101
|
Lu F, Wang M, Li N, Tang B. Polyoxometalate-Based Nanomaterials Toward Efficient Cancer Diagnosis and Therapy. Chemistry 2021; 27:6422-6434. [PMID: 33314442 DOI: 10.1002/chem.202004500] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/26/2020] [Indexed: 12/11/2022]
Abstract
As an emerging class of inorganic metal oxides, organically functionalized polyoxometalates (POMs) or POM-based nanohybrids have been demonstrated promising potential for the inhibition of various cancer types by the virtue of their diversity in structures and significantly reduced toxicity. This contribution summarizes the latest achievement of POM-based nanomaterials in cancer diagnosis and various therapeutics to put forward our fundamental viewpoints on the design principles of modified POMs based on their application. In addition, major challenges and perspectives in this field are also discussed. We expect that this review will provide a valuable and systematic reference for the further development of POM-based nanomaterials.
Collapse
Affiliation(s)
- Fei Lu
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical, Imaging in Universities of Shandong, Institute of Molecular and Nanoscience, Shandong Normal University, Jinan, 250014, P. R. China
| | - Mengzhen Wang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical, Imaging in Universities of Shandong, Institute of Molecular and Nanoscience, Shandong Normal University, Jinan, 250014, P. R. China
| | - Na Li
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical, Imaging in Universities of Shandong, Institute of Molecular and Nanoscience, Shandong Normal University, Jinan, 250014, P. R. China
| | - Bo Tang
- College of Chemistry, Chemical Engineering and Materials Science, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Collaborative Innovation Center of Functionalized Probes for Chemical, Imaging in Universities of Shandong, Institute of Molecular and Nanoscience, Shandong Normal University, Jinan, 250014, P. R. China
| |
Collapse
|
102
|
Hancock JT, Russell G. Downstream Signalling from Molecular Hydrogen. PLANTS (BASEL, SWITZERLAND) 2021; 10:367. [PMID: 33672953 PMCID: PMC7918658 DOI: 10.3390/plants10020367] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/23/2022]
Abstract
Molecular hydrogen (H2) is now considered part of the suite of small molecules that can control cellular activity. As such, H2 has been suggested to be used in the therapy of diseases in humans and in plant science to enhance the growth and productivity of plants. Treatments of plants may involve the creation of hydrogen-rich water (HRW), which can then be applied to the foliage or roots systems of the plants. However, the molecular action of H2 remains elusive. It has been suggested that the presence of H2 may act as an antioxidant or on the antioxidant capacity of cells, perhaps through the scavenging of hydroxyl radicals. H2 may act through influencing heme oxygenase activity or through the interaction with reactive nitrogen species. However, controversy exists around all the mechanisms suggested. Here, the downstream mechanisms in which H2 may be involved are critically reviewed, with a particular emphasis on the H2 mitigation of stress responses. Hopefully, this review will provide insight that may inform future research in this area.
Collapse
Affiliation(s)
- John T. Hancock
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | | |
Collapse
|
103
|
Sun F, Xie X, Zhang Y, Ma M, Wang Y, Duan J, Lu X, Yang G, He G. Wheat gliadin in ethanol solutions treated using cold air plasma at atmospheric pressure. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2020.100808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
104
|
Kambe T, Taylor KM, Fu D. Zinc transporters and their functional integration in mammalian cells. J Biol Chem 2021; 296:100320. [PMID: 33485965 PMCID: PMC7949119 DOI: 10.1016/j.jbc.2021.100320] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 12/14/2022] Open
Abstract
Zinc is a ubiquitous biological metal in all living organisms. The spatiotemporal zinc dynamics in cells provide crucial cellular signaling opportunities, but also challenges for intracellular zinc homeostasis with broad disease implications. Zinc transporters play a central role in regulating cellular zinc balance and subcellular zinc distributions. The discoveries of two complementary families of mammalian zinc transporters (ZnTs and ZIPs) in the mid-1990s spurred much speculation on their metal selectivity and cellular functions. After two decades of research, we have arrived at a biochemical description of zinc transport. However, in vitro functions are fundamentally different from those in living cells, where mammalian zinc transporters are directed to specific subcellular locations, engaged in dedicated macromolecular machineries, and connected with diverse cellular processes. Hence, the molecular functions of individual zinc transporters are reshaped and deeply integrated in cells to promote the utilization of zinc chemistry to perform enzymatic reactions, tune cellular responsiveness to pathophysiologic signals, and safeguard cellular homeostasis. At present, the underlying mechanisms driving the functional integration of mammalian zinc transporters are largely unknown. This knowledge gap has motivated a shift of the research focus from in vitro studies of purified zinc transporters to in cell studies of mammalian zinc transporters in the context of their subcellular locations and protein interactions. In this review, we will outline how knowledge of zinc transporters has been accumulated from in-test-tube to in-cell studies, highlighting new insights and paradigm shifts in our understanding of the molecular and cellular basis of mammalian zinc transporter functions.
Collapse
Affiliation(s)
- Taiho Kambe
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kathryn M Taylor
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Dax Fu
- Department of Physiology, Johns Hopkins School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.
| |
Collapse
|
105
|
Biehn SE, Lindert S. Accurate protein structure prediction with hydroxyl radical protein footprinting data. Nat Commun 2021; 12:341. [PMID: 33436604 PMCID: PMC7804018 DOI: 10.1038/s41467-020-20549-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 12/08/2020] [Indexed: 01/10/2023] Open
Abstract
Hydroxyl radical protein footprinting (HRPF) in combination with mass spectrometry reveals the relative solvent exposure of labeled residues within a protein, thereby providing insight into protein tertiary structure. HRPF labels nineteen residues with varying degrees of reliability and reactivity. Here, we are presenting a dynamics-driven HRPF-guided algorithm for protein structure prediction. In a benchmark test of our algorithm, usage of the dynamics data in a score term resulted in notable improvement of the root-mean-square deviations of the lowest-scoring ab initio models and improved the funnel-like metric Pnear for all benchmark proteins. We identified models with accurate atomic detail for three of the four benchmark proteins. This work suggests that HRPF data along with side chain dynamics sampled by a Rosetta mover ensemble can be used to accurately predict protein structure.
Collapse
Affiliation(s)
- Sarah E Biehn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
106
|
Yin V, Konermann L. Probing the Effects of Heterogeneous Oxidative Modifications on the Stability of Cytochrome c in Solution and in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:73-83. [PMID: 32401029 DOI: 10.1021/jasms.0c00089] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Covalent modifications by reactive oxygen species can modulate the function and stability of proteins. Thermal unfolding experiments in solution are a standard tool for probing oxidation-induced stability changes. Complementary to such solution investigations, the stability of electrosprayed protein ions can be assessed in the gas phase by collision-induced unfolding (CIU) and ion-mobility spectrometry. A question that remains to be explored is whether oxidation-induced stability alterations in solution are mirrored by the CIU behavior of gaseous protein ions. Here, we address this question using chloramine-T-oxidized cytochrome c (CT-cyt c) as a model system. CT-cyt c comprises various proteoforms that have undergone MetO formation (+16 Da) and Lys carbonylation (LysCH2-NH2 → LysCHO, -1 Da). We found that CT-cyt c in solution was destabilized, with a ∼5 °C reduced melting temperature compared to unmodified controls. Surprisingly, CIU experiments revealed the opposite trend, i.e., a stabilization of CT-cyt c in the gas phase. To pinpoint the source of this effect, we performed proteoform-resolved CIU on CT-cyt c fractions that had been separated by cation exchange chromatography. In this way, it was possible to identify MetO formation at residue 80 as the key modification responsible for stabilization in the gas phase. Possibly, this effect is caused by newly formed contacts of the sulfoxide with aromatic residues in the protein core. Overall, our results demonstrate that oxidative modifications can affect protein stability in solution and in the gas phase very differently.
Collapse
Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
107
|
Jayasundara K, Li C, DeBastiani A, Sharif D, Li P, Valentine SJ. Physicochemical Property Correlations with Ionization Efficiency in Capillary Vibrating Sharp-Edge Spray Ionization (cVSSI). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:84-94. [PMID: 32856909 PMCID: PMC8130659 DOI: 10.1021/jasms.0c00100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The relative contributions to ionization efficiency by three molecular chemical properties have been examined for field-free and field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) using mass spectrometry (MS) analysis. Ion intensities have been recorded for model compounds under each operational ionization mode as well as for aqueous and nonaqueous (methanol) solvent systems. Multiple regression analysis suggests that for field-free cVSSI, ion intensity is mostly associated with the log of the base dissociation constant (pKb) and proton affinity (PA) for both aqueous and methanol solutions. Comparatively, for field-enabled cVSSI using aqueous solutions, the dominant factor correlated with ion intensity is the log of the partition coefficient (log P). To a lesser degree, this is observed for methanol solutions as well. For ESI, pKb is the dominant factor associated with ion signal levels from methanol and aqueous solutions. These results are supported by studies conducted on two different mass spectrometers employing different cVSSI emitter tips. The relationship of ion intensity and pKb in ESI is supported by multiple studies; however, the shift to other chemical properties with the addition of cVSSI suggests the possibility that a different (or combinations of) ionization mechanism(s) may be operative for these ionization modes. These results are briefly considered in light of the different ESI mechanisms.
Collapse
Affiliation(s)
| | | | | | | | - Peng Li
- To whom correspondence should be addressed: , and .
| | | |
Collapse
|
108
|
Gatin A, Billault I, Duchambon P, Van der Rest G, Sicard-Roselli C. Oxidative radicals (HO • or N 3•) induce several di-tyrosine bridge isomers at the protein scale. Free Radic Biol Med 2021; 162:461-470. [PMID: 33217505 DOI: 10.1016/j.freeradbiomed.2020.10.324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/27/2020] [Accepted: 10/31/2020] [Indexed: 11/17/2022]
Abstract
Among protein oxidative damages, di-tyrosine bridges formation has been evidenced in many neuropathological diseases. Combining oxidative radical production by gamma radiolysis with very performant chromatographic separation coupled to mass spectrometry detection, we brought into light new insights of tyrosine dimerization. Hydroxyl and azide radical tyrosine oxidation leading to di-tyrosine bridges formation was studied for different biological compounds: a full-length protein (Δ25-centrin 2), a five amino acid peptide (KTSLY) and free tyrosine. We highlighted that both radicals generate high proportion of dimers even for low doses. Surprisingly, no less than five different di-tyrosine isomers were evidenced for the protein and the peptide. For tyrosine alone, at least four distinct dimers were evidenced. These results raise some questions about their respective role in vivo and hence their relative toxicity. Also, as di-tyrosine is often used as a biomarker, a better knowledge of the type of dimer detected in vivo is now required.
Collapse
Affiliation(s)
- Anouchka Gatin
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay Cedex, France
| | - Isabelle Billault
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay Cedex, France
| | - Patricia Duchambon
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405, Orsay Cedex, France
| | - Guillaume Van der Rest
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay Cedex, France
| | - Cécile Sicard-Roselli
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR 8000, 91405, Orsay Cedex, France.
| |
Collapse
|
109
|
Ruan H, Kiselar J, Zhang W, Li S, Xiong R, Liu Y, Yang S, Lai L. Integrative structural modeling of a multidomain polo-like kinase. Phys Chem Chem Phys 2020; 22:27581-27589. [PMID: 33236741 DOI: 10.1039/d0cp05030j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polo-like kinase 1 (PLK1) is a key regulator and coordinator for mitotic signaling that contains two major functional units of a kinase domain (KD) and a polo-box domain (PBD). While individual domain structures of the KD and the PBD are known, how they interact and assemble into a functional complex remains an open question. The structural model from the KD-PBD-Map205PBM heterotrimeric crystal structure of zebrafish PLK1 represents a major step in understanding the KD and the PBD interactions. However, how these two domains interact when connected by a linker in the full length PLK1 needs further investigation. By integrating different sources of structural data from small-angle X-ray scattering, hydroxyl radical protein footprinting, and computational sampling, here we report an overall architecture for PLK1 multidomain assembly between the KD and the PBD. Our model revealed that the KD uses its C-lobe to interact with the PBD via the site near the phosphopeptide binding site in its auto-inhibitory state in solution. Disruption of this auto-inhibition via site-directed mutagenesis at the KD-PBD interface increases its kinase activity, supporting the functional role of KD-PBD interactions predicted for regulating the PLK1 kinase function. Our results indicate that the full length human PLK1 takes dynamic structures with a variety of domain-domain interfaces in solution.
Collapse
Affiliation(s)
- Hao Ruan
- BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | | | | | | | | | | | | | | |
Collapse
|
110
|
Liu XR, Rempel DL, Gross ML. Protein higher-order-structure determination by fast photochemical oxidation of proteins and mass spectrometry analysis. Nat Protoc 2020; 15:3942-3970. [PMID: 33169002 PMCID: PMC10476649 DOI: 10.1038/s41596-020-0396-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/03/2020] [Indexed: 11/09/2022]
Abstract
The higher-order structure (HOS) of proteins plays a critical role in their function; therefore, it is important to our understanding of their function that we have as much information as possible about their three-dimensional structure and how it changes with time. Mass spectrometry (MS) has become an important tool for determining protein HOS owing to its high throughput, mid-to-high spatial resolution, low sample amount requirement and broad compatibility with various protein systems. Modern MS-based protein HOS analysis relies, in part, on footprinting, where a reagent reacts 'to mark' the solvent-accessible surface of the protein, and MS-enabled proteomic analysis locates the modifications to afford a footprint. Fast photochemical oxidation of proteins (FPOP), first introduced in 2005, has become a powerful approach for protein footprinting. Laser-induced hydrogen peroxide photolysis generates hydroxyl radicals that react with solvent-accessible side chains (14 out of 20 amino acid side chains) to fulfill the footprinting. The reaction takes place at sub-milliseconds, faster than most of labeling-induced protein conformational changes, thus enabling a 'snapshot' of protein HOS in solution. As a result, FPOP has been employed in solving several important problems, including mapping epitopes, following protein aggregation, locating small molecule binding, measuring ligand-binding affinity, monitoring protein folding and unfolding and determining hidden conformational changes invisible to other methods. Broader adoption will be promoted by dissemination of the technical details for assembling the FPOP platform and for dealing with the complexities of analyzing FPOP data. In this protocol, we describe the FPOP platform, the conditions for successful footprinting and its examination by mass measurements of the intact protein, the post-labeling sample handling and digestion, the liquid chromatography-tandem MS analysis of the digested sample and the data analysis with Protein Metrics Suite. This protocol is intended not only as a guide for investigators trying to establish an FPOP platform in their own lab but also for those willing to incorporate FPOP as an additional tool in addressing their questions of interest.
Collapse
Affiliation(s)
- Xiaoran Roger Liu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
| |
Collapse
|
111
|
Moosmann B. Redox Biochemistry of the Genetic Code. Trends Biochem Sci 2020; 46:83-86. [PMID: 33250285 DOI: 10.1016/j.tibs.2020.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
New findings on the chemistry of the amino acids, their role in protein folding, and their sequential primordial introduction have uncovered concealed causalities in genetic code evolution. The genetically encoded amino acids successively provided (i) membrane anchors, (ii) halophilic protein folds, (iii) mesophilic protein folds, (iv) metal ligation, and (v) antioxidation.
Collapse
Affiliation(s)
- Bernd Moosmann
- Evolutionary Biochemistry and Redox Medicine, Institute for Pathobiochemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
| |
Collapse
|
112
|
Stachowski TR, Snell ME, Snell EH. SAXS studies of X-ray induced disulfide bond damage: Engineering high-resolution insight from a low-resolution technique. PLoS One 2020; 15:e0239702. [PMID: 33201877 PMCID: PMC7671560 DOI: 10.1371/journal.pone.0239702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/12/2020] [Indexed: 12/17/2022] Open
Abstract
A significant problem in biological X-ray crystallography is the radiation chemistry caused by the incident X-ray beam. This produces both global and site-specific damage. Site specific damage can misdirect the biological interpretation of the structural models produced. Cryo-cooling crystals has been successful in mitigating damage but not eliminating it altogether; however, cryo-cooling can be difficult in some cases and has also been shown to limit functionally relevant protein conformations. The doses used for X-ray crystallography are typically in the kilo-gray to mega-gray range. While disulfide bonds are among the most significantly affected species in proteins in the crystalline state at both cryogenic and higher temperatures, there is limited information on their response to low X-ray doses in solution, the details of which might inform biomedical applications of X-rays. In this work we engineered a protein that dimerizes through a susceptible disulfide bond to relate the radiation damage processes seen in cryo-cooled crystals to those closer to physiologic conditions. This approach enables a low-resolution technique, small angle X-ray scattering (SAXS), to detect and monitor a residue specific process. A dose dependent fragmentation of the engineered protein was seen that can be explained by a dimer to monomer transition through disulfide bond cleavage. This supports the crystallographically derived mechanism and demonstrates that results obtained crystallographically can be usefully extrapolated to physiologic conditions. Fragmentation was influenced by pH and the conformation of the dimer, providing information on mechanism and pointing to future routes for investigation and potential mitigation. The novel engineered protein approach to generate a large-scale change through a site-specific interaction represents a promising tool for advancing radiation damage studies under solution conditions.
Collapse
Affiliation(s)
- Timothy R. Stachowski
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, United States of America
| | - Mary E. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
| | - Edward H. Snell
- Hauptman-Woodward Medical Research Institute, Buffalo, New York, United States of America
- Department of Materials Design and Innovation, State University at New York at Buffalo, Buffalo, New York, United States of America
| |
Collapse
|
113
|
Zeng H, Zhang G, Ji Q, Liu H, Hua X, Xia H, Sillanpää M, Qu J. pH-Independent Production of Hydroxyl Radical from Atomic H*-Mediated Electrocatalytic H 2O 2 Reduction: A Green Fenton Process without Byproducts. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14725-14731. [PMID: 33151053 DOI: 10.1021/acs.est.0c04694] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydroxyl radical (•OH) can hydroxylate or dehydrogenate organics without forming extra products and is thereby expediently applied in extensive domains. Although it can be efficiently produced through single-electron transfer from transition-metal-containing activators to hydrogen peroxide (H2O2), narrow applicable pH range, strict activator/H2O2 ratio requirement, and byproducts that are formed in the mixture with the background matrix necessitate the need for additional energy-intensive up/downstream treatments. Here, we show a green Fenton process in an electrochemical cell, where the electro-generated atomic H* on a Pd/graphite cathode enables the efficient conversion of H2O2 into •OH and subsequent degradation of organic pollutants (80% efficiency). Operando liquid time-of-fight secondary ion mass spectrometry verified that H2O2 activation takes place through a transition state of the Pd-H*-H2O2 adduct with a low reaction energy barrier of 0.92 eV, whereby the lone electron in atomic H* can readily cleave the peroxide bridge, with •OH and H2O as products (ΔGr = -1.344 eV). Using H+ or H2O as the resource, we demonstrate that the well-directed output of H* determines the pH-independent production of •OH for stable conversion of organic contaminants in wider pH ranges (3-12). The research pioneers a novel path for eliminating the restrictions that are historically challenging in the traditional Fenton process.
Collapse
Affiliation(s)
- Huabin Zeng
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Department of Separation Science, School of Engineering Science, Lappeenranta-Lahti University of Technology LUT, Sammonkatu 12, Mikkeli FI-50130, Finland
| | - Gong Zhang
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Qinghua Ji
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xin Hua
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hailun Xia
- Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Mika Sillanpää
- Department of Civil and Environmental Engineering, Florida International University, Miami FL 33199, United States
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| |
Collapse
|
114
|
Gao HY, Huang CH, Mao L, Shao B, Shao J, Yan ZY, Tang M, Zhu BZ. First Direct and Unequivocal Electron Spin Resonance Spin-Trapping Evidence for pH-Dependent Production of Hydroxyl Radicals from Sulfate Radicals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14046-14056. [PMID: 33064470 DOI: 10.1021/acs.est.0c04410] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recently, the sulfate radical (SO4•-) has been found to exhibit broad application prospects in various research fields such as chemical, biomedical, and environmental sciences. It has been suggested that SO4•- could be transformed into a more reactive hydroxyl radical (•OH); however, no direct and unequivocal experimental evidence has been reported yet. In this study, using an electron spin resonance (ESR) secondary radical spin-trapping method coupled with the classic spin-trapping agent 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and the typical •OH-scavenging agent dimethyl sulfoxide (DMSO), we found that •OH can be produced from three SO4•--generating systems from weakly acidic (pH = 5.5) to alkaline conditions (optimal at pH = 13.0), while SO4•- is the predominant radical species at pH < 5.5. A comparative study with three typical •OH-generating systems strongly supports the above conclusion. This is the first direct and unequivocal ESR spin-trapping evidence for •OH formation from SO4•- over a wide pH range, which is of great significance to understand and study the mechanism of many SO4•--related reactions and processes. This study also provides an effective and direct method for unequivocally distinguishing •OH from SO4•-.
Collapse
Affiliation(s)
- Hui-Ying Gao
- Science and Technology College, North China Electric Power University, Baoding 071051, P. R. China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
| | - Chun-Hua Huang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Li Mao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Bo Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jie Shao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhu-Ying Yan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Miao Tang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Ben-Zhan Zhu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Joint Institute of Environmental Sciences of Hong Kong Baptist University and the Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P. R. China
| |
Collapse
|
115
|
Yin V, Holzscherer D, Konermann L. Delineating Heme-Mediated versus Direct Protein Oxidation in Peroxidase-Activated Cytochrome c by Top-Down Mass Spectrometry. Biochemistry 2020; 59:4108-4117. [PMID: 32991149 DOI: 10.1021/acs.biochem.0c00609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Oxidation of key residues in cytochrome c (cyt c) by chloramine T (CT) converts the protein from an electron transporter to a peroxidase. This peroxidase-activated state represents an important model system for exploring the early steps of apoptosis. CT-induced transformations include oxidation of the distal heme ligand Met80 (MetO, +16 Da) and carbonylation (LysCHO, -1 Da) in the range of Lys53/55/72/73. Remarkably, the 15 remaining Lys residues in cyt c are not susceptible to carbonylation. The cause of this unusual selectivity is unknown. Here we applied top-down mass spectrometry (MS) to examine whether CT-induced oxidation is catalyzed by heme. To this end, we compared the behavior of cyt c with (holo-cyt c) and without heme (apoSS-cyt c). CT caused MetO formation at Met80 for both holo- and apoSS-cyt c, implying that this transformation can proceed independently of heme. The aldehyde-specific label Girard's reagent T (GRT) reacted with oxidized holo-cyt c, consistent with the presence of several LysCHO. In contrast, oxidized apo-cyt c did not react with GRT, revealing that LysCHO forms only in the presence of heme. The heme dependence of LysCHO formation was further confirmed using microperoxidase-11 (MP11). CT exposure of apoSS-cyt c in the presence of MP11 caused extensive nonselective LysCHO formation. Our results imply that the selectivity of LysCHO formation at Lys53/55/72/73 in holo-cyt c is caused by the spatial proximity of these sites to the reactive (distal) heme face. Overall, this work highlights the utility of top-down MS for unravelling complex oxidative modifications.
Collapse
Affiliation(s)
- Victor Yin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Derek Holzscherer
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
116
|
Chai YL, Gao ZB, Li Z, He LL, Yu F, Yu SC, Wang J, Tian YM, Liu LE, Wang YL, Wu YJ. A novel fluorescent nanoprobe that based on poly(thymine) single strand DNA-templated copper nanocluster for the detection of hydrogen peroxide. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118546. [PMID: 32505107 DOI: 10.1016/j.saa.2020.118546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
In this paper, a label-free fluorescence nanoprobe is constructed based on poly(thymine) single strand DNA-templated Copper nanocluster (denote as: T-CuNCs) for the detection of hydrogen peroxide. In the assay, the fluorescent T-CuNCs will generate though the reaction of Cu2+, poly(thymine) and sodium ascorbate. However, the hydroxyl radical (.OH) will generated in the presence of H2O2, which is able to induced the oxidative lesions of poly(thymine) single chain DNA and lead to the poly(thymine) being splitted into shorter or single oligonucleotide fragments and lose the ability to template the fluorescent T-CuNCs again. Therefore, H2O2 can be detected by monitoring the fluorescence strength change of T-CuNCs. The experimental results show that the fluorescence intensity change of T-CuNCs has fantastic linearity versus H2O2 concentration in the range of 1-30 μM (R2 = 0.9947) and 30-80 μM (R2 = 0.9972) with the limit of detection (LOD) as low as 0.5 μM (S/N = 3). More important, the fluorescent nanoprobe was also successfully utilized on the detection of H2O2 in serum samples. Therefore, a label-free, costless and effective fluorescence method has been established for the detection of H2O2, the intrinsic properties of the nanoprobe endow its more potential applications in chemical and biological study.
Collapse
Affiliation(s)
- Yi-Lin Chai
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Zi-Bo Gao
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Zhuang Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China
| | - Lei-Liang He
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Fei Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Song-Cheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Jia Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Yong-Mei Tian
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China
| | - Yi-Lin Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
| | - Yong-Jun Wu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, People's Republic of China.
| |
Collapse
|
117
|
Van QN, López CA, Tonelli M, Taylor T, Niu B, Stanley CB, Bhowmik D, Tran TH, Frank PH, Messing S, Alexander P, Scott D, Ye X, Drew M, Chertov O, Lösche M, Ramanathan A, Gross ML, Hengartner NW, Westler WM, Markley JL, Simanshu DK, Nissley DV, Gillette WK, Esposito D, McCormick F, Gnanakaran S, Heinrich F, Stephen AG. Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane. Proc Natl Acad Sci U S A 2020; 117:24258-24268. [PMID: 32913056 PMCID: PMC7533834 DOI: 10.1073/pnas.2006504117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The small GTPase KRAS is localized at the plasma membrane where it functions as a molecular switch, coupling extracellular growth factor stimulation to intracellular signaling networks. In this process, KRAS recruits effectors, such as RAF kinase, to the plasma membrane where they are activated by a series of complex molecular steps. Defining the membrane-bound state of KRAS is fundamental to understanding the activation of RAF kinase and in evaluating novel therapeutic opportunities for the inhibition of oncogenic KRAS-mediated signaling. We combined multiple biophysical measurements and computational methodologies to generate a consensus model for authentically processed, membrane-anchored KRAS. In contrast to the two membrane-proximal conformations previously reported, we identify a third significantly populated state using a combination of neutron reflectivity, fast photochemical oxidation of proteins (FPOP), and NMR. In this highly populated state, which we refer to as "membrane-distal" and estimate to comprise ∼90% of the ensemble, the G-domain does not directly contact the membrane but is tethered via its C-terminal hypervariable region and carboxymethylated farnesyl moiety, as shown by FPOP. Subsequent interaction of the RAF1 RAS binding domain with KRAS does not significantly change G-domain configurations on the membrane but affects their relative populations. Overall, our results are consistent with a directional fly-casting mechanism for KRAS, in which the membrane-distal state of the G-domain can effectively recruit RAF kinase from the cytoplasm for activation at the membrane.
Collapse
Affiliation(s)
- Que N Van
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Troy Taylor
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Ben Niu
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Christopher B Stanley
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Debsindhu Bhowmik
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
| | - Timothy H Tran
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Peter H Frank
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Simon Messing
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Patrick Alexander
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Daniel Scott
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaoying Ye
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Matt Drew
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Oleg Chertov
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Mathias Lösche
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439
| | - Michael L Gross
- National Mass Spectrometry Resource, Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130
| | - Nicolas W Hengartner
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - William M Westler
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - John L Markley
- National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706
| | - Dhirendra K Simanshu
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dwight V Nissley
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - William K Gillette
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Dominic Esposito
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702
| | - Frank McCormick
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899
| | - Andrew G Stephen
- National Cancer Institute RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21702;
| |
Collapse
|
118
|
Hu J, Tian J, Wang K, Deng J, Luo G. Reaction Pathway and Selectivity Control of Tetraethyl Thiuram Disulfide Synthesis with NaHCO 3 as a pH Regulator. ACS OMEGA 2020; 5:23736-23742. [PMID: 32984692 PMCID: PMC7513355 DOI: 10.1021/acsomega.0c02707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/28/2020] [Indexed: 06/11/2023]
Abstract
The selectivity of a chemical reaction is related to the effective utilization of raw materials as well as the cleanliness and economy of the process. Herein, it has been first proposed to synthesize tetraethyl thiuram disulfide (TETD) with sodium bicarbonate as the pH regulator with a reaction selectivity of ∼100%. The existence of a reaction intermediate, a sodium salt of diethyl dithiocarbamoylsulfenic acid (NaEt2DTCS), has been proved by experiments and theoretical calculations. The results indicate that TETD can not only be generated from NaEt2DTCS oxidized by H2O2 directly, but also from the conjugation of NaEt2DTC and NaEt2DTCS generated in the first stage of oxidation meanwhile. Accordingly, an oxidation reaction pathway has been proposed. The reaction selectivity with NaHCO3 or CO2 as the pH regulator has been compared, and the selectivity control mechanism is discussed. At relatively higher pH values with NaHCO3 as the pH regulator, peroxidation could be almost avoided.
Collapse
|
119
|
Niu B, Mackness BC, Zitzewitz JA, Matthews CR, Gross ML. Trifluoroethanol Partially Unfolds G93A SOD1 Leading to Protein Aggregation: A Study by Native Mass Spectrometry and FPOP Protein Footprinting. Biochemistry 2020; 59:3650-3659. [PMID: 32924445 DOI: 10.1021/acs.biochem.0c00425] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Misfolding of Cu, Zn superoxide dismutase (SOD1) variants may lead to protein aggregation and ultimately amyotrophic lateral sclerosis (ALS). The mechanism and protein conformational changes during this process are complex and remain unclear. To study SOD1 variant aggregation at the molecular level and in solution, we chemically induced aggregation of a mutant variant (G93A SOD1) with trifluoroethanol (TFE) and used both native mass spectrometry (MS) to analyze the intact protein and fast photochemical oxidation of proteins (FPOP) to characterize the structural changes induced by TFE. We found partially unfolded G93A SOD1 monomers prior to oligomerization and identified regions of the N-terminus, C-terminus, and strands β5, β6 accountable for the partial unfolding. We propose that exposure of hydrophobic interfaces of these unstructured regions serves as a precursor to aggregation. Our results provide a possible mechanism and molecular basis for ALS-linked SOD1 misfolding and aggregation.
Collapse
Affiliation(s)
- Ben Niu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Brian C Mackness
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - C Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| |
Collapse
|
120
|
Misra SK, Sharp JS. Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes. J Vis Exp 2020. [PMID: 32955502 DOI: 10.3791/61580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.
Collapse
Affiliation(s)
- Sandeep K Misra
- Department of Biomolecular Sciences, University of Mississippi
| | - Joshua S Sharp
- Department of Biomolecular Sciences, University of Mississippi; Department of Chemistry and Biochemistry, University of Mississippi; GenNext Technologies, Inc.;
| |
Collapse
|
121
|
Bruckbauer ST, Minkoff BB, Yu D, Cryns VL, Cox MM, Sussman MR. Ionizing Radiation-induced Proteomic Oxidation in Escherichia coli. Mol Cell Proteomics 2020; 19:1375-1395. [PMID: 32536603 PMCID: PMC8015010 DOI: 10.1074/mcp.ra120.002092] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/10/2020] [Indexed: 12/12/2022] Open
Abstract
Recent work has begun to investigate the role of protein damage in cell death because of ionizing radiation (IR) exposure, but none have been performed on a proteome-wide basis, nor have they utilized MS (MS) to determine chemical identity of the amino acid side chain alteration. Here, we use Escherichia coli to perform the first MS analysis of IR-treated intact cells on a proteome scale. From quintuplicate IR-treated (1000 Gy) and untreated replicates, we successfully quantified 13,262 peptides mapping to 1938 unique proteins. Statistically significant, but low in magnitude (<2-fold), IR-induced changes in peptide abundance were observed in 12% of all peptides detected, although oxidative alterations were rare. Hydroxylation (+15.99 Da) was the most prevalent covalent adduct detected. In parallel with these studies on E. coli, identical experiments with the IR-resistant bacterium, Deinococcus radiodurans, revealed orders of magnitude less effect of IR on the proteome. In E. coli, the most significant target of IR by a wide margin was glyceraldehyde 3'-phosphate dehydrogenase (GAPDH), in which the thiol side chain of the catalytic Cys residue was oxidized to sulfonic acid. The same modification was detected in IR-treated human breast carcinoma cells. Sensitivity of GAPDH to reactive oxygen species (ROS) has been described previously in microbes and here, we present GAPDH as an immediate, primary target of IR-induced oxidation across all domains of life.
Collapse
Affiliation(s)
- Steven T Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Benjamin B Minkoff
- Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Deyang Yu
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Vincent L Cryns
- Department of Medicine, University of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Wisconsin, USA
| | - Michael M Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.
| | - Michael R Sussman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Center for Genomic Science Innovation, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA.
| |
Collapse
|
122
|
Gericke SM, Mulhearn WD, Goodacre DE, Raso J, Miller DJ, Carver L, Nemšák S, Karslıoğlu O, Trotochaud L, Bluhm H, Stafford CM, Buechner C. Water-polyamide chemical interplay in desalination membranes explored by ambient pressure X-ray photoelectron spectroscopy. Phys Chem Chem Phys 2020; 22:15658-15663. [PMID: 32618298 PMCID: PMC7671007 DOI: 10.1039/d0cp01842b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reverse osmosis using aromatic polyamide membranes is currently the most important technology for seawater desalination. The performance of reverse osmosis membranes is highly dependent on the interplay of their surface chemical groups with water and water contaminants. In order to better understand the underlying mechanisms of these membranes, we study ultrathin polyamide films that chemically resemble reverse osmosis membranes, using ambient pressure X-ray photoelectron spectroscopy. This technique can identify the functional groups at the membrane-water interface and allows monitoring of small shifts in the electron binding energy that indicate interaction with water. We observe deprotonation of free acid groups and formation of a 'water complex' with nitrogen groups in the polymer upon exposure of the membrane to water vapour. The chemical changes are reversed when water is removed from the membrane. While the correlation between functional groups and water uptake is an established one, this experiment serves to understand the nature of their chemical interaction, and opens up possibilities for tailoring future materials to specific requirements.
Collapse
Affiliation(s)
- Sabrina M Gericke
- Chemical Sciences Division and Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
123
|
Wu S, Ma C, Gao Y, Su Y, Xia Q, Chen Z, Zhu JJ. Dynamic Detection of Endogenous Hydroxyl Radicals at Single-Cell Level with Individual Ag-Au Nanocages. Anal Chem 2020; 92:9940-9947. [PMID: 32567299 DOI: 10.1021/acs.analchem.0c01501] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hydroxyl radicals (•OH) are a type of short-lived radical which is the most aggressive reactive oxygen species due to its high reactivity to biomolecules. Dynamic measurement of •OH level in living cells is critical for understanding cell physiology and pathology. In this manuscript, we prepare individual Ag-Au@PEG/RGD nanocages for in situ determination of endogenous •OH at single-cell level, whose spectral shift rate correlate to the •OH concentration. The high-selective response to •OH relies on the specific oxidization of the conjugated PEG/RGD outside and the silver etching inside the nanocages that resulted in a significant LSPR signal and scattered color changes. The spectral red-shift rate of LSPR has a linear relationship with the logarithm of •OH concentration in range of 100 pM to 1 μM, suitable for the measurement of endogenous •OH. Thus, the individual nanocages were successfully used to monitor the dynamic intracellular •OH level of single tumor cells under oxidative stress. This strategy has great potential in promoting •OH mediated cell homeostasis and injury research.
Collapse
Affiliation(s)
- Shaojun Wu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Cheng Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yu Su
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Qing Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zixuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| |
Collapse
|
124
|
Liu T, Marcinko TM, Vachet RW. Protein-Ligand Affinity Determinations Using Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1544-1553. [PMID: 32501685 PMCID: PMC7332385 DOI: 10.1021/jasms.0c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Determining the binding affinity is an important aspect of characterizing protein-ligand complexes. Here, we describe an approach based on covalent labeling (CL)-mass spectrometry (MS) that can accurately provide protein-ligand dissociation constants (Kd values) using diethylpyrocarbonate (DEPC) as the labeling reagent. Even though DEPC labeling reactions occur on a time scale that is similar to the dissociation/reassociation rates of many protein-ligand complexes, we demonstrate that relatively accurate binding constants can still be obtained as long as the extent of protein labeling is kept below 30%. Using two well-established model systems and one insufficiently characterized system, we find that Kd values can be determined that are close to values obtained in previous measurements. The CL-MS-based strategy that is described here should serve as an alternative for characterizing protein-ligand complexes that are challenging to measure by other methods. Moreover, this method has the potential to provide, simultaneously, the affinity and binding site information.
Collapse
Affiliation(s)
| | | | - Richard W. Vachet
- Corresponding author: Prof. Richard W. Vachet, Department of Chemistry, University of Massachusetts, Amherst, MA 01003, , Phone: (413) 545-2733
| |
Collapse
|
125
|
Garcia NK, Sreedhara A, Deperalta G, Wecksler AT. Optimizing Hydroxyl Radical Footprinting Analysis of Biotherapeutics Using Internal Standard Dosimetry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1563-1571. [PMID: 32407079 DOI: 10.1021/jasms.0c00146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydroxyl radical footprinting-mass spectrometry (HRF-MS) is a powerful technique for measuring protein structure by quantitating the solvent accessibility of amino acid side-chains; and when used in comparative analysis, HRF-MS data can provide detailed information on changes in protein structure. However, consistently controlling the amount of hydroxyl radical labeling of a protein requires the precise understanding of both the amount of radicals generated and half-life of the radicals in solution. The latter is particularly important for applications such as protein-protein and protein-ligand interactions, which may have different characteristics such as intrinsic reactivity and buffer components, and can cause differences in radical scavenging (herein termed "scavenging potential") between samples. To address this inherent challenge with HRF-MS analysis, we describe the comprehensive implementation of an internal standard (IS) dosimeter peptide leucine enkephalin (LeuEnk) for measuring the scavenging potential of pharmaceutically relevant proteins and formulation components. This further enabled evaluation of the critical method parameters affecting the scavenging potential of samples subjected to HRF-MS using fast photochemical oxidation of proteins. We demonstrate a direct correlation between the oxidation of the IS peptide and biotherapeutic target proteins, and show the oxidation of the IS can be used as a guide for ensuring equivalent scavenging potentials when comparing multiple samples. Establishing this strategy enables optimization of sample parameters, a system suitability approach, normalization of data, and comparison/harmonization of HRF-MS analysis across different laboratories.
Collapse
Affiliation(s)
- Natalie K Garcia
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, 1 DNA Way, South San Francisco, California 94080, United States
| | - Alavattam Sreedhara
- Late Stage Pharmaceutical Development, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Galahad Deperalta
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, 1 DNA Way, South San Francisco, California 94080, United States
| | - Aaron T Wecksler
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, 1 DNA Way, South San Francisco, California 94080, United States
| |
Collapse
|
126
|
Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
Collapse
|
127
|
Espino JA, Zhang Z, Jones LM. Chemical Penetration Enhancers Increase Hydrogen Peroxide Uptake in C. elegans for In Vivo Fast Photochemical Oxidation of Proteins. J Proteome Res 2020; 19:3708-3715. [PMID: 32506919 PMCID: PMC7861136 DOI: 10.1021/acs.jproteome.0c00245] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical protein
footprinting method that covalently labels solvent-accessible amino acids by photolysis
of hydrogen peroxide. Recently, we expanded the use of FPOP for in vivo
(IV-FPOP) covalent labeling in C. elegans. In initial IV-FPOP studies,
545 proteins were oxidatively modified in all body systems within the worm. Here, with
the use of chemical penetration enhancers (CPEs), we increased the number of modified
proteins as well as the number of modifications per protein to gain more structural
information. CPEs aid in the delivery of hydrogen peroxide inside C.
elegans by disturbing the highly ordered lipid bilayer of the worm cuticle
without affecting worm viability. IV-FPOP experiments performed using the CPE azone
showed an increase in oxidatively modified proteins and peptides. This increase
correlated with greater hydrogen peroxide uptake by C. elegans
quantified using a chemical fluorophore demonstrating the efficacy of using CPEs with
IV-FPOP. Mass spectrometry proteomics data are available via ProteomeXchange with
identifier PXD019290.
Collapse
Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| | - Zhihui Zhang
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21202, United States
| |
Collapse
|
128
|
Na S, Paek E. Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions. Comput Struct Biotechnol J 2020; 18:1391-1402. [PMID: 32637038 PMCID: PMC7322682 DOI: 10.1016/j.csbj.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS) has made enormous contributions to comprehensive protein identification and quantification in proteomics. MS is also gaining momentum for structural biology in a variety of ways, complementing conventional structural biology techniques. Here, we will review how MS-based techniques, such as hydrogen/deuterium exchange, covalent labeling, and chemical cross-linking, enable the characterization of protein structure, dynamics, and interactions, especially from a perspective of their data analyses. Structural information encoded by chemical probes in intact proteins is decoded by interpreting MS data at a peptide level, i.e., revealing conformational and dynamic changes in local regions of proteins. The structural MS data are not amenable to data analyses in traditional proteomics workflow, requiring dedicated software for each type of data. We first provide basic principles of data interpretation, including isotopic distribution and peptide sequencing. We then focus particularly on computational methods for structural MS data analyses and discuss outstanding challenges in a proteome-wide large scale analysis.
Collapse
Affiliation(s)
- Seungjin Na
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Eunok Paek
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| |
Collapse
|
129
|
Limpikirati PK, Zhao B, Pan X, Eyles SJ, Vachet RW. Covalent Labeling/Mass Spectrometry of Monoclonal Antibodies with Diethylpyrocarbonate: Reaction Kinetics for Ensuring Protein Structural Integrity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1223-1232. [PMID: 32310649 PMCID: PMC7370534 DOI: 10.1021/jasms.0c00067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Diethylpyrocarbonate (DEPC)-based covalent labeling together with mass spectrometry is a promising tool for the higher-order structural analysis of antibody therapeutics. Reliable information about antibody higher-order structure can be obtained, though, only when the protein's structural integrity is preserved during labeling. In this work, we have evaluated the applicability of DEPC reaction kinetics for ensuring the structural integrity of monoclonal antibodies (mAbs) during labeling. By monitoring the modification extent of selected proteolytic fragments as a function of DEPC concentration, we find that a common DEPC concentration can be used for different monoclonal antibodies in formulated samples without perturbing their higher-order structure. Under these labeling conditions, we find that the antibodies can accommodate up to four DEPC modifications without being structurally perturbed, indicating that multidomain proteins can withstand more than one label, which contrasts to previously studied single-domain proteins. This more extensive labeling provides a more sensitive measure of structure, making DEPC-based covalent labeling-mass spectrometry suitable for the higher-order structural analyses of mAbs.
Collapse
Affiliation(s)
- Patanachai K. Limpikirati
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Bo Zhao
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Xiao Pan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Corresponding author, Phone: (413) 545-2733 (R.W.V.)
| |
Collapse
|
130
|
Xu Y, Xiao H, Wu D, Long C. Abiotic and Biological Degradation of Atmospheric Proteinaceous Matter Can Contribute Significantly to Dissolved Amino Acids in Wet Deposition. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:6551-6561. [PMID: 32391688 DOI: 10.1021/acs.est.0c00421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Atmospheric proteinaceous matter is characterized by ubiquity and potential bioavailability. However, little is known about the origins, secondary production processes, and biogeochemical role of proteinaceous matter in wet deposition. Precipitation samples were collected in suburban Guiyang (southwestern China) over a 1 year period to investigate their chemical components, mainly including dissolved combined amino acids (DCAAs), dissolved free AAs (DFAAs), and nonleachable particulate AAs (PAAs). Glycine was most abundant in the DFAAs, while the dominant species in DCAAs and PAAs was glutamic acid (including deaminated glutamine). The total DCAA, DFAA, and PAA concentrations peaked on average in spring (min. in summer). On average, the contribution of DCAA-nitrogen (median of 3.44%) to dissolved organic nitrogen was 5-fold higher than that of DFAA-nitrogen (median of 0.60%). Correlation analyses of AAs with ozone, nitrogen dioxide, and the quantitative degradation index suggest that DC(/F)AAs are linked with both abiotic and biological degradation of proteinaceous matter. Moreover, the high FAA scavenging ratios indicate the presence of postdepositional degradation of atmospheric proteinaceous matter. Further, the positive matrix factorization results suggest that the degradation of atmospheric proteinaceous matter markedly contributes to DCAAs and DFAAs in precipitation. Overall, the results suggest that the secondary processes involved in the degradation of atmospheric proteinaceous matter significantly promote direct bioavailability of AA-nitrogen.
Collapse
Affiliation(s)
- Yu Xu
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Resource, Environmental and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Huayun Xiao
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daishe Wu
- Key Laboratory of Poyang Lake Environment and Resource Utilization of Ministry of Education, School of Resource, Environmental and Chemical Engineering, Nanchang University, Nanchang 330031, China
| | - Chaojun Long
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, No. 99, Linchengxi Road, Guiyang 550081, China
| |
Collapse
|
131
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
132
|
Espino JA, King CD, Jones LM, Robinson RAS. In Vivo Fast Photochemical Oxidation of Proteins Using Enhanced Multiplexing Proteomics. Anal Chem 2020; 92:7596-7603. [PMID: 32383586 PMCID: PMC7815197 DOI: 10.1021/acs.analchem.0c00174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
In vivo fast photochemical oxidation of proteins
(IV-FPOP) is a hydroxyl radical protein footprinting method used to
study protein structure and protein–protein interactions. Oxidatively
modified proteins by IV-FPOP are analyzed by mass spectrometry (MS),
and the extent of oxidation is quantified by label-free MS. Peptide
oxidation changes yield useful information about protein structure,
due to changes in solvent accessibility. However, the sample size
necessary for animal studies requires increased sample preparation
and instrument time. Here, we report the combined application of IV-FPOP
and the enhanced multiplexing strategy combined precursor isotopic
labeling and isobaric tagging (cPILOT) for higher-throughput analysis
of oxidative modifications in C. elegans. Key differences
in the performance of label-free MS and cPILOT were identified. The
addition of oxygen (+16) was the most abundant modification identified
among all known possible FPOP modifications. This study presents IV-FPOP
coupled with enhanced multiplexing strategies such as cPILOT to increase
throughput of studies seeking to examine oxidative protein modifications.
Collapse
Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
133
|
Cheng M, Asuru A, Kiselar J, Mathai G, Chance MR, Gross ML. Fast Protein Footprinting by X-ray Mediated Radical Trifluoromethylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1019-1024. [PMID: 32255631 PMCID: PMC7486011 DOI: 10.1021/jasms.0c00085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Synchrotron radiolysis generates hydroxyl radicals (•OH) that are successful footprinting reagents. Here, we describe a new reagent for the synchrotron platform, the trifluoromethyl radical (•CF3). The radical is produced by •OH displacement of •CF3 from sodium triflinate (Langlois reagent). Upon X-ray beam exposure, the reagent labels proteins extensively without any additional chemicals on a millisecond or shorter time scale. The •CF3 is comparably reactive to •OH and produces footprinting information that complements that of •OH alone. This reagent in combination with •OH should enable novel chemistry for protein footprinting on the synchrotron platform.
Collapse
Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Awuri Asuru
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - George Mathai
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala 682013, India
| | - Mark R. Chance
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
| |
Collapse
|
134
|
Evaluation of NHS-Acetate and DEPC labelling for determination of solvent accessible amino acid residues in protein complexes. J Proteomics 2020; 222:103793. [PMID: 32348883 DOI: 10.1016/j.jprot.2020.103793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/27/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023]
Abstract
The activity of most proteins and protein complexes relies on the formation of defined three-dimensional structures. The analysis of these arrangements is therefore key for understanding their function and regulation in the cell. Besides the traditional structural techniques, structural mass spectrometry delivers insights into the various aspects of protein structure, including stoichiometry, protein-ligand interactions and solvent accessibility. The latter is usually obtained from labelling experiments. In this study, we evaluate two chemical labelling strategies using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate as labelling reagents. We characterised the mass spectra of modified peptides and assessed labelling reactivity of individual amino acid residues in intact proteins. Importantly, we uncovered neutral losses from diethylpyrocarbonate modified amino acids improving the assignments of the peptide fragment spectra. We further established a quantitative labelling workflow to determine labelling percentage and unambiguously distinguish solvent accessible amino acid residues from stochastically labelled residues. Finally, we used ion mobility MS to explore whether labelled proteins maintain their structures and remain stable. We conclude that labelling using N-hydroxysuccinimidyl acetate and diethylpyrocarbonate delivers comparable results, however, N-hydroxysuccinimidyl acetate labelling is compatible with standard proteomic workflows while diethylpyrocarbonate labelling requires specialised experimental conditions and data analysis. SIGNIFICANCE: Covalent labelling is widely used to identify solvent accessible amino acid residues of proteins or protein complexes. However, with increasing sensitivity of available MS instrumentation, a high number of modified residues is usually observed making an unambiguous assignment of solvent accessible residues necessary. In this study, we establish a quantitative labelling workflow for two different labelling strategies to identify accessible amino acid residues. In addition, we characterise observed mass spectra of modified peptides and identified neutral loss of DEPC modified amino acid residues during HCD fragmentation improving their assignments.
Collapse
|
135
|
Chance MR, Farquhar ER, Yang S, Lodowski DT, Kiselar J. Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution. J Mol Biol 2020; 432:2973-2984. [PMID: 32088185 PMCID: PMC7245549 DOI: 10.1016/j.jmb.2020.02.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/25/2022]
Abstract
Structural biology is entering an exciting time where many new high-resolution structures of large complexes and membrane proteins are determined regularly. These advances have been driven by over fifteen years of technology advancements, first in macromolecular crystallography, and recently in Cryo-electron microscopy. These structures are allowing detailed questions about functional mechanisms of the structures, and the biology enabled by these structures, to be addressed for the first time. At the same time, mass spectrometry technologies for protein structure analysis, "footprinting" studies, have improved their sensitivity and resolution dramatically and can provide detailed sub-peptide and residue level information for validating structures and interactions or understanding the dynamics of structures in the context of ligand binding or assembly. In this perspective, we review the use of protein footprinting to extend our understanding of macromolecular systems, particularly for systems challenging for analysis by other techniques, such as intrinsically disordered proteins, amyloidogenic proteins, and other proteins/complexes so far recalcitrant to existing methods. We also illustrate how the availability of high-resolution structural information can be a foundation for a suite of hybrid approaches to divine structure-function relationships beyond what individual techniques can deliver.
Collapse
Affiliation(s)
- Mark R Chance
- Case Center for Proteomics and Bioinformatics, USA; Case Center for Synchrotron Biosciences, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA.
| | | | - Sichun Yang
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - David T Lodowski
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| | - Janna Kiselar
- Case Center for Proteomics and Bioinformatics, USA; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Ave., Cleveland, OH, 44106, USA
| |
Collapse
|
136
|
Di Gaspero M, Ruzza P, Hussain R, Honisch C, Biondi B, Siligardi G, Marangon M, Curioni A, Vincenzi S. The Secondary Structure of a Major Wine Protein is Modified upon Interaction with Polyphenols. Molecules 2020; 25:E1646. [PMID: 32260104 PMCID: PMC7180857 DOI: 10.3390/molecules25071646] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 01/20/2023] Open
Abstract
Polyphenols are an important constituent of wines and they are largely studied due to their antioxidant properties and for their effects on wine quality and stability, which is also related to their capacity to bind to proteins. The effects of some selected polyphenols, including procyanidins B1 and B2, tannic acid, quercetin, and rutin, as well as those of a total white wine procyanidin extract on the conformational properties of the major wine protein VVTL1 (Vitis vinifera Thaumatin-Like-1) were investigated by Synchrotron Radiation Circular Dichroism (SRCD). Results showed that VVTL1 interacts with polyphenols as demonstrated by the changes in the secondary (far-UV) and tertiary (near-UV) structures, which were differently affected by different polyphenols. Additionally, polyphenols modified the two melting temperatures (TM) that were found for VVTL1 (32.2 °C and 53.9 °C for the protein alone). The circular dichroism (CD) spectra in the near-UV region revealed an involvement of the aromatic side-chains of the protein in the interaction with phenolics. The data demonstrate the existence of an interaction between polyphenols and VVTL1, which results in modification of its thermal and UV denaturation pattern. This information can be useful in understanding the behavior of wine proteins in presence of polyphenols, thus giving new insights on the phenomena that are involved in wine stability.
Collapse
Affiliation(s)
- Mattia Di Gaspero
- Department of Land, Environment, Agriculture and Forestry (TESAF), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy;
| | - Paolo Ruzza
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
| | - Rohanah Hussain
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; (R.H.); (G.S.)
| | - Claudia Honisch
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
- Department of Chemical Sciences, University of Padua, Via Marzolo 1, 35131 Padua, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry of CNR, Padua Unit, via Marzolo 1, 35131 Padua, Italy; (P.R.); (C.H.); (B.B.)
| | - Giuliano Siligardi
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK; (R.H.); (G.S.)
| | - Matteo Marangon
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
| | - Andrea Curioni
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
| | - Simone Vincenzi
- Department of Agronomy, Food, Natural Resources Animals and Environment (DAFNAE), University of Padua, Viale dell’Università, 16, 35020 Legnaro (PD), Italy; (A.C.); (S.V.)
| |
Collapse
|
137
|
Espino JA, Jones LM. In Vivo Hydroxyl Radical Protein Footprinting for the Study of Protein Interactions in Caenorhabditis elegans. J Vis Exp 2020. [PMID: 32310230 DOI: 10.3791/60910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fast oxidation of proteins (FPOP) is a hydroxyl radical protein footprinting (HRPF) method used to study protein structure, protein-ligand interactions, and protein-protein interactions. FPOP utilizes a KrF excimer laser at 248 nm for photolysis of hydrogen peroxide to generate hydroxyl radicals which in turn oxidatively modify solvent-accessible amino acid side chains. Recently, we expanded the use of FPOP of in vivo oxidative labeling in Caenorhabditis elegans (C. elegans), entitled IV-FPOP. The transparent nematodes have been used as model systems for many human diseases. Structural studies in C. elegans by IV-FPOP is feasible because of the animal's ability to uptake hydrogen peroxide, their transparency to laser irradiation at 248 nm, and the irreversible nature of the modification. The assembly of a microfluidic flow system for IV-FPOP labeling, IV-FPOP parameters, protein extraction, and LC-MS/MS optimized parameters are described herein.
Collapse
Affiliation(s)
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland;
| |
Collapse
|
138
|
Pan X, Limpikirati P, Chen H, Liu T, Vachet RW. Higher-Order Structure Influences the Kinetics of Diethylpyrocarbonate Covalent Labeling of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:658-665. [PMID: 32013423 PMCID: PMC7077735 DOI: 10.1021/jasms.9b00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The combination of covalent labeling (CL) and mass spectrometry (MS) has emerged as a useful tool for studying protein structure due to its good structural coverage, the ability to study proteins in mixtures, and its high sensitivity. Diethylpyrocarbonate (DEPC) is an effective CL reagent that can label N-termini and the side chains of several nucleophilic residues, providing information for about 30% of the residues in the average protein. For DEPC to provide accurate structural information, the extent of labeling must be controlled to minimize label-induced structural perturbations. In this work, we establish a quantitative correlation between general protein structural factors and DEPC reaction rates by measuring the reaction rate coefficients for several model proteins. Using principal component and regression analyses, we find that the solvent accessible surface areas of histidine and lysine residues in proteins are the primary factors that determine a protein's reactivity toward DEPC, despite the fact that other more abundant residues, such as tyrosine, threonine, and serine, are also labeled by DEPC. From the statistical analysis, a model emerges that can be used to predict the reactivity of a protein based on its structure and sequence, allowing the optimal DEPC concentration to be chosen for a given protein. The resulting model is supported by cross-validation studies and by accurately predicting of the reactivity of five test proteins. Overall, our model reveals interesting insight into the reactivity of proteins with DEPC, and it will facilitate identification of optimal DEPC labeling conditions for proteins.
Collapse
Affiliation(s)
- Xiao Pan
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Patanachai Limpikirati
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Huan Chen
- Department of Mathematical Sciences, School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX 75080, United States
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
| | - Richard W. Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, MA 01003, United States
- Corresponding Author:; Phone: (413) 545-2733 (R.W.V.)
| |
Collapse
|
139
|
Honisch C, Donadello V, Hussain R, Peterle D, De Filippis V, Arrigoni G, Gatto C, Giurgola L, Siligardi G, Ruzza P. Application of Circular Dichroism and Fluorescence Spectroscopies To Assess Photostability of Water-Soluble Porcine Lens Proteins. ACS OMEGA 2020; 5:4293-4301. [PMID: 32149259 PMCID: PMC7057709 DOI: 10.1021/acsomega.9b04234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The eye lens is mainly composed of the highly ordered water-soluble (WS) proteins named crystallins. The aggregation and insolubilization of these proteins lead to progressive lens opacification until cataract onset. Although this is a well-known disease, the mechanism of eye lens protein aggregation is not well understood; however, one of the recognized causes of proteins modification is related to the exposure to UV light. For this reason, the spectroscopic properties of WS lens proteins and their stability to UV irradiation have been evaluated by different biophysical methods including synchrotron radiation circular dichroism, fluorescence, and circular dichroism spectroscopies. Moreover, dynamic light scattering, gel electrophoresis, transmission electron microscopy, and protein digestion followed by tandem LC-MS/MS analysis were used to study the morphological and structural changes in protein aggregates induced by exposure to UV light. Our results clearly indicated that the exposure to UV radiation modified the protein conformation, inducing a loss of ordered structure and aggregation. Furthermore, we confirmed that these changes were attributable to the generation of reactive oxygen species due to the irradiation of the protein sample. This approach, involving the photodenaturation of proteins, provides a benchmark in high-throughput screening of small molecules suitable to prevent protein denaturation and aggregation.
Collapse
Affiliation(s)
- Claudia Honisch
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Viola Donadello
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
| | - Rohanah Hussain
- Diamond
Light Source Ltd., Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Daniele Peterle
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Vincenzo De Filippis
- Department
of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Giorgio Arrigoni
- Department
of Biomedical Sciences, University of Padova, 35131 Padova, Italy
- Proteomics
Center, University of Padova and Azienda
Ospedaliera di Padova, 35129 Padova, Italy
| | - Claudio Gatto
- Alchilife
Srl, R&D, Viale Austria
14, 35020 Ponte
San Nicolò (PD), Italy
| | - Laura Giurgola
- Alchilife
Srl, R&D, Viale Austria
14, 35020 Ponte
San Nicolò (PD), Italy
| | - Giuliano Siligardi
- Diamond
Light Source Ltd., Harwell Science and
Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Paolo Ruzza
- Institute
of Biomolecular Chemistry of CNR, Padua
Unit, 35131 Padova, Italy
| |
Collapse
|
140
|
Halgand F, Houée-Lévin C, Weik M, Madern D. Remote oxidative modifications induced by oxygen free radicals modify T/R allosteric equilibrium of a hyperthermophilic lactate dehydrogenase. J Struct Biol 2020; 210:107478. [PMID: 32087239 DOI: 10.1016/j.jsb.2020.107478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/01/2022]
Abstract
L-Lactate dehydrogenase (LDH) is a model protein allowing to shed light on the fundamental molecular mechanisms that drive the acquisition, evolution and regulation of enzyme properties. In this study, we test the hypothesis of a link between thermal stability of LDHs and their capacity against unfolding induced by reactive oxygen species (ROS) generated by γ-rays irradiation. By using circular dichroism spectroscopy, we analysed that high thermal stability of a thermophilic LDH favours strong resistance against ROS-induced unfolding, in contrast to its psychrophilic and mesophilic counterparts that are less resistant. We suggest that a protein's phenotype linking strong thermal stability and resistance against ROS damages would have been a selective evolutionary advantage. We also find that the enzymatic activity of the thermophilic LDH that is strongly resistant against ROS-unfolding is very sensitive to inactivation by irradiation. To address this counter-intuitive observation, we combined mass spectrometry analyses and enzymatic activity measurements. We demonstrate that the dramatic change on LDH activity was linked to remote chemical modifications away from the active site, that change the equilibrium between low-affinity tense (T-inactive) and high-affinity relaxed (R-active) forms. We found the T-inactive thermophilic enzyme obtained after irradiation can recover its LDH activity by addition of the allosteric effector 1, 6 fructose bis phosphate. We analyse our data within the general framework of allosteric regulation, which requires that an enzyme in solution populates a large diversity of dynamically-interchanging conformations. Our work demonstrates that the radiation-induced inactivation of an enzyme is controlled by its dynamical properties.
Collapse
Affiliation(s)
- Frédéric Halgand
- Université Paris Sud-CNRS, UMR 8000, bâtiments 201 P2 and 350, 91405 Orsay, France
| | - Chantal Houée-Lévin
- Université Paris Sud-CNRS, UMR 8000, bâtiments 201 P2 and 350, 91405 Orsay, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | |
Collapse
|
141
|
Bender J, Schmidt C. Mass spectrometry of membrane protein complexes. Biol Chem 2020; 400:813-829. [PMID: 30956223 DOI: 10.1515/hsz-2018-0443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. In addition, their natural lipid environment is crucial for their structure and function further hampering their analysis. Alternative approaches are therefore required when the analysis by conventional techniques proves difficult. In this review, we highlight the broad application of mass spectrometry (MS) for the characterisation of membrane proteins and their interactions with lipids. We show that MS unambiguously identifies the protein and lipid components of membrane protein complexes, unravels their three-dimensional arrangements and further provides clues of protein-lipid interactions.
Collapse
Affiliation(s)
- Julian Bender
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| |
Collapse
|
142
|
Khaje NA, Sharp JS. Rapid Quantification of Peptide Oxidation Isomers From Complex Mixtures. Anal Chem 2020; 92:3834-3843. [PMID: 32039584 DOI: 10.1021/acs.analchem.9b05268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a powerful technique for probing changes in protein topography, based on quantifying the amount of oxidation of different regions of a protein. While quantification of HRPF oxidation at the peptide level is relatively common and straightforward, quantification at the residue level is challenging because of the influence of oxidation on MS/MS fragmentation and the large number of complex and only partially chromatographically resolved isomeric peptide oxidation products. HRPF quantification of isomeric peptide oxidation products (where the peptide sequence is the same but isomeric oxidation products are formed at different sites) at the residue level by electron transfer dissociation tandem mass spectrometry (ETD MS/MS) has been demonstrated in both model peptides and HRPF products, but the method is hampered by the partial separation of oxidation isomers by reversed phase chromatography. This requires custom MS/MS methods to equally sample all isomeric oxidation products across their elution window, greatly increasing method development time and reducing the oxidation products quantified in a single LC-MS/MS run. Here, we present a zwitterionic hydrophilic interaction capillary chromatography (ZIC-HILIC) method to ideally coelute all isomeric peptide oxidation products while separating different peptides. This allows us to relatively quantify peptide oxidation isomers using an ETD MS/MS spectrum acquired at any point across the single peptide oxidation isomer peak, greatly simplifying data acquisition and data analysis.
Collapse
Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States.,Depertmant of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| |
Collapse
|
143
|
Ziemianowicz DS, MacCallum JL, Schriemer DC. Correlation between Labeling Yield and Surface Accessibility in Covalent Labeling Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:207-216. [PMID: 32031402 DOI: 10.1021/jasms.9b00083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The functional properties of a protein are strongly influenced by its topography, or the solvent-facing contour map of its surface. Together with crosslinking, covalent labeling mass spectrometry (CL-MS) has the potential to contribute topographical data through the measurement of surface accessibility. However, recent efforts to correlate measures of surface accessibility with labeling yield have been met with mixed success. Most applications of CL-MS involve differential analysis of protein interactions (i.e., footprinting experiments) where such inconsistencies have limited effect. Extending CL-MS into structural analysis requires an improved evaluation of the relationship between labeling and surface exposure. In this study, we applied recently developed diazirine reagents to obtain deep coverage of the large motor domain of Eg5 (a mitotic kinesin), and together with computational methods we correlated labeling yields with accessibility data in a number of ways. We observe that correlations can indeed be seen at a local structural level, but these correlations do not extend across the structure. The lack of correlation arises from the influence of protein dynamics and chemical composition on reagent partitioning and, thus, also on labeling yield. We conclude that our use of CL-MS data should be considered in light of "chemical accessibility" rather than "solvent accessibility" and suggest that CL-MS data would be a useful tool in the fundamental study of protein-solute interactions.
Collapse
Affiliation(s)
- Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - Justin L MacCallum
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute , University of Calgary , Calgary , Alberta , Canada T2N 4N1
- Department of Chemistry , University of Calgary , Calgary , Alberta , Canada T2N 4N1
| |
Collapse
|
144
|
Sun F, Xie X, Zhang Y, Duan J, Ma M, Wang Y, Qiu D, Lu X, Yang G, He G. Effects of Cold Jet Atmospheric Pressure Plasma on the Structural Characteristics and Immunoreactivity of Celiac-Toxic Peptides and Wheat Storage Proteins. Int J Mol Sci 2020; 21:ijms21031012. [PMID: 32033029 PMCID: PMC7036898 DOI: 10.3390/ijms21031012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 01/09/2023] Open
Abstract
The present research reported the effects of structural properties and immunoreactivity of celiac-toxic peptides and wheat storage proteins modified by cold jet atmospheric pressure (CJAP) plasma. It could generate numerous high-energy excited atoms, photons, electrons, and reactive oxygen and nitrogen species, including O3, H2O2, •OH, NO2- and NO3- etc., to modify two model peptides and wheat storage proteins. The Orbitrap HR-LC-MS/MS was utilized to identify and quantify CJAP plasma-modified model peptide products. Backbone cleavage of QQPFP and PQPQLPY at specific proline and glutamine residues, accompanied by hydroxylation at the aromatic ring of phenylalanine and tyrosine residues, contributed to the reduction and modification of celiac-toxic peptides. Apart from fragmentation, oxidation, and agglomeration states were evaluated, including carbonyl formation and the decline of γ-gliadin. The immunoreactivity of gliadin extract declined over time, demonstrating a significant decrease by 51.95% after 60 min of CJAP plasma treatment in vitro. The CJAP plasma could initiate depolymerization of gluten polymer, thereby reducing the amounts of large-sized polymers. In conclusion, CJAP plasma could be employed as a potential technique in the modification and reduction of celiac-toxic peptides and wheat storage proteins.
Collapse
Affiliation(s)
- Fusheng Sun
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
| | - Xiaoxue Xie
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
| | - Yufan Zhang
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
| | - Jiangwei Duan
- State Key Laboratory of Advanced Electromagnetic Engineering and Technology, School of Electrical and Electronic Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; (J.D.); (M.M.); (X.L.)
| | - Mingyu Ma
- State Key Laboratory of Advanced Electromagnetic Engineering and Technology, School of Electrical and Electronic Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; (J.D.); (M.M.); (X.L.)
| | - Yaqiong Wang
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
| | - Ding Qiu
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
| | - Xinpei Lu
- State Key Laboratory of Advanced Electromagnetic Engineering and Technology, School of Electrical and Electronic Engineering, Huazhong University of Science and Technology, Wuhan 430074, China; (J.D.); (M.M.); (X.L.)
| | - Guangxiao Yang
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
- Correspondence: (G.Y.); (G.H.); Tel.: +86-27-87792271 (G.Y. & G.H.); Fax: +86-27-87792272 (G.Y. & G.H.)
| | - Guangyuan He
- The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (F.S.); (X.X.); (Y.Z.); (Y.W.); (D.Q.)
- Correspondence: (G.Y.); (G.H.); Tel.: +86-27-87792271 (G.Y. & G.H.); Fax: +86-27-87792272 (G.Y. & G.H.)
| |
Collapse
|
145
|
Salem S, Sakir M, Sahin K, Korkmaz I, Yavuz E, Sarp G, Onses MS, Yilmaz E. Low bandgap microsphere-like magnetic nanocomposite: An enhanced photocatalyst for degradation of organic contaminants and fabrication of SERS-active surfaces. Colloids Surf A Physicochem Eng Asp 2020. [DOI: 10.1016/j.colsurfa.2020.124436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
146
|
Kuznetsova V, Dominguez-Martin MA, Bao H, Gupta S, Sutter M, Kloz M, Rebarz M, Přeček M, Chen Y, Petzold CJ, Ralston CY, Kerfeld CA, Polívka T. Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2020; 1861:148120. [PMID: 31734194 PMCID: PMC6943196 DOI: 10.1016/j.bbabio.2019.148120] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/09/2019] [Accepted: 11/04/2019] [Indexed: 01/12/2023]
Abstract
The orange carotenoid protein (OCP) is a structurally and functionally modular photoactive protein involved in cyanobacterial photoprotection. Recently, based on bioinformatic analysis and phylogenetic relationships, new families of OCP have been described, OCP2 and OCPx. The first characterization of the OCP2 showed both faster photoconversion and back-conversion, and lower fluorescence quenching of phycobilisomes relative to the well-characterized OCP1. Moreover, OCP2 is not regulated by the fluorescence recovery protein (FRP). In this work, we present a comprehensive study combining ultrafast spectroscopy and structural analysis to compare the photoactivation mechanisms of OCP1 and OCP2 from Tolypothrix PCC 7601. We show that despite significant differences in their functional characteristics, the spectroscopic properties of OCP1 and OCP2 are comparable. This indicates that the OCP functionality is not directly related to the spectroscopic properties of the bound carotenoid. In addition, the structural analysis by X-ray footprinting reveals that, overall, OCP1 and OCP2 have grossly the same photoactivation mechanism. However, the OCP2 is less reactive to radiolytic labeling, suggesting that the protein is less flexible than OCP1. This observation could explain fast photoconversion of OCP2.
Collapse
Affiliation(s)
- Valentyna Kuznetsova
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | | | - Han Bao
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miroslav Kloz
- ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Za Radnicí 835, 252 41 Dolní Břežany, Czech Republic
| | - Mateusz Rebarz
- ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Za Radnicí 835, 252 41 Dolní Břežany, Czech Republic
| | - Martin Přeček
- ELI Beamlines, Institute of Physics, Czech Academy of Sciences, Za Radnicí 835, 252 41 Dolní Břežany, Czech Republic
| | - Yan Chen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corie Y Ralston
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Tomáš Polívka
- Institute of Physics, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech Republic.
| |
Collapse
|
147
|
Anderson AP, Luo X, Russell W, Yin YW. Oxidative damage diminishes mitochondrial DNA polymerase replication fidelity. Nucleic Acids Res 2020; 48:817-829. [PMID: 31799610 PMCID: PMC6954441 DOI: 10.1093/nar/gkz1018] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/12/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial DNA (mtDNA) resides in a high ROS environment and suffers more mutations than its nuclear counterpart. Increasing evidence suggests that mtDNA mutations are not the results of direct oxidative damage, rather are caused, at least in part, by DNA replication errors. To understand how the mtDNA replicase, Pol γ, can give rise to elevated mutations, we studied the effect of oxidation of Pol γ on replication errors. Pol γ is a high fidelity polymerase with polymerase (pol) and proofreading exonuclease (exo) activities. We show that Pol γ exo domain is far more sensitive to oxidation than pol; under oxidative conditions, exonuclease activity therefore declines more rapidly than polymerase. The oxidized Pol γ becomes editing-deficient, displaying a 20-fold elevated mutations than the unoxidized enzyme. Mass spectrometry analysis reveals that Pol γ exo domain is a hotspot for oxidation. The oxidized exo residues increase the net negative charge around the active site that should reduce the affinity to mismatched primer/template DNA. Our results suggest that the oxidative stress induced high mutation frequency on mtDNA can be indirectly caused by oxidation of the mitochondrial replicase.
Collapse
Affiliation(s)
- Andrew P Anderson
- Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Xuemei Luo
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - William Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Y Whitney Yin
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77550, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77550, USA
| |
Collapse
|
148
|
Chen C, Lu B, Zhao X, Qian W, Liu J, Trabelsi T, Francisco JS, Qin J, Li J, Wang L, Zeng X. Capture of the Sulfur Monoxide–Hydroxyl Radical Complex. J Am Chem Soc 2020; 142:2175-2179. [DOI: 10.1021/jacs.9b12152] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Changyun Chen
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
| | - Bo Lu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
| | - Xiaofang Zhao
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
| | - Weiyu Qian
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
| | - Jie Liu
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
| | - Tarek Trabelsi
- Department of Earth and Environment Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
| | - Joseph S. Francisco
- Department of Earth and Environment Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6243, United States
| | - Jie Qin
- School of Chemistry and Chemical Engineering and Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, 401331 Chongqing, China
| | - Jun Li
- School of Chemistry and Chemical Engineering and Chongqing Key Laboratory of Theoretical and Computational Chemistry, Chongqing University, 401331 Chongqing, China
| | - Lina Wang
- Department of Chemistry, Fudan University, 200433 Shanghai, China
| | - Xiaoqing Zeng
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, 215123 Suzhou, China
- Department of Chemistry, Fudan University, 200433 Shanghai, China
| |
Collapse
|
149
|
Gupta S, Chen Y, Petzold CJ, DePonte DP, Ralston CY. Development of Container Free Sample Exposure for Synchrotron X-ray Footprinting. Anal Chem 2020; 92:1565-1573. [PMID: 31790200 DOI: 10.1021/acs.analchem.9b04849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The method of X-ray footprinting and mass spectrometry (XFMS) on large protein assemblies and membrane protein samples requires high flux density to overcome the hydroxyl radical scavenging reactions produced by the buffer constituents and the total protein content. Previously, we successfully developed microsecond XFMS using microfluidic capillary flow and a microfocused broadband X-ray source at the Advanced Light Source synchrotron beamlines, but the excessive radiation damage incurred when using capillaries prevented the full usage of a high-flux density beam. Here we present another significant advance for the XFMS method: the instrumentation of a liquid injection jet to deliver container free samples to the X-ray beam. Our preliminary experiments with a liquid jet at a bending magnet X-ray beamline demonstrate the feasibility of the approach and show a significant improvement in the effective dose for both the Alexa fluorescence assay and protein samples compared to conventional capillary flow methods. The combination of precisely controlled high dose delivery, shorter exposure times, and elimination of radiation damage due to capillary effects significantly increases the signal quality of the hydroxyl radical modification products and the dose-response data. This new approach is the first application of container free sample handling for XFMS and opens up the method for even further advances, such as high-quality microsecond time-resolved XFMS studies.
Collapse
Affiliation(s)
- Sayan Gupta
- Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Yan Chen
- Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | | | - Daniel P DePonte
- Stanford Linear Accelerator Center , Menlo Park , California 94025 , United States
| | - Corie Y Ralston
- Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| |
Collapse
|
150
|
Milosavljević AR, Jänkälä K, Ranković ML, Canon F, Bozek J, Nicolas C, Giuliani A. Oxygen K-shell spectroscopy of isolated progressively solvated peptide. Phys Chem Chem Phys 2020; 22:12909-12917. [DOI: 10.1039/d0cp00994f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray spectroscopy of an isolated controllably hydrated peptide: core excitation of the first solvation shell enhances peptide backbone fragmentation.
Collapse
Affiliation(s)
| | - Kari Jänkälä
- Nano and Molecular Systems Research Unit
- University of Oulu
- 90014 Oulu
- Finland
| | | | - Francis Canon
- Centre des Sciences du Goût et de l’Alimentation
- CNRS
- INRAE
- Université de Bourgogne Franche-Comté
- France
| | - John Bozek
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | | | - Alexandre Giuliani
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- INRAE
- UAR1008
| |
Collapse
|