotrophin receptors resulted in opto-RTKs controlled with light above 650 nm. To expand this engineering approach to RTKs of other families, here we combined the DrBpP-PCM with the cytoplasmic domains of EGFR and FGFR1. The resultant Dr-EGFR and Dr-FGFR1 opto-RTKs are rapidly activated with near-infrared and inactivated with far-red light. The opto-RTKs efficiently trigger ERK1/2, PI3K/Akt, and PLCγ signaling. Absence of spectral crosstalk between the opto-RTKs and green fluorescent protein-based biosensors enables simultaneous Dr-FGFR1 activation and detection of calcium transients. Action mechanism of the DrBphP-PCM-based opto-RTKs is considered using the available RTK structures. DrBphP-PCM represents a versatile scaffold for engineering of opto-RTKs that are reversibly regulated with far-red and near-infrared light.
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Affiliation(s)
- Anna V Leopold
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Sergei Pletnev
- Macromolecular Crystallography Laboratory, National Cancer Institute, Basic Science Program, Leidos Biomedical Research Inc., Argonne, IL 60439, USA
| | - Vladislav V Verkhusha
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland; Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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9
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Berntsson O, Rodriguez R, Henry L, Panman MR, Hughes AJ, Einholz C, Weber S, Ihalainen JA, Henning R, Kosheleva I, Schleicher E, Westenhoff S. Photoactivation of Drosophila melanogaster cryptochrome through sequential conformational transitions. Sci Adv 2019; 5:eaaw1531. [PMID: 31328161 PMCID: PMC6636987 DOI: 10.1126/sciadv.aaw1531] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/13/2019] [Indexed: 05/27/2023]
Abstract
Cryptochromes are blue-light photoreceptor proteins, which provide input to circadian clocks. The cryptochrome from Drosophila melanogaster (DmCry) modulates the degradation of Timeless and itself. It is unclear how light absorption by the chromophore and the subsequent redox reactions trigger these events. Here, we use nano- to millisecond time-resolved x-ray solution scattering to reveal the light-activated conformational changes in DmCry and the related (6-4) photolyase. DmCry undergoes a series of structural changes, culminating in the release of the carboxyl-terminal tail (CTT). The photolyase has a simpler structural response. We find that the CTT release in DmCry depends on pH. Mutation of a conserved histidine, important for the biochemical activity of DmCry, does not affect transduction of the structural signal to the CTT. Instead, molecular dynamics simulations suggest that it stabilizes the CTT in the resting-state conformation. Our structural photocycle unravels the first molecular events of signal transduction in an animal cryptochrome.
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Affiliation(s)
- Oskar Berntsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
- MAX IV Laboratory, Lund University, 224 84 Lund, Sweden
| | - Ryan Rodriguez
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Léocadie Henry
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Matthijs R. Panman
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Ashley J. Hughes
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Christopher Einholz
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Stefan Weber
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Janne A. Ihalainen
- Nanoscience Center, Department of Biological and Environmental Sciences, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Robert Henning
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, IL 60637, USA
| | - Erik Schleicher
- Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
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10
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Mirarefi P, Ted Lee C. Reversible control of enzyme-inhibitor interactions with light illumination using a photoresponsive surfactant. Proteins 2019; 87:715-722. [PMID: 30980557 DOI: 10.1002/prot.25695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 11/07/2022]
Abstract
The effects of a photoresponsive surfactant and light illumination on the complex formed between ribonuclease A (RNase A) and a protein ribonuclease inhibitor (RI) have been investigated to develop a light-based technique to reactivate an enzyme through surfactant-induced dissociation of the enzyme-inhibitor complex. The photoresponsive surfactant undergoes a photoisomerization from the relatively hydrophobic trans isomer under visible light to the relatively hydrophilic cis isomer upon UV illumination, providing a means to reversibly control protein-inhibitor interactions. In the absence of surfactant, RI binds tightly to RNase A through noncovalent interactions, which inhibits the enzyme activity. Upon addition of the surfactant under visible light, RNase A is reactivated, regaining ~75% of the native activity in the absence of RI. In the presence of the surfactant under UV light, however, the enzyme remains inhibited. Fluorescence spectroscopy, dynamic light scattering, and circular dichroism spectroscopy reveal that RI dramatically unfolds upon addition of the trans form of the surfactant, while RNase A does not undergo noticeable structural changes under the same conditions. This indicates that RNase A reactivation occurs through dissociation of the enzyme-inhibitor complex arising from surfactant-induced unfolding of the inhibitor. As a result, photoresponsive surfactant and light illumination can be used as a novel light-based technique to dissociate enzyme-inhibitor complexes and, thus, reactivate an inhibited enzyme.
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Affiliation(s)
- Panteha Mirarefi
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
| | - C Ted Lee
- Department of Chemical Engineering and Materials Science, University of Southern California, California, Los Angeles
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11
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Abstract
A synthetic data set demonstrating a particularly challenging case of indexing ambiguity in the context of radiation damage was generated. This set shall serve as a standard benchmark and reference point for the ongoing development of new methods and new approaches to robust structure solution when single-crystal methods are insufficient. Of the 100 short wedges of data, only the first 36 are currently necessary to solve the structure by `cheating', or using the correct reference structure as a guide. The total wall-clock time and number of crystals required to solve the structure without cheating is proposed as a metric for the efficacy and efficiency of a given multi-crystal automation pipeline.
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Affiliation(s)
- James M. Holton
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA
- Divison of Molecular Biophysics and Bioengineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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12
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Ebrahim A, Appleby MV, Axford D, Beale J, Moreno-Chicano T, Sherrell DA, Strange RW, Hough MA, Owen RL. Resolving polymorphs and radiation-driven effects in microcrystals using fixed-target serial synchrotron crystallography. Acta Crystallogr D Struct Biol 2019; 75:151-159. [PMID: 30821704 PMCID: PMC6400251 DOI: 10.1107/s2059798318010240] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/16/2018] [Indexed: 11/11/2022] Open
Abstract
The ability to determine high-quality, artefact-free structures is a challenge in micro-crystallography, and the rapid onset of radiation damage and requirement for a high-brilliance X-ray beam mean that a multi-crystal approach is essential. However, the combination of crystal-to-crystal variation and X-ray-induced changes can make the formation of a final complete data set challenging; this is particularly true in the case of metalloproteins, where X-ray-induced changes occur rapidly and at the active site. An approach is described that allows the resolution, separation and structure determination of crystal polymorphs, and the tracking of radiation damage in microcrystals. Within the microcrystal population of copper nitrite reductase, two polymorphs with different unit-cell sizes were successfully separated to determine two independent structures, and an X-ray-driven change between these polymorphs was followed. This was achieved through the determination of multiple serial structures from microcrystals using a high-throughput high-speed fixed-target approach coupled with robust data processing.
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Affiliation(s)
- Ali Ebrahim
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Martin V. Appleby
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - John Beale
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Tadeo Moreno-Chicano
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Richard W. Strange
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Michael A. Hough
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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13
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Baaske J, Mühlhäuser WWD, Yousefi OS, Zanner S, Radziwill G, Hörner M, Schamel WWA, Weber W. Optogenetic control of integrin-matrix interaction. Commun Biol 2019; 2:15. [PMID: 30652127 PMCID: PMC6325061 DOI: 10.1038/s42003-018-0264-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022] Open
Abstract
Optogenetic approaches have gathered momentum in precisely modulating and interrogating cellular signalling and gene expression. The use of optogenetics on the outer cell surface to interrogate how cells receive stimuli from their environment, however, has so far not reached its full potential. Here we demonstrate the development of an optogenetically regulated membrane receptor-ligand pair exemplified by the optically responsive interaction of an integrin receptor with the extracellular matrix. The system is based on an integrin engineered with a phytochrome-interacting factor domain (OptoIntegrin) and a red light-switchable phytochrome B-functionalized matrix (OptoMatrix). This optogenetic receptor-ligand pair enables light-inducible and -reversible cell-matrix interaction, as well as the controlled activation of downstream mechanosensory signalling pathways. Pioneering the application of optogenetic switches in the extracellular environment of cells, this OptoMatrix-OptoIntegrin system may serve as a blueprint for rendering matrix-receptor interactions amendable to precise control with light.
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Affiliation(s)
- Julia Baaske
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Wignand W. D. Mühlhäuser
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - O. Sascha Yousefi
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian Zanner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Gerald Radziwill
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | - Maximilian Hörner
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
| | - Wolfgang W. A. Schamel
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Wilfried Weber
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstr. 19A, 79104 Freiburg, Germany
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14
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Heyes DJ, Hardman SJO, Pedersen MN, Woodhouse J, De La Mora E, Wulff M, Weik M, Cammarata M, Scrutton NS, Schirò G. Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering. Commun Biol 2019; 2:1. [PMID: 30740537 PMCID: PMC6318211 DOI: 10.1038/s42003-018-0242-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
Phytochromes are photoreceptor proteins that transmit a light signal from a photosensory region to an output domain. Photoconversion involves protein conformational changes whose nature is not fully understood. Here, we use time-resolved X-ray scattering and optical spectroscopy to study the kinetics of structural changes in a full-length cyanobacterial phytochrome and in a truncated form with no output domain. X-ray and spectroscopic signals on the µs/ms timescale are largely independent of the presence of the output domain. On longer time-scales, large differences between the full-length and truncated proteins indicate the timeframe during which the structural transition is transmitted from the photosensory region to the output domain and represent a large quaternary motion. The suggested independence of the photosensory-region dynamics on the µs/ms timescale defines a time window in which the photoreaction can be characterized (e.g. for optogenetic design) independently of the nature of the engineered output domain.
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Affiliation(s)
- Derren J. Heyes
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Samantha J. O. Hardman
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Martin N. Pedersen
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Joyce Woodhouse
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Eugenio De La Mora
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Michael Wulff
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Marco Cammarata
- Univ. Rennes 1, CNRS, UBL, Institut de Physique de Rennes (IPR) - UMR 6251, 263 avenue du Général Leclerc, 35042 Rennes, France
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
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15
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Yang W, Tu Z, Wang H, Zhang L, Song Q. Glycation of ovalbumin after high-intensity ultrasound pretreatment: effects on conformation, immunoglobulin (Ig)G/IgE binding ability and antioxidant activity. J Sci Food Agric 2018; 98:3767-3773. [PMID: 29344948 DOI: 10.1002/jsfa.8890] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 10/26/2017] [Accepted: 01/11/2018] [Indexed: 06/07/2023]
Abstract
BACKGROUND Ovalbumin (OVA), a protein with excellent nutritional and processing properties, is the major allergen of hen egg white. High-intensity ultrasound treatment increases the immunoglobulin (Ig)G and IgE binding abilities by unfolding the conformational structure of OVA. This may allow a modification of the IgG and IgE binding of OVA by combining high-intensity ultrasound with other methods, such as glycation, thus representing a promising method for the improvement of protein properties. RESULTS Glycation with mannose (M) after ultrasound pretreatment at 0-600 W significantly reduced the IgG and IgE binding abilities and dramatically enhanced the antioxidant activity of OVA-M conjugates, with the lowest values of IgG and IgE binding and highest values of antioxidant capacity observed at 600 W. Polyacrylamide gel electrophoresis showed that the molecular weight of OVA-M conjugates with ultrasound pretreatment increased more than non-pretreatment sample, implying that ultrasound pretreatment promoted glycation. The α-helix content and ultraviolet absorption of OVA were observably increased, whereas β-sheet content, intrinsic fluorescence and surface hydrophobicity were notably decreased, indicating that the tertiary and secondary structures of OVA were markedly changed. CONCLUSION High-intensity ultrasound pretreatment can be conducive to reducing the binding abilities of IgG and IgE and enhancing the antioxidant activity of OVA-M conjugates. Therefore, glycation combined with high-intensity ultrasound pretreatment might be a promising method for producing hypo-allergenic and high-antioxidant OVA products. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Wenhua Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Zongcai Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Lu Zhang
- College of Life Science, Jiangxi Normal University, Nanchang, Jiangxi, China
| | - Qidong Song
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
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16
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Gao Y, Westfield G, Erickson JW, Cerione RA, Skiniotis G, Ramachandran S. Isolation and structure-function characterization of a signaling-active rhodopsin-G protein complex. J Biol Chem 2017; 292:14280-14289. [PMID: 28655769 PMCID: PMC5572916 DOI: 10.1074/jbc.m117.797100] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 05/16/2017] [Revised: 06/26/2017] [Indexed: 01/06/2023] Open
Abstract
The visual photo-transduction cascade is a prototypical G protein-coupled receptor (GPCR) signaling system, in which light-activated rhodopsin (Rho*) is the GPCR catalyzing the exchange of GDP for GTP on the heterotrimeric G protein transducin (GT). This results in the dissociation of GT into its component αT-GTP and β1γ1 subunit complex. Structural information for the Rho*-GT complex will be essential for understanding the molecular mechanism of visual photo-transduction. Moreover, it will shed light on how GPCRs selectively couple to and activate their G protein signaling partners. Here, we report on the preparation of a stable detergent-solubilized complex between Rho* and a heterotrimer (GT*) comprising a GαT/Gαi1 chimera (αT*) and β1γ1 The complex was formed on native rod outer segment membranes upon light activation, solubilized in lauryl maltose neopentyl glycol, and purified with a combination of affinity and size-exclusion chromatography. We found that the complex is fully functional and that the stoichiometry of Rho* to GαT* is 1:1. The molecular weight of the complex was calculated from small-angle X-ray scattering data and was in good agreement with a model consisting of one Rho* and one GT*. The complex was visualized by negative-stain electron microscopy, which revealed an architecture similar to that of the β2-adrenergic receptor-GS complex, including a flexible αT* helical domain. The stability and high yield of the purified complex should allow for further efforts toward obtaining a high-resolution structure of this important signaling complex.
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Affiliation(s)
- Yang Gao
- From the Department of Chemistry and Chemical Biology, Baker Laboratory, and Ithaca, New York 14853
| | - Gerwin Westfield
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Jon W Erickson
- From the Department of Chemistry and Chemical Biology, Baker Laboratory, and Ithaca, New York 14853
| | - Richard A Cerione
- From the Department of Chemistry and Chemical Biology, Baker Laboratory, and Ithaca, New York 14853; Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853.
| | - Georgios Skiniotis
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sekar Ramachandran
- From the Department of Chemistry and Chemical Biology, Baker Laboratory, and Ithaca, New York 14853
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17
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Majkowska-Skrobek G, Łątka A, Berisio R, Maciejewska B, Squeglia F, Romano M, Lavigne R, Struve C, Drulis-Kawa Z. Capsule-Targeting Depolymerase, Derived from Klebsiella KP36 Phage, as a Tool for the Development of Anti-Virulent Strategy. Viruses 2016; 8:v8120324. [PMID: 27916936 PMCID: PMC5192385 DOI: 10.3390/v8120324] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/13/2023] Open
Abstract
The rise of antibiotic-resistant Klebsiella pneumoniae, a leading nosocomial pathogen, prompts the need for alternative therapies. We have identified and characterized a novel depolymerase enzyme encoded by Klebsiella phage KP36 (depoKP36), from the Siphoviridae family. To gain insights into the catalytic and structural features of depoKP36, we have recombinantly produced this protein of 93.4 kDa and showed that it is able to hydrolyze a crude exopolysaccharide of a K. pneumoniae host. Using in vitro and in vivo assays, we found that depoKP36 was also effective against a native capsule of clinical K. pneumoniae strains, representing the K63 type, and significantly inhibited Klebsiella-induced mortality of Galleria mellonella larvae in a time-dependent manner. DepoKP36 did not affect the antibiotic susceptibility of Klebsiella strains. The activity of this enzyme was retained in a broad range of pH values (4.0–7.0) and temperatures (up to 45 °C). Consistently, the circular dichroism (CD) spectroscopy revealed a highly stability with melting transition temperature (Tm) = 65 °C. In contrast to other phage tailspike proteins, this enzyme was susceptible to sodium dodecyl sulfate (SDS) denaturation and proteolytic cleavage. The structural studies in solution showed a trimeric arrangement with a high β-sheet content. Our findings identify depoKP36 as a suitable candidate for the development of new treatments for K. pneumoniae infections.
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Affiliation(s)
- Grażyna Majkowska-Skrobek
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
| | - Agnieszka Łątka
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Barbara Maciejewska
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Maria Romano
- Institute of Biostructures and Bioimaging, National Research Council, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Kasteelpark Arenberg 21, box 2462, B-3001 Leuven, Belgium.
| | - Carsten Struve
- Department of Microbiology and Infection Control, Statens Serum Institut, Artillerivej 5, DK-2300S Copenhagen, Denmark.
- World Health Organization Collaborating Centre for Reference and Research on Escherichia and Klebsiella, Statens Serum Institut, Artillerivej 5, DK-2300S Copenhagen, Denmark.
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland.
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18
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Kyriakidou M, Mavrogenis AF, Kyriazis S, Markouizou A, Theophanides T, Anastassopoulou J. An FT-IR Spectral Analysis of the Effects of γ-Radiation on Normal and Cancerous Cartilage. In Vivo 2016; 30:599-604. [PMID: 27566078] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 07/01/2016] [Indexed: 06/06/2023]
Abstract
In the present study we used non-distractive physicochemical methods to investigate the effect of γ-radiation on human articular cartilage. Comparison between the FT-IR (Fourier transform infrared) spectra before and after irradiation of the cartilage with different doses of radiation showed considerable changes in the spectra. It was found that for doses up to 2 Gy the collagen helices changed their structure from α-helix to random coil. By increasing the radiation dose it was found that the proteins' structure changed further to amyloid-like protein formation and to fragments of glycosaminoglycan chains, which were indicated in the IR spectra. Furthermore, comparison between the spectra of normal and irradiated cartilage, cancerous cartilage and cartilage from patients who received radiotherapy showed similarities in the spectra together with the formation of an aldehyde absorption band at 1740 cm(-1) suggesting that in all cases of cartilage examined,oxidative stress played major role in the damage progression of cartilage.
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Affiliation(s)
- Maria Kyriakidou
- School of Chemical Engineering Laboratory of Radiation Chemistry & Biospectroscopy, National Technical University of Athens, Athens, Greece
| | - Andreas F Mavrogenis
- First Department of Orthopaedics, National and Kapodistrian University of Athens, Athens, Greece
| | - Stylianos Kyriazis
- School of Chemical Engineering Laboratory of Radiation Chemistry & Biospectroscopy, National Technical University of Athens, Athens, Greece
| | - Athina Markouizou
- 2 Radiation Oncology Department, General Metaxa Anticancer Hospital of Piraeus, Piraeus, Greece
| | - Theophile Theophanides
- School of Chemical Engineering Laboratory of Radiation Chemistry & Biospectroscopy, National Technical University of Athens, Athens, Greece
| | - Jane Anastassopoulou
- School of Chemical Engineering Laboratory of Radiation Chemistry & Biospectroscopy, National Technical University of Athens, Athens, Greece
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19
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Liu R, Liang QN, Du SQ, Hu XJ, Ding Y. The crystal structure of red fluorescent protein TagRFP-T reveals the mechanism of its superior photostability. Biochem Biophys Res Commun 2016; 477:229-34. [PMID: 27297107 DOI: 10.1016/j.bbrc.2016.06.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 06/09/2016] [Indexed: 10/21/2022]
Abstract
The red fluorescent protein variant TagRFP-T has greatly improved photostability over its parent molecule, TagRFP, but the underlying mechanism leading to this improvement is to date unknown. The 1.95 Å resolution crystallographic structure of TagRFP-T showed that its chromophore exists as a mixture of cis and trans coplanar isomers in roughly equal proportions. Interestingly, both isomers are able to fluoresce, a property that has never been observed in any other fluorescent protein. We propose a "circular restoration model" for TagRFP-T to explain its superior photostability: There are four co-existing chromophore states (cis/trans protonated/ionized state) that can be driven by light to transform from one state into another. This model also explains how TagRPF-T essentially eliminates the temporary dark state (reversible photobleaching).
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Affiliation(s)
- Rui Liu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qing-Nan Liang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shu-Qi Du
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiao-Jian Hu
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Yu Ding
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China.
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20
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Owen RL, Sherrell DA. Radiation damage and derivatization in macromolecular crystallography: a structure factor's perspective. Acta Crystallogr D Struct Biol 2016; 72:388-94. [PMID: 26960125 PMCID: PMC4784669 DOI: 10.1107/s2059798315021555] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 11/13/2015] [Indexed: 11/11/2022] Open
Abstract
During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on very short time (dose) scales well before global damage becomes apparent. A result of both site-specific radiation damage and derivatization is a change in the relative intensity of reflections. The size and approximate rate of onset of X-ray-induced transformations is compared with the changes expected from derivatization, and strategies for minimizing radiation damage are discussed.
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Affiliation(s)
- Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Darren A. Sherrell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
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21
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Lee SS, Jung HS, Park SK, Lee EM, Singh S, Lee Y, Lee KO, Lee SY, Chung BY. Enhancement of Chaperone Activity of Plant-Specific Thioredoxin through γ-Ray Mediated Conformational Change. Int J Mol Sci 2015; 16:27302-12. [PMID: 26580605 PMCID: PMC4661877 DOI: 10.3390/ijms161126019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/01/2015] [Accepted: 10/23/2015] [Indexed: 11/24/2022] Open
Abstract
AtTDX, a thioredoxin-like plant-specific protein present in Arabidospis is a thermo-stable and multi-functional enzyme. This enzyme is known to act as a thioredoxin and as a molecular chaperone depending upon its oligomeric status. The present study examines the effects of γ-irradiation on the structural and functional changes of AtTDX. Holdase chaperone activity of AtTDX was increased and reached a maximum at 10 kGy of γ-irradiation and declined subsequently in a dose-dependent manner, together with no effect on foldase chaperone activity. However, thioredoxin activity decreased gradually with increasing irradiation. Electrophoresis and size exclusion chromatography analysis showed that AtTDX had a tendency to form high molecular weight (HMW) complexes after γ-irradiation and γ-ray-induced HMW complexes were tightly associated with a holdase chaperone activity. The hydrophobicity of AtTDX increased with an increase in irradiation dose till 20 kGy and thereafter decreased further. Analysis of the secondary structures of AtTDX using far UV-circular dichroism spectra revealed that the irradiation remarkably increased the exposure of β-sheets and random coils with a dramatic decrease in α-helices and turn elements in a dose-dependent manner. The data of the present study suggest that γ-irradiation may be a useful tool for increasing holdase chaperone activity without adversely affecting foldase chaperone activity of thioredoxin-like proteins.
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Affiliation(s)
- Seung Sik Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup 580-185, Korea.
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 200-701, Korea.
| | - Soo-Kwon Park
- Crop Foundation Division, National Institute of Crop Science, Rural Development Administration, 181 Hyeoksin-ro, Iseo-myeon, Wanju-gun 565-851, Korea.
| | - Eun Mi Lee
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup 580-185, Korea.
| | - Sudhir Singh
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup 580-185, Korea.
| | - Yuno Lee
- Division of Applied Life Science (Brain Korea 21 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 660-701, Korea.
| | - Kyun Oh Lee
- Division of Applied Life Science (Brain Korea 21 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 660-701, Korea.
| | - Sang Yeol Lee
- Division of Applied Life Science (Brain Korea 21 Program), Gyeongsang National University, 501 Jinju-daero, Jinju 660-701, Korea.
| | - Byung Yeoup Chung
- Research Division for Biotechnology, Advanced Radiation Technology Institute (ARTI), Korea Atomic Energy Research Institute (KAERI), 29 Geumgu-gil, Jeongeup 580-185, Korea.
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22
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Orekhov PS, Klose D, Mulkidjanian AY, Shaitan KV, Engelhard M, Klare JP, Steinhoff HJ. Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis. PLoS Comput Biol 2015; 11:e1004561. [PMID: 26496122 PMCID: PMC4651059 DOI: 10.1371/journal.pcbi.1004561] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 09/18/2015] [Indexed: 11/19/2022] Open
Abstract
Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors. Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.
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Affiliation(s)
- Philipp S. Orekhov
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Daniel Klose
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
| | - Armen Y. Mulkidjanian
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
- Department of Bioengineering and Bioinformatics and A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Martin Engelhard
- Max-Planck-Institute for Molecular Physiology, Dortmund, Germany
| | - Johann P. Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
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23
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Galli L, Son SK, White TA, Santra R, Chapman HN, Nanao MH. Towards RIP using free-electron laser SFX data. J Synchrotron Radiat 2015; 22:249-55. [PMID: 25723926 DOI: 10.1107/s1600577514027854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/21/2014] [Indexed: 05/03/2023]
Abstract
Here, it is shown that simulated native serial femtosecond crystallography (SFX) cathepsin B data can be phased by rapid ionization of sulfur atoms. Utilizing standard software adopted for radiation-damage-induced phasing (RIP), the effects on both substructure determination and phasing of the number of collected patterns and fluences are explored for experimental conditions already available at current free-electron laser facilities.
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Affiliation(s)
- Lorenzo Galli
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Sang Kil Son
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Robin Santra
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Max H Nanao
- EMBL, Grenoble Outstation, Rue Jules Horowitz 6, 38042 Grenoble, France
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24
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Bury C, Garman EF, Ginn HM, Ravelli RBG, Carmichael I, Kneale G, McGeehan JE. Radiation damage to nucleoprotein complexes in macromolecular crystallography. J Synchrotron Radiat 2015; 22:213-24. [PMID: 25723923 PMCID: PMC4344358 DOI: 10.1107/s1600577514026289] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 11/30/2014] [Indexed: 05/23/2023]
Abstract
Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses.
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Affiliation(s)
- Charles Bury
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Helen Mary Ginn
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Raimond B. G. Ravelli
- Institute of Nanoscopy, Maastricht University, PO Box 616, Maastricht 6200 MD, The Netherlands
| | - Ian Carmichael
- Notre Dame Radiation Laboratory, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Geoff Kneale
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
| | - John E. McGeehan
- Molecular Biophysics, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY, UK
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25
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Lórenz-Fonfría VA, Heberle J. Proton transfer and protein conformation dynamics in photosensitive proteins by time-resolved step-scan Fourier-transform infrared spectroscopy. J Vis Exp 2014:e51622. [PMID: 24998200 PMCID: PMC4208678 DOI: 10.3791/51622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as -10(-) (4), sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent.
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Affiliation(s)
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin;
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26
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Wickstrand C, Dods R, Royant A, Neutze R. Bacteriorhodopsin: Would the real structural intermediates please stand up? Biochim Biophys Acta Gen Subj 2014; 1850:536-53. [PMID: 24918316 DOI: 10.1016/j.bbagen.2014.05.021] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined. SCOPE OF REVIEW We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data. MAJOR CONCLUSIONS An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212. GENERAL SIGNIFICANCE A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Antoine Royant
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France; European Synchrotron Radiation Facility, F-38043 Grenoble, France.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.
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27
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Muders V, Kerruth S, Lórenz-Fonfría VA, Bamann C, Heberle J, Schlesinger R. Resonance Raman and FTIR spectroscopic characterization of the closed and open states of channelrhodopsin-1. FEBS Lett 2014; 588:2301-6. [PMID: 24859039 DOI: 10.1016/j.febslet.2014.05.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 11/17/2022]
Abstract
Channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) is a light-activated cation channel, which is a promising optogenetic tool. We show by resonance Raman spectroscopy and retinal extraction followed by high pressure liquid chromatography (HPLC) that the isomeric ratio of all-trans to 13-cis of solubilized channelrhodopsin-1 is with 70:30 identical to channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Critical frequency shifts in the retinal vibrations are identified in the Raman spectrum upon transition to the open (conductive P2(380)) state. Fourier transform infrared spectroscopy (FTIR) spectra indicate different structures of the open states in the two channelrhodopsins as reflected by the amide I bands and the protonation pattern of acidic amino acids.
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Affiliation(s)
- Vera Muders
- Genetic Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Silke Kerruth
- Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | | | - Christian Bamann
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, 60438 Frankfurt/Main, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
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28
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Sridharan V, Aykin-Burns N, Tripathi P, Krager KJ, Sharma SK, Moros EG, Corry PM, Nowak G, Hauer-Jensen M, Boerma M. Radiation-induced alterations in mitochondria of the rat heart. Radiat Res 2014; 181:324-34. [PMID: 24568130 PMCID: PMC4029615 DOI: 10.1667/rr13452.1] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Radiation therapy for the treatment of thoracic cancers may be associated with radiation-induced heart disease (RIHD), especially in long-term cancer survivors. Mechanisms by which radiation causes heart disease are largely unknown. To identify potential long-term contributions of mitochondria in the development of radiation-induced heart disease, we examined the time course of effects of irradiation on cardiac mitochondria. In this study, Sprague-Dawley male rats received image-guided local X irradiation of the heart with a single dose ranging from 3-21 Gy. Two weeks after irradiation, left ventricular mitochondria were isolated to assess the dose-dependency of the mitochondrial permeability transition pore (mPTP) opening in a mitochondrial swelling assay. At time points from 6 h to 9 months after a cardiac dose of 21 Gy, the following analyses were performed: left ventricular Bax and Bcl-2 protein levels; apoptosis; mitochondrial inner membrane potential and mPTP opening; mitochondrial mass and expression of mitophagy mediators Parkin and PTEN induced putative kinase-1 (PINK-1); mitochondrial respiration and protein levels of succinate dehydrogenase A (SDHA); and the 70 kDa subunit of complex II. Local heart irradiation caused a prolonged increase in Bax/Bcl-2 ratio and induced apoptosis between 6 h and 2 weeks. The mitochondrial membrane potential was reduced until 2 weeks, and the calcium-induced mPTP opening was increased from 6 h up to 9 months. An increased mitochondrial mass together with unaltered levels of Parkin suggested that mitophagy did not occur. Lastly, we detected a significant decrease in succinate-driven state 2 respiration in isolated mitochondria from 2 weeks up to 9 months after irradiation, coinciding with reduced mitochondrial levels of succinate dehydrogenase A. Our results suggest that local heart irradiation induces long-term changes in cardiac mitochondrial membrane functions, levels of SDH and state 2 respiration. At any time after exposure to radiation, cardiac mitochondria are more prone to mPTP opening. Future studies will determine whether this makes the heart more susceptible to secondary stressors such as calcium overload or ischemia/reperfusion.
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Affiliation(s)
- Vijayalakshmi Sridharan
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
| | - Nukhet Aykin-Burns
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
| | - Preeti Tripathi
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
| | - Kimberly J. Krager
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
| | - Sunil K. Sharma
- University of Arkansas for Medical Sciences, Department of Radiation Oncology, Little Rock, Arkansas
| | - Eduardo G. Moros
- Moffitt Cancer Center and Research Institute, Department of Radiation Oncology, Tampa, Florida
| | - Peter M. Corry
- University of Arkansas for Medical Sciences, Department of Radiation Oncology, Little Rock, Arkansas
| | - Grazyna Nowak
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Little Rock, Arkansas
| | - Martin Hauer-Jensen
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
- Surgical Service, Central Arkansas Veterans Healthcare System, Little Rock, Arkansas
| | - Marjan Boerma
- University of Arkansas for Medical Sciences, Department of Pharmaceutical Sciences, Division of Radiation Health, Little Rock, Arkansas
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29
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Abstract
Fluorescent proteins have revolutionized life sciences because they allow noninvasive and highly specific labeling of biological samples. The subset of "phototransformable" fluorescent proteins recently attracted a widespread interest, as their fluorescence state can be modified upon excitation at defined wavelengths. The fluorescence emission of Reversibly Switchable Fluorescent Proteins (RSFPs), in particular, can be repeatedly switched on and off. RSFPs enable many new exciting modalities in fluorescence microscopy and biotechnology, including protein tracking, photochromic Förster Resonance Energy Transfer, super-resolution microscopy, optogenetics, and ultra-high-density optical data storage. Photoswitching in RSFPs typically results from chromophore cis-trans isomerization accompanied by a protonation change, but other switching schemes based on, e.g., chromophore hydration/dehydration have also been discovered. In this chapter, we review the main structural features at the basis of photoswitching in RSFPs.
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Affiliation(s)
- Chenxi Duan
- Institut de Biologie Structurale, Université Grenoble Alpes, Grenoble, France
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Sutton KA, Black PJ, Mercer KR, Garman EF, Owen RL, Snell EH, Bernhard WA. Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies. Acta Crystallogr D Biol Crystallogr 2013; 69:2381-94. [PMID: 24311579 PMCID: PMC3852651 DOI: 10.1107/s0907444913022117] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/07/2013] [Indexed: 11/24/2022]
Abstract
Electron paramagnetic resonance (EPR) and online UV-visible absorption microspectrophotometry with X-ray crystallography have been used in a complementary manner to follow X-ray-induced disulfide-bond cleavage. Online UV-visible spectroscopy showed that upon X-irradiation, disulfide radicalization appeared to saturate at an absorbed dose of approximately 0.5-0.8 MGy, in contrast to the saturating dose of ∼0.2 MGy observed using EPR at much lower dose rates. The observations suggest that a multi-track model involving product formation owing to the interaction of two separate tracks is a valid model for radiation damage in protein crystals. The saturation levels are remarkably consistent given the widely different experimental parameters and the range of total absorbed doses studied. The results indicate that even at the lowest doses used for structural investigations disulfide bonds are already radicalized. Multi-track considerations offer the first step in a comprehensive model of radiation damage that could potentially lead to a combined computational and experimental approach to identifying when damage is likely to be present, to quantitate it and to provide the ability to recover the native unperturbed structure.
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Affiliation(s)
- Kristin A. Sutton
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086, USA
| | - Paul J. Black
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Kermit R. Mercer
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, Oxfordshire OX1 3QU, England
| | - Robin L. Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, England
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14086, USA
- Department of Structural Biology, SUNY Buffalo Medical School, 700 Ellicott Street, Buffalo, NY 14203, USA
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31
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Zou M, Zhang L, Wang J, Wang Q, Gao J, Fan P. Investigation on interaction and sonodynamic damage of fluorescein derivants to bovine serum albumin (BSA) under ultrasonic irradiation. Spectrochim Acta A Mol Biomol Spectrosc 2013; 110:364-376. [PMID: 23583854 DOI: 10.1016/j.saa.2013.03.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 02/13/2013] [Accepted: 03/17/2013] [Indexed: 06/02/2023]
Abstract
The fluorescein derivants (Fluorescein: (2-(6-Hydroxy-3-oxo-(3H)-xanthen-9-yl) benzoic acid), Fluorescein-DA: (Bis [N,N-bis (carboxymethyl) aminomethyl] fluorescein) and Fluorescein-DA-Fe(III): (Bis [N,N-bis (carboxymethyl) aminomethyl] fluorescein-Ferrous(III)) with a tricyclic plane structure were used to study the interaction and sonodynamic damage to bovine serum albumin (BSA) under ultrasonic irradiation through fluorospectrometry and UV-vis spectrophotometry. Besides, because of the existence of Fe(III) ion in Fluorescein-DA-Fe(III), under ultrasonic irradiation the sonocatalytic activity in the damage of BSA molecules was also found. Three-dimensional fluorescence spectra and three-dimensional fluorescence contour profile spectra were mentioned to determine the fluorescence quenching and the conformation change of BSA in the absence and presence of these fluorescein derivants. As judged from the experimental results, the fluorescence quenching of BSA in aqueous solution caused by these fluorescein derivants were all attributed to static quenching process. The damage degree and mode were related to some factors such as ultrasonic irradiation time, fluorescein derivant concentration and ionic strength. Finally, several quenchers were used to determine the amount and kind of generated reactive oxygen species (ROS) during sonodynamic and sonocatalytic reaction processes. It suggests that these fluorescein derivants induce protein damage via various ROS, at least, including singlet oxygen ((1)O2) and hydroxyl radicals (OH). Perhaps, this paper may offer some important subjects for broadening the application of these fluorescein derivants in sonodynamic therapy (SDT) and sonocatalytic therapy (SCT) technologies for tumor treatment.
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Affiliation(s)
- Mingming Zou
- College of Chemistry, Liaoning University, Shenyang 110036, PR China
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Chen Y, Cruz-Chu ER, Woodard J, Gartia MR, Schulten K, Liu L. Electrically induced conformational change of peptides on metallic nanosurfaces. ACS Nano 2012; 6:8847-8856. [PMID: 22897498 PMCID: PMC3482133 DOI: 10.1021/nn3027408] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Surface immobilized biomolecular probes are used in many areas of biomedical research, such as genomics, proteomics, immunology, and pathology. Although the structural conformations of small DNA and peptide molecules in free solution are well studied both theoretically and experimentally, the conformation of small biomolecules bound on surfaces, especially under the influence of external electric fields, is poorly understood. Using a combination of molecular dynamics simulation and surface-enhanced Raman spectroscopy, we study the external electric field-induced conformational change of dodecapeptide probes tethered to a nanostructured metallic surface. Surface-tethered peptides with and without phosphorylated tyrosine residues are compared to show that peptide conformational change under electric field is sensitive to biochemical modification. Our study proposes a highly sensitive in vitro nanoscale electro-optical detection and manipulation method for biomolecule conformation and charge at bio-nano interfaces.
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Affiliation(s)
- Yi Chen
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
| | - Eduardo R. Cruz-Chu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Jaie Woodard
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
| | - Manas Ranjan Gartia
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign
- Department of Nuclear, Plasma and Radiological Engineering, University of Illinois at Urbana-Champaign
| | - Klaus Schulten
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
- Department of Physics, University of Illinois at Urbana-Champaign
| | - Logan Liu
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign
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33
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Liu B, Zhang Y, Sage JT, Soltis SM, Doukov T, Chen Y, Stout CD, Fee JA. Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: a combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B). Biochim Biophys Acta 2012; 1817:658-65. [PMID: 22226917 PMCID: PMC3294259 DOI: 10.1016/j.bbabio.2011.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/09/2011] [Accepted: 12/09/2011] [Indexed: 11/30/2022]
Abstract
The purpose of the work was to provide a crystallographic demonstration of the venerable idea that CO photolyzed from ferrous heme-a(3) moves to the nearby cuprous ion in the cytochrome c oxidases. Crystal structures of CO-bound cytochrome ba(3)-oxidase from Thermus thermophilus, determined at ~2.8-3.2Å resolution, reveal a Fe-C distance of ~2.0Å, a Cu-O distance of 2.4Å and a Fe-C-O angle of ~126°. Upon photodissociation at 100K, X-ray structures indicate loss of Fe(a3)-CO and appearance of Cu(B)-CO having a Cu-C distance of ~1.9Å and an O-Fe distance of ~2.3Å. Absolute FTIR spectra recorded from single crystals of reduced ba(3)-CO that had not been exposed to X-ray radiation, showed several peaks around 1975cm(-1); after photolysis at 100K, the absolute FTIR spectra also showed a significant peak at 2050cm(-1). Analysis of the 'light' minus 'dark' difference spectra showed four very sharp CO stretching bands at 1970cm(-1), 1977cm(-1), 1981cm(-1), and 1985cm(-1), previously assigned to the Fe(a3)-CO complex, and a significantly broader CO stretching band centered at ~2050cm(-1), previously assigned to the CO stretching frequency of Cu(B) bound CO. As expected for light propagating along the tetragonal axis of the P4(3)2(1)2 space group, the single crystal spectra exhibit negligible dichroism. Absolute FTIR spectrometry of a CO-laden ba(3) crystal, exposed to an amount of X-ray radiation required to obtain structural data sets before FTIR characterization, showed a significant signal due to photogenerated CO(2) at 2337cm(-1) and one from traces of CO at 2133cm(-1); while bands associated with CO bound to either Fe(a3) or to Cu(B) in "light" minus "dark" FTIR difference spectra shifted and broadened in response to X-ray exposure. In spite of considerable radiation damage to the crystals, both X-ray analysis at 2.8 and 3.2Å and FTIR spectra support the long-held position that photolysis of Fe(a3)-CO in cytochrome c oxidases leads to significant trapping of the CO on the Cu(B) atom; Fe(a3) and Cu(B) ligation, at the resolutions reported here, are otherwise unaltered.
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Affiliation(s)
- Bin Liu
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Yang Zhang
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 110 Forsyth St., Boston MA 02115
| | - J. Timothy Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, 110 Forsyth St., Boston MA 02115
| | - S. Michael Soltis
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park CA 94025
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park CA 94025
| | - Ying Chen
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - C. David Stout
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - James A. Fee
- The Scripps Research Institute, Department of Molecular Biology, MB-8, 10550 North Torrey Pines Road, La Jolla, CA 92037
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Koopmann R, Cupelli K, Redecke L, Nass K, Deponte DP, White TA, Stellato F, Rehders D, Liang M, Andreasson J, Aquila A, Bajt S, Barthelmess M, Barty A, Bogan MJ, Bostedt C, Boutet S, Bozek JD, Caleman C, Coppola N, Davidsson J, Doak RB, Ekeberg T, Epp SW, Erk B, Fleckenstein H, Foucar L, Graafsma H, Gumprecht L, Hajdu J, Hampton CY, Hartmann A, Hartmann R, Hauser G, Hirsemann H, Holl P, Hunter MS, Kassemeyer S, Kirian RA, Lomb L, Maia FRNC, Kimmel N, Martin AV, Messerschmidt M, Reich C, Rolles D, Rudek B, Rudenko A, Schlichting I, Schulz J, Seibert MM, Shoeman RL, Sierra RG, Soltau H, Stern S, Strüder L, Timneanu N, Ullrich J, Wang X, Weidenspointner G, Weierstall U, Williams GJ, Wunderer CB, Fromme P, Spence JCH, Stehle T, Chapman HN, Betzel C, Duszenko M. In vivo protein crystallization opens new routes in structural biology. Nat Methods 2012; 9:259-62. [PMID: 22286384 PMCID: PMC3429599 DOI: 10.1038/nmeth.1859] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 12/21/2011] [Indexed: 11/08/2022]
Abstract
Protein crystallization in cells has been observed several times in nature. However, owing to their small size these crystals have not yet been used for X-ray crystallographic analysis. We prepared nano-sized in vivo-grown crystals of Trypanosoma brucei enzymes and applied the emerging method of free-electron laser-based serial femtosecond crystallography to record interpretable diffraction data. This combined approach will open new opportunities in structural systems biology.
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Affiliation(s)
- Rudolf Koopmann
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
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35
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Chandrapala J, Zisu B, Palmer M, Kentish S, Ashokkumar M. Effects of ultrasound on the thermal and structural characteristics of proteins in reconstituted whey protein concentrate. Ultrason Sonochem 2011; 18:951-7. [PMID: 21262585 DOI: 10.1016/j.ultsonch.2010.12.016] [Citation(s) in RCA: 393] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Revised: 12/24/2010] [Accepted: 12/27/2010] [Indexed: 05/22/2023]
Abstract
The sonication-induced changes in the structural and thermal properties of proteins in reconstituted whey protein concentrate (WPC) solutions were examined. Differential scanning calorimetry, UV-vis, fluorescence and circular dichroism spectroscopic techniques were used to determine the thermal properties of proteins, measure thiol groups and monitor changes to protein hydrophobicity and secondary structure, respectively. The enthalpy of denaturation decreased when WPC solutions were sonicated for up to 5 min. Prolonged sonication increased the enthalpy of denaturation due to protein aggregation. Sonication did not alter the thiol content but resulted in minor changes to the secondary structure and hydrophobicity of the protein. Overall, the sonication process had little effect on the structure of proteins in WPC solutions which is critical to preserving functional properties during the ultrasonic processing of whey protein based dairy products.
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36
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Kondoh M, Shiraishi C, Müller P, Ahmad M, Hitomi K, Getzoff ED, Terazima M. Light-induced conformational changes in full-length Arabidopsis thaliana cryptochrome. J Mol Biol 2011; 413:128-37. [PMID: 21875594 DOI: 10.1016/j.jmb.2011.08.031] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 08/11/2011] [Accepted: 08/15/2011] [Indexed: 11/17/2022]
Abstract
Cryptochromes (CRYs) are widespread flavoproteins with homology to photolyases (PHRs), a class of blue-light-activated DNA repair enzymes. Unlike PHRs, both plant and animal CRYs have a C-terminal domain. This cryptochrome C-terminal (CCT) domain mediates interactions with other proteins, while the PHR-like domain converts light energy into a signal via reduction and radical formation of the flavin adenine dinucleotide cofactor. However, the mechanism by which the PHR-like domain regulates the CCT domain is not known. Here, we applied the pulsed-laser-induced transient grating method to detect conformational changes induced by blue-light excitation of full-length Arabidopsis thaliana cryptochrome 1 (AtCRY1). A significant reduction in the diffusion coefficient of AtCRY1 was observed upon photoexcitation, indicating that a large conformational change occurs in this monomeric protein. AtCRY1 containing a single mutation (W324F) that abolishes an intra-protein electron transfer cascade did not exhibit this conformational change. Moreover, the conformational change was much reduced in protein lacking the CCT domain. Thus, we conclude that the observed large conformational changes triggered by light excitation of the PHR-like domain result from C-terminal domain rearrangement. This inter-domain modulation would be critical for CRYs' ability to transduce a blue-light signal into altered protein-protein interactions for biological activity. Lastly, we demonstrate that the transient grating technique provides a powerful method for the direct observation and understanding of photoreceptor dynamics.
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Affiliation(s)
- Masato Kondoh
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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37
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Dean K, Lubbeck J, Binder J, Schwall L, Jimenez R, Palmer A. Analysis of red-fluorescent proteins provides insight into dark-state conversion and photodegradation. Biophys J 2011; 101:961-9. [PMID: 21843488 PMCID: PMC3175071 DOI: 10.1016/j.bpj.2011.06.055] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Revised: 06/03/2011] [Accepted: 06/28/2011] [Indexed: 01/30/2023] Open
Abstract
Fluorescent proteins (FPs) are powerful tools that permit real-time visualization of cellular processes. The utility of a given FP for a specific experiment depends strongly on its effective brightness and overall photostability. However, the brightness of FPs is limited by dark-state conversion (DSC) and irreversible photobleaching, which occur on different timescales. Here, we present in vivo ensemble assays for measuring DSC and irreversible photobleaching under continuous and pulsed illumination. An analysis of closely related red FPs reveals that DSC and irreversible photobleaching are not always connected by the same mechanistic pathway. DSC occurs out of the first-excited singlet state, and its magnitude depends predominantly on the kinetics for recovery out of the dark state. The experimental results can be replicated through kinetic simulations of a four-state model of the electronic states. The methodology presented here allows light-driven dynamics to be studied at the ensemble level over six orders of magnitude in time (microsecond to second timescales).
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Affiliation(s)
- Kevin M. Dean
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Jennifer L. Lubbeck
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
- JILA/National Institute of Standards and Technology, University of Colorado, Boulder, Colorado
| | - Jennifer K. Binder
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
| | - Linda R. Schwall
- JILA/National Institute of Standards and Technology, University of Colorado, Boulder, Colorado
| | - Ralph Jimenez
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
- JILA/National Institute of Standards and Technology, University of Colorado, Boulder, Colorado
| | - Amy E. Palmer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado
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Dalsgaard TK, Nielsen JH, Brown BE, Stadler N, Davies MJ. Dityrosine, 3,4-dihydroxyphenylalanine (DOPA), and radical formation from tyrosine residues on milk proteins with globular and flexible structures as a result of riboflavin-mediated photo-oxidation. J Agric Food Chem 2011; 59:7939-7947. [PMID: 21696221 DOI: 10.1021/jf200277r] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Riboflavin-mediated photo-oxidative damage to protein Tyr residues has been examined to determine whether protein structure influences competing protein oxidation pathways in single proteins and protein mixtures. EPR studies resulted in the detection of Tyr-derived o-semiquione radicals, with this species suggested to arise from oxidation of 3,4-dihydroxyphenylalanine (DOPA). The yield of this radical was lower in samples containing β-casein than in samples containing only globular proteins. Consistent with this observation, the yield of DOPA detected on β-casein was lower than that on two globular proteins, BSA and β-lactoglobulin. In contrast, samples with β-casein gave higher yields of dityrosine than samples containing BSA and β-lactoglobulin. These results indicate that the flexible structure of β-casein favors radical-radical termination of tyrosyl radicals to give dityrosine, whereas the less flexible structure of globular proteins decreases the propensity for tyrosyl radicals to dimerize, with this resulting in higher yields of DOPA and its secondary radical.
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Affiliation(s)
- Trine K Dalsgaard
- Department of Food Science, Aarhus University, DK-8830 Tjele, Denmark.
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39
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Ibrahimkutty S, Kim J, Cammarata M, Ewald F, Choi J, Ihee H, Plech A. Ultrafast structural dynamics of the photocleavage of protein hybrid nanoparticles. ACS Nano 2011; 5:3788-94. [PMID: 21504177 DOI: 10.1021/nn200120e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Protein-coated gold nanoparticles in suspension are excited by intense laser pulses to mimic the light-induced effect on biomolecules that occur in photothermal laser therapy with nanoparticles as photosensitizer. Ultrafast X-ray scattering employed to access the nanoscale structural modifications of the protein-nanoparticle hybrid reveals that the protein shell is expelled as a whole without denaturation at a laser fluence that coincides with the bubble formation threshold. In this ultrafast heating mediated by the nanoparticles, time-resolved scattering data show that proteins are not denatured in terms of secondary structure even at much higher temperatures than the static thermal denaturation temperature, probably because time is too short for the proteins to unfold and the temperature stimulus has vanished before this motion sets in. Consequently the laser pulse length has a strong influence on whether the end result is the ligand detachment (for example drug delivery) or biomaterial degradation.
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Affiliation(s)
- Shyjumon Ibrahimkutty
- Institute for Synchrotron Radiation, Karlsruhe Institute of Technology, Postfach 3640, D-76021 Karlsruhe, EU
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40
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Liu B, Wang DJ, Wang X, Liu BM, Kong YM, He LL, Wang J, Xu SK. Spectroscopic investigation on protein damage by ciprofloxacin under ultrasonic irradiation. Spectrochim Acta A Mol Biomol Spectrosc 2011; 78:712-717. [PMID: 21177138 DOI: 10.1016/j.saa.2010.11.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 11/16/2010] [Accepted: 11/30/2010] [Indexed: 05/30/2023]
Abstract
In recent years, sonodynamic activities of many drugs have attracted more and more attention of researchers. The correlative study will promote the development of sonodynamic therapy (SDT) in anti-tumor treatment. In this work, bovine serum albumin (BSA) was used as a protein model to investigate the intensifying effects of ciprofloxacin (CPFX) ultrasonically induced protein damage by UV-vis and fluorescence spectra. Meanwhile, the conformation of BSA is changed upon the addition of CPFX and metal ions under ultrasound (US) so that the damaging site of BSA is considered. Various influencing factors, such as US irradiation time, metal ions, solution temperature and ionic strength, on the ultrasonically induced BSA damage are discussed. It was showed that CPFX could enhance ultrasonically induced BSA damage. The damage degree of BSA was aggravated with the increasing of US irradiation time, solution temperature, ionic strength as well as the addition of metal ions. Furthermore, the reactive oxygen species (ROS) in reaction system were detected by oxidation-extraction photometry (OEP). Experimental results also showed that US could activate CPFX to produce ROS, which were mainly determined as superoxide radical anion (.O2-) and hydroxyl radical (.OH).
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Affiliation(s)
- Bin Liu
- Department of Chemistry, Northeastern University, Shenyang 110819, PR China
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41
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Estey T, Chen Y, Carpenter JF, Vasiliou V. Structural and functional modifications of corneal crystallin ALDH3A1 by UVB light. PLoS One 2010; 5:e15218. [PMID: 21203538 PMCID: PMC3006428 DOI: 10.1371/journal.pone.0015218] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 10/29/2010] [Indexed: 11/18/2022] Open
Abstract
As one of the most abundantly expressed proteins in the mammalian corneal epithelium, aldehyde dehydrogenase 3A1 (ALDH3A1) plays critical and multifaceted roles in protecting the cornea from oxidative stress. Recent studies have demonstrated that one protective mechanism of ALDH3A1 is the direct absorption of UV-energy, which reduces damage to other corneal proteins such as glucose-6-phosphate dehydrogenase through a competition mechanism. UV-exposure, however, leads to the inactivation of ALDH3A1 in such cases. In the current study, we demonstrate that UV-light caused soluble, non-native aggregation of ALDH3A1 due to both covalent and non-covalent interactions, and that the formation of the aggregates was responsible for the loss of ALDH3A1 enzymatic activity. Spectroscopic studies revealed that as a result of aggregation, the secondary and tertiary structure of ALDH3A1 were perturbed. LysC peptide mapping using MALDI-TOF mass spectrometry shows that UV-induced damage to ALDH3A1 also includes chemical modifications to Trp, Met, and Cys residues. Surprisingly, the conserved active site Cys of ALDH3A1 does not appear to be affected by UV-exposure; this residue remained intact after exposure to UV-light that rendered the enzyme completely inactive. Collectively, our data suggest that the UV-induced inactivation of ALDH3A1 is a result of non-native aggregation and associated structural changes rather than specific damage to the active site Cys.
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Affiliation(s)
- Tia Estey
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Ying Chen
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - John F. Carpenter
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Vasilis Vasiliou
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- Molecular Toxicology & Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
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42
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Warkentin M, Thorne RE. Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements. Acta Crystallogr D Biol Cryst 2010; 66:1092-100. [PMID: 20944242 PMCID: PMC2954455 DOI: 10.1107/s0907444910035523] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Accepted: 09/03/2010] [Indexed: 11/10/2022]
Abstract
The temperature-dependence of radiation damage to thaumatin crystals between T = 300 and 100 K is reported. The amount of damage for a given dose decreases sharply as the temperature decreases from 300 to 220 K and then decreases more gradually on further cooling below the protein-solvent glass transition. Two regimes of temperature-activated behavior were observed. At temperatures above ∼200 K the activation energy of 18.0 kJ mol(-1) indicates that radiation damage is dominated by diffusive motions in the protein and solvent. At temperatures below ∼200 K the activation energy is only 1.00 kJ mol(-1), which is of the order of the thermal energy. Similar activation energies describe the temperature-dependence of radiation damage to a variety of solvent-free small-molecule organic crystals over the temperature range T = 300-80 K. It is suggested that radiation damage in this regime is vibrationally assisted and that the freezing-out of amino-acid scale vibrations contributes to the very weak temperature-dependence of radiation damage below ∼80 K. Analysis using the radiation-damage model of Blake and Phillips [Blake & Phillips (1962), Biological Effects of Ionizing Radiation at the Molecular Level, pp. 183-191] indicates that large-scale conformational and molecular motions are frozen out below T = 200 K but become increasingly prevalent and make an increasing contribution to damage at higher temperatures. Possible alternative mechanisms for radiation damage involving the formation of hydrogen-gas bubbles are discussed and discounted. These results have implications for mechanistic studies of proteins and for studies of the protein glass transition. They also suggest that data collection at T ≃ 220 K may provide a viable alternative for structure determination when cooling-induced disorder at T = 100 is excessive.
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Vreede J, Juraszek J, Bolhuis PG. Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proc Natl Acad Sci U S A 2010; 107:2397-402. [PMID: 20133754 PMCID: PMC2823881 DOI: 10.1073/pnas.0908754107] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the dynamics of large-scale conformational changes in proteins still poses a challenge for molecular simulations. We employ transition path sampling of explicit solvent molecular dynamics trajectories to obtain atomistic insight in the reaction network of the millisecond timescale partial unfolding transition in the photocycle of the bacterial sensor photoactive yellow protein. Likelihood maximization analysis predicts the best model for the reaction coordinates of each substep as well as tentative transition states, without further simulation. We find that the unfolding of the alpha-helical region 43-51 is followed by sequential solvent exposure of both Glu46 and the chromophore. Which of these two residues is exposed first is correlated with the presence of a salt bridge that is part of the N-terminal domain. Additional molecular dynamics simulations indicate that the exposure of the chromophore does not result in a productive pathway. We discuss several possibilities for experimental validation of these predictions. Our results open the way for studying millisecond conformational changes in other medium-sized (signaling) proteins.
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Affiliation(s)
- Jocelyne Vreede
- Van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands.
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Hayashi T. JSCTR-CTR commentary. What is the function of proline in the collagen molecule? Connect Tissue Res 2010; 51:81. [PMID: 20067421 DOI: 10.3109/03008200903471776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Orlova MA, Kuznetsov DA, Latysheva AV, Orlov AP. [The study of the creatine kinase radiation stability in 25Mg-enzyme enrichment experiment]. Radiats Biol Radioecol 2009; 49:580-584. [PMID: 19947522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The radiation inactivation technique was applied to conduct the study on catalytic activity changes of creatine kinase species isolated from the Mid-Asian Death Adder venom. Both intact and the 25Mg-enriched enzyme samples were separately tested. Some differences in radiation stability levels were found to be indicating to a shift in conformational condition (a so called "conformational distribution") of the native enzyme that had happen in the presence of the magnetic nuclei excess.
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46
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Yamamoto M, Hayakawa N, Murakami M, Kouyama T. Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels. J Mol Biol 2009; 393:559-73. [PMID: 19712684 DOI: 10.1016/j.jmb.2009.08.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [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: 04/20/2009] [Revised: 08/18/2009] [Accepted: 08/19/2009] [Indexed: 11/16/2022]
Abstract
The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.
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Affiliation(s)
- Masataka Yamamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
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Macedo S, Pechlaner M, Schmid W, Weik M, Sato K, Dennison C, Djinović-Carugo K. Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection? J Synchrotron Radiat 2009; 16:191-204. [PMID: 19240331 DOI: 10.1107/s0909049509003331] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 01/27/2009] [Indexed: 05/27/2023]
Abstract
One of the first events taking place when a crystal of a metalloprotein is exposed to X-ray radiation is photoreduction of the metal centres. The oxidation state of a metal cannot always be determined from routine X-ray diffraction experiments alone, but it may have a crucial impact on the metal's environment and on the analysis of the structural data when considering the functional mechanism of a metalloenzyme. Here, UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects. UV-Vis absorption spectra of native crystals, as well as those soaked in 18 different radioprotectants, show dramatic metal reduction occurring in the first 60 s of irradiation with an X-ray beam from a third-generation synchrotron source. Among the tested radioprotectants only potassium hexacyanoferrate(III) seems to be capable of partially mitigating the rate of metal photoreduction at the concentrations used, but not to a sufficient extent that would allow a complete data set to be recorded from a fully oxidized crystal. On the other hand, analysis of the X-ray crystallographic data confirms ascorbate as an efficient protecting agent against radiation damage, other than metal centre reduction, and suggests further testing of HEPES and 2,3-dichloro-1,4-naphtoquinone as potential scavengers.
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Affiliation(s)
- Sofia Macedo
- Department for Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, 1030 Vienna, Austria
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Abstract
Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to radiation damage issues, and to provide references to the more exacting and detailed work. No attempt has been made to report precise numbers (a factor of two is considered satisfactory), and, since there are aspects of radiation damage that are demonstrably unpredictable, the 'worst case scenario' as well as the 'average crystal' are discussed in terms of the practicalities of data collection.
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Affiliation(s)
- James M Holton
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2330, USA.
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Fischetti RF, Xu S, Yoder DW, Becker M, Nagarajan V, Sanishvili R, Hilgart MC, Stepanov S, Makarov O, Smith JL. Mini-beam collimator enables microcrystallography experiments on standard beamlines. J Synchrotron Radiat 2009; 16:217-25. [PMID: 19240333 PMCID: PMC2725011 DOI: 10.1107/s0909049508040612] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 12/02/2008] [Indexed: 05/20/2023]
Abstract
The high-brilliance X-ray beams from undulator sources at third-generation synchrotron facilities are excellent tools for solving crystal structures of important and challenging biological macromolecules and complexes. However, many of the most important structural targets yield crystals that are too small or too inhomogeneous for a ;standard' beam from an undulator source, approximately 25-50 microm (FWHM) in the vertical and 50-100 microm in the horizontal direction. Although many synchrotron facilities have microfocus beamlines for other applications, this capability for macromolecular crystallography was pioneered at ID-13 of the ESRF. The National Institute of General Medical Sciences and National Cancer Institute Collaborative Access Team (GM/CA-CAT) dual canted undulator beamlines at the APS deliver high-intensity focused beams with a minimum focal size of 20 microm x 65 microm at the sample position. To meet growing user demand for beams to study samples of 10 microm or less, a ;mini-beam' apparatus was developed that conditions the focused beam to either 5 microm or 10 microm (FWHM) diameter with high intensity. The mini-beam has a symmetric Gaussian shape in both the horizontal and vertical directions, and reduces the vertical divergence of the focused beam by 25%. Significant reduction in background was achieved by implementation of both forward- and back-scatter guards. A unique triple-collimator apparatus, which has been in routine use on both undulator beamlines since February 2008, allows users to rapidly interchange the focused beam and conditioned mini-beams of two sizes with a single mouse click. The device and the beam are stable over many hours of routine operation. The rapid-exchange capability has greatly facilitated sample screening and resulted in several structures that could not have been obtained with the larger focused beam.
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Affiliation(s)
- Robert F Fischetti
- GM/CA CAT at the APS, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.
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Barker AI, Southworth-Davies RJ, Paithankar KS, Carmichael I, Garman EF. Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay. J Synchrotron Radiat 2009; 16:205-216. [PMID: 19240332 DOI: 10.1107/s0909049509003343] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Accepted: 01/27/2009] [Indexed: 05/27/2023]
Abstract
The advent of highly intense wiggler and undulator beamlines has reintroduced the problem of X-ray radiation damage in protein crystals even at cryogenic temperatures (100 K). Although cryocrystallography can be utilized for the majority of protein crystals, certain macromolecular crystals (e.g. of viruses) suffer large increases in mosaicity upon flash cooling and data are still collected at room temperature (293 K). An alternative mechanism to cryocooling for prolonging crystal lifetime is the use of radioprotectants. These compounds are able to scavenge the free radical species formed upon X-ray irradiation which are thought to be responsible for part of the observed damage. Three putative radioprotectants, ascorbate, 1,4-benzoquinone and 2,2,6,6-tetramethyl-4-piperidone (TEMP), were tested for their ability to prolong lysozyme crystal lifetimes at 293 K. Plots of relative summed intensity against dose were used as a metric to assess radioprotectant ability: ascorbate and 1,4-benzoquinone appear to be effective, whereas studies on TEMP were inconclusive. Ascorbate, which scavenges OH* radicals (k(OH) = 8 x 10(9) M(-1) s(-1)) and electrons with a lower rate constant (k(e-(aq)) = 3.0 x 10(8) M(-1) s(-1)), doubled the crystal dose tolerance, whereas 1,4-benzoquinone, which also scavenges both OH* radicals (k(OH) = 1.2 x 10(9) M(-1) s(-1)) and electrons (k(e-(aq)) = 1.2 x 10(10) M(-1) s(-1)), offered a ninefold increase in dose tolerance at the dose rates used. Pivotally, these preliminary results on a limited number of samples show that the two scavengers also induced a striking change in the dose dependence of the intensity decay from a first-order to a zeroth-order process.
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Affiliation(s)
- Adam I Barker
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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