1
|
Salazar Marcano DE, Savić ND, Declerck K, Abdelhameed SAM, Parac-Vogt TN. Reactivity of metal-oxo clusters towards biomolecules: from discrete polyoxometalates to metal-organic frameworks. Chem Soc Rev 2024; 53:84-136. [PMID: 38015569 DOI: 10.1039/d3cs00195d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Metal-oxo clusters hold great potential in several fields such as catalysis, materials science, energy storage, medicine, and biotechnology. These nanoclusters of transition metals with oxygen-based ligands have also shown promising reactivity towards several classes of biomolecules, including proteins, nucleic acids, nucleotides, sugars, and lipids. This reactivity can be leveraged to address some of the most pressing challenges we face today, from fighting various diseases, such as cancer and viral infections, to the development of sustainable and environmentally friendly energy sources. For instance, metal-oxo clusters and related materials have been shown to be effective catalysts for biomass conversion into renewable fuels and platform chemicals. Furthermore, their reactivity towards biomolecules has also attracted interest in the development of inorganic drugs and bioanalytical tools. Additionally, the structural versatility of metal-oxo clusters allows for the efficiency and selectivity of the biomolecular reactions they promote to be readily tuned, thereby providing a pathway towards reaction optimization. The properties of the catalyst can also be improved through incorporation into solid supports or by linking metal-oxo clusters together to form Metal-Organic Frameworks (MOFs), which have been demonstrated to be powerful heterogeneous catalysts. Therefore, this review aims to provide a comprehensive and critical analysis of the state of the art on biomolecular transformations promoted by metal-oxo clusters and their applications, with a particular focus on structure-activity relationships.
Collapse
Affiliation(s)
| | - Nada D Savić
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
| | - Kilian Declerck
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
| | | | | |
Collapse
|
2
|
Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022; 215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
|
3
|
Zehnder J, Cadalbert R, Yulikov M, Künze G, Wiegand T. Paramagnetic spin labeling of a bacterial DnaB helicase for solid-state NMR. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 332:107075. [PMID: 34597956 DOI: 10.1016/j.jmr.2021.107075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
Labeling of biomolecules with a paramagnetic probe for nuclear magnetic resonance (NMR) spectroscopy enables determining long-range distance restraints, which are otherwise not accessible by classically used dipolar coupling-based NMR approaches. Distance restraints derived from paramagnetic relaxation enhancements (PREs) can facilitate the structure determination of large proteins and protein complexes. We herein present the site-directed labeling of the large oligomeric bacterial DnaB helicase from Helicobacter pylori with cysteine-reactive maleimide tags carrying either a nitroxide radical or a lanthanide ion. The success of the labeling reaction was followed by quantitative continuous-wave electron paramagnetic resonance (EPR) experiments performed on the nitroxide-labeled protein. PREs were extracted site-specifically from 2D and 3D solid-state NMR spectra. A good agreement with predicted PRE values, derived by computational modeling of nitroxide and Gd3+ tags in the low-resolution DnaB crystal structure, was found. Comparison of experimental PREs and model-predicted spin label-nucleus distances indicated that the size of the "blind sphere" around the paramagnetic center, in which NMR resonances are not detected, is slightly larger for Gd3+ (∼14 Å) than for nitroxide (∼11 Å) in 13C-detected 2D spectra of DnaB. We also present Gd3+-Gd3+ dipolar electron-electron resonance EPR experiments on DnaB supporting the conclusion that DnaB was present as a hexameric assembly.
Collapse
Affiliation(s)
| | | | - Maxim Yulikov
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Georg Künze
- Institute for Drug Discovery, Medical School, Leipzig University, 04103 Leipzig, Germany.
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland; Max-Planck-Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany; Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany.
| |
Collapse
|
4
|
McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
Collapse
Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| |
Collapse
|
5
|
Lai SM, Gopalan V. Using an L7Ae-Tethered, Hydroxyl Radical-Mediated Footprinting Strategy to Identify and Validate Kink-Turns in RNAs. Methods Mol Biol 2021; 2167:147-169. [PMID: 32712919 DOI: 10.1007/978-1-0716-0716-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Kink-turns are important RNA structural modules that facilitate long-range tertiary interactions and form binding sites for members of the L7Ae family of proteins. Present in a wide variety of functional RNAs, kink-turns play key organizational roles in many RNA-based cellular processes, including translation, modification, and tRNA biogenesis. It is important to determine the contribution of kink-turns to the overall architecture of resident RNAs, as these modules dictate ribonucleoprotein (RNP) assembly and function. This chapter describes a site-directed, hydroxyl radical-mediated footprinting strategy that utilizes L7Ae-tethered chemical nucleases to experimentally validate computationally identified kink-turns in any RNA and under a wide variety of conditions. The work plan described here uses the catalytic RNase P RNA as an example to provide a blueprint for using this footprinting method to map RNA-protein interactions in other RNP complexes.
Collapse
Affiliation(s)
- Stella M Lai
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
| |
Collapse
|
6
|
Peng KC, Chang KC, Ke SC, Chen J, Liu SY. Novel protein photocleavers: Chrysophanol and pachybasin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2020. [DOI: 10.1016/j.jpap.2020.100008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
|
7
|
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: 128] [Impact Index Per Article: 32.0] [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
|
8
|
Loosen A, de Azambuja F, Smolders S, Moons J, Simms C, De Vos D, Parac-Vogt TN. Interplay between structural parameters and reactivity of Zr 6-based MOFs as artificial proteases. Chem Sci 2020; 11:6662-6669. [PMID: 34094124 PMCID: PMC8159359 DOI: 10.1039/d0sc02136a] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/21/2020] [Indexed: 12/15/2022] Open
Abstract
Structural parameters influencing the reactivity of metal-organic frameworks (MOF) are challenging to establish. However, understanding their effect is crucial to further develop their catalytic potential. Here, we uncovered a correlation between reaction kinetics and the morphological structure of MOF-nanozymes using the hydrolysis of a dipeptide under physiological pH as model reaction. Comparison of the activation parameters in the presence of NU-1000 with those observed with MOF-808 revealed the reaction outcome is largely governed by the Zr6 cluster. Additionally, its structural environment completely changes the energy profile of the hydrolysis step, resulting in a higher energy barrier ΔG ‡ for NU-1000 due to a much larger ΔS ‡ term. The reactivity of NU-1000 towards a hen egg white lysozyme protein under physiological pH was also evaluated, and the results pointed to a selective cleavage at only 3 peptide bonds. This showcases the potential of Zr-MOFs to be developed into heterogeneous catalysts for non-enzymatic but selective transformation of biomolecules, which are crucial for many modern applications in biotechnology and proteomics.
Collapse
Affiliation(s)
- Alexandra Loosen
- Department of Chemistry, KU Leuven Celestijnenlaan 200F Leuven Belgium
| | | | - Simon Smolders
- Department Microbial and Molecular Systems, KU Leuven Celestijnenlaan 200F Leuven Belgium
| | - Jens Moons
- Department of Chemistry, KU Leuven Celestijnenlaan 200F Leuven Belgium
| | - Charlotte Simms
- Department of Chemistry, KU Leuven Celestijnenlaan 200F Leuven Belgium
| | - Dirk De Vos
- Department Microbial and Molecular Systems, KU Leuven Celestijnenlaan 200F Leuven Belgium
| | | |
Collapse
|
9
|
Jayasinghe‐Arachchige VM, Hu Q, Sharma G, Paul TJ, Lundberg M, Quinonero D, Parac‐Vogt TN, Prabhakar R. Hydrolysis of chemically distinct sites of human serum albumin by polyoxometalate: A hybrid QM/MM (ONIOM) study. J Comput Chem 2018; 40:51-61. [DOI: 10.1002/jcc.25528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 06/22/2018] [Accepted: 06/23/2018] [Indexed: 12/28/2022]
Affiliation(s)
| | - Qiaoyu Hu
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Gaurav Sharma
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Thomas J. Paul
- Department of Chemistry University of Miami Coral Gables Florida 33146
| | - Marcus Lundberg
- Department of Chemistry ‐ Ångström Laboratory Uppsala University 751 21, Uppsala Sweden
| | - David Quinonero
- Department of Chemistry Universitat de les Illes Balears Palma de Mallorca Spain
| | | | - Rajeev Prabhakar
- Department of Chemistry University of Miami Coral Gables Florida 33146
| |
Collapse
|
10
|
Yenjai S, Kumar CV, Kuno M, Liwporncharoenvong T, Samosorn S, Buranaprapuk A. Tuning the chain length of new pyrene derivatives for site-selective photocleavage of avidin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2018; 186:23-30. [PMID: 29990670 DOI: 10.1016/j.jphotobiol.2018.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/08/2018] [Accepted: 07/02/2018] [Indexed: 06/08/2023]
Abstract
Rational design of photoreagents with systematic modifications of their structures can provide valuable information for a better understanding of the protein photocleavage mechanism by these reagents. Variation of the length of the linker connecting the photoactive moiety with the protein anchoring-group allowed us to investigate the control of the protein photocleavage site. A series of new photochemical reagents (PMA-1A, PMA-2A and PMA-3A) with increasing chain lengths is examined in the current study. Using avidin as a model system, we examined the interaction of these probes by UV-Vis, fluorescence spectroscopic methods, photocleavage and computational docking studies. Hypochromism of the absorption spectrum was observed for the binding of these new photochemical reagents with estimated binding constants (Kb) of 6.2 × 105, 6.7 × 105 and 4.6 × 105 M-1, respectively. No significant changes of Stern-Volmer quenching constant (Ksv) with Co(NH3)6Cl3 has been noted and the data indicated that the probes bind near the surface of the protein with sufficient exposure to the solvent. Photoexcitation of the probe-avidin complex, in the presence of Co(NH3)6Cl3, resulted in protein fragmentation, and the cleavage yield decreased with the increase in the linker length, and paralleled with the observed Ksv values. Amino acid sequencing of the photofragments indicated that avidin is cleaved between Thr77 and Val78, as a major cleavage site for all the three photoreagents. This site is proximate to the biotin binding site on avidin, and molecular docking studies indicated that the H-bonding interactions between the polar end-group of the photoreagents and hydrophilic amino acids of avidin were important in positioning the reagent on the protein. The major cleavage site, at residues 77-78, was within 5 Å of the pyrenyl moiety of the probe, and hence, molecular tuning of the linker provided a simple approach to position the photoreagent along the potential photocleavage site.
Collapse
Affiliation(s)
- Sudarat Yenjai
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Challa V Kumar
- Department of Chemistry, 55 N. Eagleville Road, University of Connecticut, Storrs, CT 06269-3060, USA; Department of Molecular and Cellular Biology, 91 N. Eagleville Road, U-3125, University of Connecticut, Storrs, CT 06269-3125, USA
| | - Mayuso Kuno
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | - Siritron Samosorn
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | - Apinya Buranaprapuk
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand.
| |
Collapse
|
11
|
Tokmina-Lukaszewska M, Patterson A, Berry L, Scott L, Balasubramanian N, Bothner B. The Role of Mass Spectrometry in Structural Studies of Flavin-Based Electron Bifurcating Enzymes. Front Microbiol 2018; 9:1397. [PMID: 30026733 PMCID: PMC6041385 DOI: 10.3389/fmicb.2018.01397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/07/2018] [Indexed: 12/01/2022] Open
Abstract
For decades, biologists and biochemists have taken advantage of atomic resolution structural models of proteins from X-ray crystallography, nuclear magnetic resonance spectroscopy, and more recently cryo-electron microscopy. However, not all proteins relent to structural analyses using these approaches, and as the depth of knowledge increases, additional data elucidating a mechanistic understanding of protein function is desired. Flavin-based electron bifurcating enzymes, which are responsible for producing high energy compounds through the simultaneous endergonic and exergonic reduction of two intercellular electron carriers (i.e., NAD+ and ferredoxin) are one class of proteins that have challenged structural biologists and in which there is great interest to understand the mechanism behind electron gating. A limited number of X-ray crystallography projects have been successful; however, it is clear that to understand how these enzymes function, techniques that can reveal detailed in solution information about protein structure, dynamics, and interactions involved in the bifurcating reaction are needed. In this review, we cover a general set of mass spectrometry-based techniques that, combined with protein modeling, are capable of providing information on both protein structure and dynamics. Techniques discussed include surface labeling, covalent cross-linking, native mass spectrometry, and hydrogen/deuterium exchange. We cover how biophysical data can be used to validate computationally generated protein models and develop mechanistic explanations for regulation and performance of enzymes and protein complexes. Our focus will be on flavin-based electron bifurcating enzymes, but the broad applicability of the techniques will be showcased.
Collapse
Affiliation(s)
| | - Angela Patterson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Luke Berry
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Liam Scott
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| |
Collapse
|
12
|
Alqarni MH, Muharram MM, Labrou NE. Ligand-induced glutathione transferase degradation as a therapeutic modality: Investigation of a new metal-mediated affinity cleavage strategy for human GSTP1-1. Int J Biol Macromol 2018; 116:84-90. [PMID: 29727648 DOI: 10.1016/j.ijbiomac.2018.04.187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/16/2018] [Accepted: 04/30/2018] [Indexed: 02/07/2023]
Abstract
Glutathione transferases (GST, EC. 2.5.1.18) are overexpressed in cancer cell and have been shown to be involved in cancer cell growth, differentiation and the development of multi-drug resistance (MDR) mechanism. Therefore, GST inhibitors are emerging as promising chemosensitizers to manage and reverse MDR. The present work aims to the synthesis, characterization and assessment of a new active-site chimeric inhibitor towards the MDR-involved human GSTP1-1 isoenzyme (hGSTP1-1). The inhibitor [BDA-Fe(III)] was designed to possess two functional groups: the anthraquinone moiety, as recognition element by hGSTP1-1 and a metal chelated complex [iminodiacetic acid-Fe(III)] as a reactive moiety, able to generate reactive oxygen species (ROS), through Fenton reaction. Upon binding of the BDA-Fe(III) to hGSTP1-1 in the presence of hydrogen peroxide, reactive oxygen species (ROS) are generated, which promoted the specific cleavage of hGSTP1-1 in a time and concentration-dependent manner. Electrophoretic analysis showed that each enzyme subunit is cleaved at a single site. Amino acid sequencing as well as molecular modelling studies established that the cleaved peptide bond is located between the amino acids Tyr103 and Ile104. This ligand-induced hGSTP1-1 degradation and inactivation strategy is discussed as a new approach towards chemosensitization of MDR cancer cells.
Collapse
Affiliation(s)
- Mohammed Hamed Alqarni
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942 Alkharj, Saudi Arabia
| | - Magdy Mohamed Muharram
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942 Alkharj, Saudi Arabia; Department of Microbiology, College of Science, Al-Azhar University, Nasr City, 11884 Cairo, Egypt
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, 75 Iera Odos Street, GR-11855 Athens, Greece.
| |
Collapse
|
13
|
Zhang T, Sharma G, Paul TJ, Hoffmann Z, Prabhakar R. Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis. J Chem Inf Model 2017; 57:1079-1088. [PMID: 28398040 DOI: 10.1021/acs.jcim.6b00781] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimental information, these molecules were created by altering protonation states (singly protonated, doubly protonated, or doubly deprotonated) and number of their ligands. The energetics of the I'N2O4, and I'NO2 and their analogues predicted that both stepwise and concerted mechanisms occurred either with similar barriers, or the latter was more favorable than the former. They also showed that the doubly deprotonated form hydrolyzed the peptide bond with substantially lower barriers than the barriers for other protonation states. For NO2 core possessing complexes, Zr-(NO2)(OHH)(H2O/OH)n for n = 1-3, the hydroxyl group containing molecules were found to be more reactive than their water ligand possessing counterparts. The barriers for these complexes reduced with an increase in the coordination number (6-8) of the Zr(IV) ion. Among all 11 molecules, the NO2 core possessing and two hydroxyl group containing I'DNO2-2H complex was found to be the most reactive complex with a barrier of 28.9 kcal/mol. Furthermore, barriers of 27.5, 28.9, and 32.0 kcal/mol for hydrolysis of Gly-Glu (negative), Gly-Gly (neutral), and Gly-Lys (positive) substrates, respectively, by this complex were in agreement with experiments. The activities of these complexes were explained in terms of basicity of their ligand environment and nucleophilicity of the Zr(IV) center using metal-ligand distances, charge on the metal ion, and the metal-nucleophile distance as parameters. These results provide a deeper understanding of the functioning of these complexes and will help design Zr(IV)-based synthetic metallopeptidases.
Collapse
Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Gaurav Sharma
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Thomas J Paul
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Zachary Hoffmann
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami , Coral Gables, Florida 33146, United States
| |
Collapse
|
14
|
Wang T, Chen Y, Tabuchi A, Cosgrove DJ, Hong M. The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies. PLANT PHYSIOLOGY 2016; 172:2107-2119. [PMID: 27729469 PMCID: PMC5129719 DOI: 10.1104/pp.16.01311] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/07/2016] [Indexed: 05/18/2023]
Abstract
The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing 13C-enriched maize CWs with EXPB1 functionalized with a Mn2+ tag, we measured Mn2+-induced PRE Strong 1H and 13C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.
Collapse
Affiliation(s)
- Tuo Wang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Yuning Chen
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Akira Tabuchi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Daniel J Cosgrove
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (T.W., M.H.); and
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802 (Y.C., A.T., D.J.C.)
| |
Collapse
|
15
|
Oxidative footprinting in the study of structure and function of membrane proteins: current state and perspectives. Biochem Soc Trans 2016; 43:983-94. [PMID: 26517913 DOI: 10.1042/bst20150130] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Membrane proteins, such as receptors, transporters and ion channels, control the vast majority of cellular signalling and metabolite exchange processes and thus are becoming key pharmacological targets. Obtaining structural information by usage of traditional structural biology techniques is limited by the requirements for the protein samples to be highly pure and stable when handled in high concentrations and in non-native buffer systems, which is often difficult to achieve for membrane targets. Hence, there is a growing requirement for the use of hybrid, integrative approaches to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions. In recent years, significant progress has been made in the field of oxidative labelling techniques and in particular the X-ray radiolytic footprinting in combination with mass spectrometry (MS) (XF-MS), which provide residue-specific information on the solvent accessibility of proteins. In combination with both low- and high-resolution data from other structural biology approaches, it is capable of providing valuable insights into dynamics of membrane proteins, which have been difficult to obtain by other structural techniques, proving a highly complementary technique to address structure and function of membrane targets. XF-MS has demonstrated a unique capability for identification of structural waters and conformational changes in proteins at both a high degree of spatial and a high degree of temporal resolution. Here, we provide a perspective on the place of XF-MS among other structural biology methods and showcase some of the latest developments in its usage for studying water-mediated transmembrane (TM) signalling, ion transport and ligand-induced allosteric conformational changes in membrane proteins.
Collapse
|
16
|
Abstract
Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function. Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides inhibit these pathways and this may contribute to the accumulation of modified proteins in cells. Available evidence supports an association between protein oxidation and multiple human pathologies, but whether this link is causal remains to be established.
Collapse
Affiliation(s)
- Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Blegdamsvej 3, Copenhagen 2200, Denmark
| |
Collapse
|
17
|
Ghattas W, Cotchico-Alonso L, Maréchal JD, Urvoas A, Rousseau M, Mahy JP, Ricoux R. Artificial Metalloenzymes with the Neocarzinostatin Scaffold: Toward a Biocatalyst for the Diels-Alder Reaction. Chembiochem 2016; 17:433-40. [DOI: 10.1002/cbic.201500445] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Wadih Ghattas
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Lur Cotchico-Alonso
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Jean-Didier Maréchal
- Departament de Química; Universitat Autònoma de Barcelona; Edifici C.n. 08193, Cerdonyola del Vallès Barcelona Spain
| | - Agathe Urvoas
- Institute for Integrative Biology of the Cell (I2BC); UMR 9198, CEA, CNRS, Université Paris-Sud; Bât. 430, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Maëva Rousseau
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Jean-Pierre Mahy
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| | - Rémy Ricoux
- Institute de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO); UMR 8182, CNRS, Université Paris-Sud; Bât. 420, rue du Doyen Georges Poitou 91405 Orsay Cedex France
| |
Collapse
|
18
|
Jaroniec CP. Structural studies of proteins by paramagnetic solid-state NMR spectroscopy. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2015; 253:50-9. [PMID: 25797004 PMCID: PMC4371136 DOI: 10.1016/j.jmr.2014.12.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/17/2014] [Indexed: 05/03/2023]
Abstract
Paramagnetism-based nuclear pseudocontact shifts and spin relaxation enhancements contain a wealth of information in solid-state NMR spectra about electron-nucleus distances on the ∼20 Å length scale, far beyond that normally probed through measurements of nuclear dipolar couplings. Such data are especially vital in the context of structural studies of proteins and other biological molecules that suffer from a sparse number of experimentally-accessible atomic distances constraining their three-dimensional fold or intermolecular interactions. This perspective provides a brief overview of the recent developments and applications of paramagnetic magic-angle spinning NMR to biological systems, with primary focus on the investigations of metalloproteins and natively diamagnetic proteins modified with covalent paramagnetic tags.
Collapse
Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| |
Collapse
|
19
|
Mahy JP, Maréchal JD, Ricoux R. Various strategies for obtaining oxidative artificial hemoproteins with a catalytic oxidative activity: from "Hemoabzymes" to "Hemozymes"? J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424614500813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The design of artificial hemoproteins that could lead to new biocatalysts for selective oxidation reactions using clean oxidants such as O 2 or H 2 O 2 under ecocompatible conditions constitutes a really promising challenge for a wide range of industrial applications. In vivo, such reactions are performed by heme-thiolate proteins, cytochromes P450, that catalyze the oxidation of drugs by dioxygen in the presence of electrons delivered from NADPH by cytochrome P450 reductase. Several strategies were used to design new artificial hemoproteins to mimic these enzymes, that associate synthetic metalloporphyrin derivatives to a protein that is supposed to induce a selectivity in the catalyzed reaction. A first generation of artificial hemoproteins or "hemoabzymes" was obtained by the non-covalent association of synthetic hemes such as N-methyl-mesoporphyrin IX, Fe(III) -α3β-tetra-o-carboxyphenylporphyrin or microperoxidase 8 with monoclonal antibodies raised against these cofactors. The obtained antibody-metalloporphyrin complexes displayed a peroxidase activity and some of them catalyzed the regio-selective nitration of phenols by H 2 O 2/ NO 2 and the stereo-selective oxidation of sulphides by H 2 O 2. A second generation of artificial hemoproteins or "hemozymes", was obtained by the non-covalent association of non-relevant proteins with metalloporphyrin derivatives. Several strategies were used, the most successful of which, named "host-guest" strategy involved the non-covalent incorporation of metalloporphyrin derivatives into easily affordable proteins. The artificial hemoproteins obtained were found to be able to perform efficiently the stereoselective oxidation of organic compounds such as sulphides and alkenes by H 2 O 2 and KHSO 5.
Collapse
Affiliation(s)
- Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie, Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola del Vallès, Barcelona, Spain
| | - Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR 8182 CNRS, Laboratoire de Chimie, Bioorganique et Bioinorganique, Bât. 420, Université Paris-sud, 91405 Orsay Cedex, France
| |
Collapse
|
20
|
Abstract
Myriad biological processes proceed through states that defy characterization by conventional atomic-resolution structural biological methods. The invisibility of these 'dark' states can arise from their transient nature, low equilibrium population, large molecular weight, and/or heterogeneity. Although they are invisible, these dark states underlie a range of processes, acting as encounter complexes between proteins and as intermediates in protein folding and aggregation. New methods have made these states accessible to high-resolution analysis by nuclear magnetic resonance (NMR) spectroscopy, as long as the dark state is in dynamic equilibrium with an NMR-visible species. These methods - paramagnetic NMR, relaxation dispersion, saturation transfer, lifetime line broadening, and hydrogen exchange - allow the exploration of otherwise invisible states in exchange with a visible species over a range of timescales, each taking advantage of some unique property of the dark state to amplify its effect on a particular NMR observable. In this review, we introduce these methods and explore two specific techniques - paramagnetic relaxation enhancement and dark state exchange saturation transfer - in greater detail.
Collapse
Affiliation(s)
- Nicholas J. Anthis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
| |
Collapse
|
21
|
Cunningham TF, Shannon MD, Putterman MR, Arachchige RJ, Sengupta I, Gao M, Jaroniec CP, Saxena S. Cysteine-specific Cu2+ chelating tags used as paramagnetic probes in double electron electron resonance. J Phys Chem B 2015; 119:2839-43. [PMID: 25608028 DOI: 10.1021/jp5103143] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Double electron electron resonance (DEER) is an attractive technique that is utilized for gaining insight into protein structure and dynamics via nanometer-scale distance measurements. The most commonly used paramagnetic tag in these measurements is a nitroxide spin label, R1. Here, we present the application of two types of high-affinity Cu(2+) chelating tags, based on the EDTA and cyclen metal-binding motifs as alternative X-band DEER probes, using the B1 immunoglobulin-binding domain of protein G (GB1) as a model system. Both types of tags have been incorporated into a variety of protein secondary structure environments and exhibit high spectral sensitivity. In particular, the cyclen-based tag displays distance distributions with comparable distribution widths and most probable distances within 1-3 Å when compared to homologous R1 distributions. The results display the viability of the cyclen tag as an alternative to the R1 side chain for X-band DEER distance measurements in proteins.
Collapse
Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh , 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Mahy JP, Maréchal JD, Ricoux R. From “hemoabzymes” to “hemozymes”: towards new biocatalysts for selective oxidations. Chem Commun (Camb) 2015; 51:2476-94. [DOI: 10.1039/c4cc08169b] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Two generations of artificial hemoproteins have been obtained: “hemoabzymes”, by non-covalent association of synthetic hemes with monoclonal antibodies raised against these cofactors and “hemozymes”, by non-covalent association of non-relevant proteins with metalloporphyrin derivatives. A review of the different strategies employed as well as their structural and catalytic properties is presented here.
Collapse
Affiliation(s)
- J.-P. Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- UMR 8182 CNRS
- Laboratoire de Chimie Bioorganique et Bioinorganique
- 91435 Orsay Cedex
- France
| | - J.-D. Maréchal
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - R. Ricoux
- Institut de Chimie Moléculaire et des Matériaux d'Orsay
- UMR 8182 CNRS
- Laboratoire de Chimie Bioorganique et Bioinorganique
- 91435 Orsay Cedex
- France
| |
Collapse
|
23
|
Abstract
Site-selective peptide/protein degradation through chemical cleavage methods is an important modification of biologically relevant macromolecules which complements enzymatic hydrolysis. In this review, recent progress in chemical, site-selective peptide bond cleavage is overviewed, with an emphasis on postulated mechanisms and their implications on reactivity, selectivity, and substrate scope.
Collapse
|
24
|
Sengupta I, Gao M, Arachchige RJ, Nadaud PS, Cunningham TF, Saxena S, Schwieters CD, Jaroniec CP. Protein structural studies by paramagnetic solid-state NMR spectroscopy aided by a compact cyclen-type Cu(II) binding tag. JOURNAL OF BIOMOLECULAR NMR 2015; 61:1-6. [PMID: 25432438 PMCID: PMC4304965 DOI: 10.1007/s10858-014-9880-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 11/18/2014] [Indexed: 05/07/2023]
Abstract
Paramagnetic relaxation enhancements (PREs) are a rich source of structural information in protein solid-state NMR spectroscopy. Here we demonstrate that PRE measurements in natively diamagnetic proteins are facilitated by a thiol-reactive compact, cyclen-based, high-affinity Cu(2+) binding tag, 1-[2-(pyridin-2-yldisulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (TETAC), that overcomes the key shortcomings associated with the use of larger, more flexible metal-binding tags. Using the TETAC-Cu(2+) K28C mutant of B1 immunoglobulin-binding domain of protein G as a model, we find that amino acid residues located within ~10 Å of the Cu(2+) center experience considerable transverse PREs leading to severely attenuated resonances in 2D (15)N-(13)C correlation spectra. For more distant residues, electron-nucleus distances are accessible via quantitative measurements of longitudinal PREs, and we demonstrate such measurements for (15)N-Cu(2+) distances up to ~20 Å.
Collapse
Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Min Gao
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rajith J. Arachchige
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Timothy F. Cunningham
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Charles D. Schwieters
- Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Corresponding author: Christopher P. Jaroniec,
| |
Collapse
|
25
|
Zhang T, Zhu X, Prabhakar R. Peptide Hydrolysis by Metal-Cyclen Complexes and Their Analogues: Insights from Theoretical Studies. Organometallics 2014. [DOI: 10.1021/om400903r] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| |
Collapse
|
26
|
Zhang T, Zhu X, Prabhakar R. Mechanistic Insights into Metal (Pd2+, Co2+, and Zn2+)−β-Cyclodextrin Catalyzed Peptide Hydrolysis: A QM/MM Approach. J Phys Chem B 2014; 118:4106-14. [DOI: 10.1021/jp502229s] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tingting Zhang
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| |
Collapse
|
27
|
|
28
|
Tanabe K, Taniguchi A, Matsumoto T, Oisaki K, Sohma Y, Kanai M. Asparagine-selective cleavage of peptide bonds through hypervalent iodine-mediated Hofmann rearrangement in neutral aqueous solution. Chem Sci 2014. [DOI: 10.1039/c3sc53037j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
29
|
Sengupta I, Nadaud PS, Jaroniec CP. Protein structure determination with paramagnetic solid-state NMR spectroscopy. Acc Chem Res 2013; 46:2117-26. [PMID: 23464364 DOI: 10.1021/ar300360q] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Many structures of the proteins and protein assemblies that play central roles in fundamental biological processes and disease pathogenesis are not readily accessible via the conventional techniques of single-crystal X-ray diffraction and solution-state nuclear magnetic resonance (NMR). On the other hand, many of these challenging biological systems are suitable targets for atomic-level structural and dynamic analysis by magic-angle spinning (MAS) solid-state NMR spectroscopy, a technique that has far less stringent limitations on the molecular size and crystalline state. Over the past decade, major advances in instrumentation and methodology have prompted rapid growth in the field of biological solid-state NMR. However, despite this progress, one challenge for the elucidation of three-dimensional (3D) protein structures via conventional MAS NMR methods is the relative lack of long-distance data. Specifically, extracting unambiguous interatomic distance restraints larger than ∼5 Å from through-space magnetic dipole-dipole couplings among the protein (1)H, (13)C, and (15)N nuclei has proven to be a considerable challenge for researchers. It is possible to circumvent this problem by extending the structural studies to include several analogs of the protein of interest, intentionally modified to contain covalently attached paramagnetic tags at selected sites. In these paramagnetic proteins, the hyperfine couplings between the nuclei and unpaired electrons can manifest themselves in NMR spectra in the form of relaxation enhancements of the nuclear spins that depend on the electron-nucleus distance. These effects can be significant for nuclei located up to ∼20 Å away from the paramagnetic center. In this Account, we discuss MAS NMR structural studies of nitroxide and EDTA-Cu(2+) labeled variants of a model 56 amino acid globular protein, B1 immunoglobulin-binding domain of protein G (GB1), in the microcrystalline solid phase. We used a set of six EDTA-Cu(2+)-tagged GB1 mutants to rapidly determine the global protein fold in a de novo fashion. Remarkably, these studies required quantitative measurements of only approximately four or five backbone amide (15)N longitudinal paramagnetic relaxation enhancements per residue, in the complete absence of the usual internuclear distance restraints. Importantly, this paramagnetic solid-state NMR methodology is general and can be directly applied to larger proteins and protein complexes for which a significant fraction of the signals can be assigned in standard 2D and 3D MAS NMR chemical shift correlation spectra.
Collapse
Affiliation(s)
- Ishita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Philippe S. Nadaud
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Christopher P. Jaroniec
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
30
|
Jityuti B, Liwporncharoenvong T, Buranaprapuk A. Use of a molybdenum(VI) complex as artificial protease in protein photocleavage. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2013; 126:55-59. [PMID: 23895865 DOI: 10.1016/j.jphotobiol.2013.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 06/05/2013] [Accepted: 07/02/2013] [Indexed: 06/02/2023]
Abstract
In this study, a molybdenum(VI) peroxo α-amino acid complex, MoO(O2)2(α-leucine) (H2O), was prepared and used as an artificial protease for site-specific cleavage of porcine pepsin, a model protein. Cleavage of pepsin by MoO(O2)2(α-leucine) (H2O) was achieved under photochemical conditions at room temperature and pH 7.0. The reaction was activated by irradiation of the MoO(O2)2(α-leucine) (H2O)-protein mixture by UV light (320 and 340nm) for up to 30min. No cleavage was observed in the absence of MoO(O2)2(α-leucine) (H2O) or the light. The photocleavage yield increased with irradiation time. The cleaved fragments were sequencable, and the cleavage site was assigned to Leu(112)-Tyr(113). The cleavage reaction was quenched by ethanol. Therefore, hydroxyl radicals may be involved in the reaction and responsible for the cleavage of the protein. This is the first demonstration of the successful photocleavage of proteins by a molybdenum complex. This observation can provide a new approach for the photochemical footprinting of metal binding sites on proteins.
Collapse
Affiliation(s)
- Benchawan Jityuti
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | | |
Collapse
|
31
|
Vanhaecht S, Absillis G, Parac-Vogt TN. Amino acid side chain induced selectivity in the hydrolysis of peptides catalyzed by a Zr(iv)-substituted Wells–Dawson type polyoxometalate. Dalton Trans 2013; 42:15437-46. [DOI: 10.1039/c3dt51893k] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
32
|
|
33
|
Jaroniec CP. Solid-state nuclear magnetic resonance structural studies of proteins using paramagnetic probes. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2012; 43-44:1-13. [PMID: 22464402 DOI: 10.1016/j.ssnmr.2012.02.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 02/27/2012] [Accepted: 02/28/2012] [Indexed: 05/31/2023]
Abstract
Determination of three-dimensional structures of biological macromolecules by magic-angle spinning (MAS) solid-state NMR spectroscopy is hindered by the paucity of nuclear dipolar coupling-based restraints corresponding to distances exceeding 5 Å. Recent MAS NMR studies of uniformly (13)C,(15)N-enriched proteins containing paramagnetic centers have demonstrated the measurements of site-specific nuclear pseudocontact shifts and spin relaxation enhancements, which report on electron-nucleus distances up to ~20 Å. These studies pave the way for the application of such long-distance paramagnetic restraints to protein structure elucidation and analysis of protein-protein and protein-ligand interactions in the solid phase. Paramagnetic species also facilitate the rapid acquisition of high resolution and sensitivity multidimensional solid-state NMR spectra of biomacromolecules using condensed data collection schemes, and characterization of solvent-accessible surfaces of peptides and proteins. In this review we discuss some of the latest applications of magic-angle spinning NMR spectroscopy in conjunction with paramagnetic probes to the structural studies of proteins in the solid state.
Collapse
Affiliation(s)
- Christopher P Jaroniec
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
| |
Collapse
|
34
|
Sengupta I, Nadaud PS, Helmus JJ, Schwieters CD, Jaroniec CP. Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy. Nat Chem 2012; 4:410-7. [PMID: 22522262 PMCID: PMC3335742 DOI: 10.1038/nchem.1299] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 02/08/2012] [Indexed: 11/16/2022]
Abstract
Biomacromolecules that are challenging for the usual structural techniques can be studied with atomic resolution by solid-state nuclear magnetic resonance. However, the paucity of >5 Å distance restraints, traditionally derived from measurements of magnetic dipole-dipole couplings between protein nuclei, is a major bottleneck that hampers such structure elucidation efforts. Here we describe a general approach that enables the rapid determination of global protein fold in the solid phase via measurements of nuclear paramagnetic relaxation enhancements (PREs) in several analogs of the protein of interest containing covalently-attached paramagnetic tags, without the use of conventional internuclear distance restraints. The method is demonstrated using six cysteine-EDTA-Cu2+ mutants of the 56-residue B1 immunoglobulin-binding domain of protein G, for which ~230 longitudinal backbone 15N PREs corresponding to ~10-20 Å distances were obtained. The mean protein fold determined in this manner agrees with the X-ray structure with a backbone atom root-mean-square deviation of 1.8 Å.
Collapse
Affiliation(s)
- Ishita Sengupta
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
| | | | | | | | | |
Collapse
|
35
|
Yenjai S, Malaikaew P, Liwporncharoenvong T, Buranaprapuk A. Selective cleavage of pepsin by molybdenum metallopeptidase. Biochem Biophys Res Commun 2012; 419:126-9. [PMID: 22330807 DOI: 10.1016/j.bbrc.2012.01.147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 01/30/2012] [Indexed: 10/14/2022]
Abstract
In this study, the cleavage of protein by molybdenum cluster is reported for the first time. The protein target used is porcine pepsin. The data presented in this study show that pepsin is cleaved to at least three fragments with molecular weights of ∼23, ∼19 and ∼16 kDa when the mixture of the protein and ammonium heptamolybdate tetrahydrate ((NH(4))(6)Mo(7)O(24)·4H(2)O) was incubated at 37°C for 24h. No self cleavage of pepsin occurs at 37 °C, 24h indicating that the reaction is mediated by the metal ions. N-terminal sequencing of the peptide fragments indicated three cleavage sites of pepsin between Leu 112-Tyr 113, Leu 166-Leu 167 and Leu 178-Asn 179. The cleavage reaction occurs after incubation of the mixture of pepsin and (NH(4))(6)Mo(7)O(24)·4H(2)O) only for 2h. However, the specificity of the cleavage decreases when incubation time is longer than 48 h. The mechanism for cleavage of pepsin is expected to be hydrolytic chemistry of the amide bonds in the protein backbone.
Collapse
Affiliation(s)
- Sudarat Yenjai
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | | | | |
Collapse
|
36
|
Gómez GE, Mundo MR, Craig PO, Delfino JM. Probing protein surface with a solvent mimetic carbene coupled to detection by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:30-42. [PMID: 22006407 DOI: 10.1007/s13361-011-0266-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/26/2011] [Accepted: 09/26/2011] [Indexed: 05/31/2023]
Abstract
Much knowledge into protein folding, ligand binding, and complex formation can be derived from the examination of the nature and size of the accessible surface area (SASA) of the polypeptide chain, a key parameter in protein science not directly measurable in an experimental fashion. To this end, an ideal chemical approach should aim at exerting solvent mimicry and achieving minimal selectivity to probe the protein surface regardless of its chemical nature. The choice of the photoreagent diazirine to fulfill these goals arises from its size comparable to water and from being a convenient source of the extremely reactive methylene carbene (:CH(2)). The ensuing methylation depends primarily on the solvent accessibility of the polypeptide chain, turning it into a valuable signal to address experimentally the measurement of SASA in proteins. The superb sensitivity and high resolution of modern mass spectrometry techniques allows us to derive a quantitative signal proportional to the extent of modification (EM) of the sample. Thus, diazirine labeling coupled to electrospray mass spectrometry (ESI-MS) detection can shed light on conformational features of the native as well as non-native states, not easily addressable by other methods. Enzymatic fragmentation of the polypeptide chain at the level of small peptides allows us to locate the covalent tag along the amino acid sequence, therefore enabling the construction of a map of solvent accessibility. Moreover, by subsequent MS/MS analysis of peptides, we demonstrate here the feasibility of attaining amino acid resolution in defining the target sites.
Collapse
Affiliation(s)
- Gabriela E Gómez
- Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires e Instituto de Química y Fisicoquímica Biológica (IQUIFIB-CONICET), Junín 956, C1113AAD, Buenos Aires, Argentina
| | | | | | | |
Collapse
|
37
|
Nadaud PS, Sengupta I, Helmus JJ, Jaroniec CP. Evaluation of the influence of intermolecular electron-nucleus couplings and intrinsic metal binding sites on the measurement of 15N longitudinal paramagnetic relaxation enhancements in proteins by solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:293-302. [PMID: 21826518 DOI: 10.1007/s10858-011-9536-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/25/2011] [Indexed: 05/31/2023]
Abstract
Magic-angle spinning solid-state NMR measurements of (15)N longitudinal paramagnetic relaxation enhancements (PREs) in (13)C,(15)N-labeled proteins modified with Cu(2+)-chelating tags can yield multiple long-range electron-nucleus distance restraints up to ~20 Å (Nadaud et al. in J Am Chem Soc 131:8108-8120, 2009). Using the EDTA-Cu(2+) K28C mutant of B1 immunoglobulin binding domain of protein G (GB1) as a model, we investigate the effects on such measurements of intermolecular electron-nucleus couplings and intrinsic metal binding sites, both of which may potentially complicate the interpretation of PRE data in terms of the intramolecular protein fold. To quantitatively assess the influence of intermolecular (15)N-Cu(2+) interactions we have determined a nearly complete set of longitudinal (15)N PREs for a series of microcrystalline samples containing ~10, 15 and 25 mol percent of the (13)C,(15)N-labeled EDTA-Cu(2+)-tagged protein diluted in a matrix of diamagnetic natural abundance GB1. The residual intermolecular interactions were found to be minor on the whole and account for only a fraction of the relatively small but systematic deviations observed between the experimental (15)N PREs and corresponding values calculated using protein structural models for residues furthest removed from the EDTA-Cu(2+) tag. This suggests that these deviations are also caused in part by other factors not related to the protein structure, such as the presence in the protein of intrinsic secondary sites capable of binding Cu(2+) ions. To probe this issue we performed a Cu(2+) titration study for K28C-EDTA GB1 monitored by 2D (15)N-(1)H solution-state NMR, which revealed that while for Cu(2+):protein molar ratios of ≤ 1.0 Cu(2+) binds primarily to the high-affinity EDTA tag, as anticipated, at even slightly super-stoichiometric ratios the Cu(2+) ions can also associate with side-chains of aspartate and glutamate residues. This in turn is expected to lead to enhanced PREs for residues located in the vicinity of the secondary Cu(2+) binding sites, and indeed many of these residues were ones found to display the elevated longitudinal (15)N PREs in the solid phase.
Collapse
Affiliation(s)
- Philippe S Nadaud
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
| | | | | | | |
Collapse
|
38
|
Malaikaew P, Svasti J, Kumar CV, Buranaprapuk A. Photocleavage of avidin by a new pyrenyl probe. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2011; 103:251-255. [PMID: 21531570 DOI: 10.1016/j.jphotobiol.2011.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Revised: 03/21/2011] [Accepted: 04/02/2011] [Indexed: 05/30/2023]
Abstract
In this study, a new small-molecule-based reagent was designed to recognize and bind to specific site in protein. A new pyrenyl probe, d-biotinyl-1(1-pyrene)methylamide (Py-biotin) was designed and synthesized by coupling of d-biotin to 1(1-pyrene)methylamine hydrochloride. Binding studies and site-specific photocleavage of avidin by Py-biotin were demonstrated. Binding of Py-biotin to avidin was studied using absorbance and fluorescence spectroscopic techniques. Red shifts of the absorption peak positions of the pyrenyl chromophore followed by hyperchromism were observed upon binding to avidin. The photocleavage of avidin was achieved when a mixture of the protein, Py-biotin, and an electron acceptor, cobalt(III) hexammine trichloride (CoHA), was irradiated at 342nm. No reaction occurred in the absence of the probe, CoHA, or light. N-terminal sequencing of the peptide fragments indicated a cleavage site of avidin between Thr 77 and Val 78. The high specificity of photocleavage may be valuable in targeting specific sites of proteins with small molecules.
Collapse
Affiliation(s)
- Pinpinat Malaikaew
- Department of Chemistry, Faculty of Science, Srinakharinwirot University, Sukhumvit 23, Bangkok 10110, Thailand
| | | | | | | |
Collapse
|
39
|
Pitié M, Pratviel G. Activation of DNA Carbon−Hydrogen Bonds by Metal Complexes. Chem Rev 2010; 110:1018-59. [DOI: 10.1021/cr900247m] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Marguerite Pitié
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| | - Geneviève Pratviel
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, F-31077 Toulouse, France, and Université de Toulouse, Toulouse, France
| |
Collapse
|
40
|
Clore GM, Iwahara J. Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes. Chem Rev 2009; 109:4108-39. [PMID: 19522502 DOI: 10.1021/cr900033p] [Citation(s) in RCA: 588] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- G Marius Clore
- Laboratory of Chemical Physics, Building 5, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| | | |
Collapse
|
41
|
Abstract
The nucleosome and other chromatin complexes are examples of complicated protein-DNA assemblies that are not easily studied by traditional structural methods. Site-directed cleavage of DNA is a method for mapping the location of interaction of a specific site in a protein such as a linker histone within a large complex such as the nucleosome. In this chapter we describe the application of the site-directed cleavage method, employing linker histones site-specifically modified with the chemical cleavage reagent Fe(II)(EDTA-2-aminoethyl) 2-pyridyl disulfide (ebr). Addition of hydrogen peroxide and a reducing agent to the complex containing the modified protein leads to the production of hydroxyl radicals from the iron center, resulting in cleavage of DNA backbones in the vicinity of the modified residue. The cleavages can then be mapped and ascribed to a particular location within the nucleosome, allowing the binding site of the protein within this structure to be determined.
Collapse
|
42
|
Nadaud PS, Helmus JJ, Kall SL, Jaroniec CP. Paramagnetic Ions Enable Tuning of Nuclear Relaxation Rates and Provide Long-Range Structural Restraints in Solid-State NMR of Proteins. J Am Chem Soc 2009; 131:8108-20. [DOI: 10.1021/ja900224z] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Philippe S. Nadaud
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Jonathan J. Helmus
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Stefanie L. Kall
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | | |
Collapse
|
43
|
Ricoux R, Dubuc R, Dupont C, Marechal JD, Martin A, Sellier M, Mahy JP. Hemozymes Peroxidase Activity Of Artificial Hemoproteins Constructed From the Streptomyces lividans Xylanase A and Iron(III)-Carboxy-Substituted Porphyrins. Bioconjug Chem 2008; 19:899-910. [DOI: 10.1021/bc700435a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rémy Ricoux
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Roger Dubuc
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Claude Dupont
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Jean-Didier Marechal
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Aurore Martin
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Marion Sellier
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d’Orsay, UMR 8182 CNRS, Laboratoire de Chimie Bioorganique et Bioinorganique, Bât. 420, Université Paris XI, 91405 Orsay Cedex, France, Institut National de la Recherche Scientifique, INRS-Institut Armand-Frappier, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada, and Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona, Edifici C.n., 08193 Cerdonyola (Barcelona), Spain
| |
Collapse
|
44
|
|
45
|
Primo ME, Klinke S, Sica MP, Goldbaum FA, Jakoncic J, Poskus E, Ermácora MR. Structure of the Mature Ectodomain of the Human Receptor-type Protein-tyrosine Phosphatase IA-2. J Biol Chem 2008; 283:4674-81. [DOI: 10.1074/jbc.m708144200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
46
|
Satake Y, Abe S, Okazaki S, Ban N, Hikage T, Ueno T, Nakajima H, Suzuki A, Yamane T, Nishiyama H, Watanabe Y. Incorporation of a Phebox Rhodium Complex into apo-Myoglobin Affords a Stable Organometallic Protein Showing Unprecedented Arrangement of the Complex in the Cavity. Organometallics 2007. [DOI: 10.1021/om700471a] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuh Satake
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Satoshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Seiji Okazaki
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Noritaka Ban
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Tatsuo Hikage
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Takafumi Ueno
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Hiroshi Nakajima
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Atsuo Suzuki
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Takashi Yamane
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Hisao Nishiyama
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| | - Yoshihito Watanabe
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan, PRESTO, Japan Science and Technology Agency (JST) Kawaguchi, Saitama, 332-0012, Japan, Department of Biotechnology, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan, Department of Applied Chemistry, Graduate School of Engineering, High Intensity X-ray Diffraction Laboratory, Nagoya University, Nagoya, 464-8603, Japan, and Research Center of Materials Science, Nagoya University,
| |
Collapse
|
47
|
|
48
|
Xu G, Chance MR. Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics. Chem Rev 2007; 107:3514-43. [PMID: 17683160 DOI: 10.1021/cr0682047] [Citation(s) in RCA: 507] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guozhong Xu
- Center for Proteomics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | | |
Collapse
|
49
|
Andberg M, Jäntti J, Heilimo S, Pihkala P, Paananen A, Koskinen AMP, Söderlund H, Linder MB. Cleavage of recombinant proteins at poly-His sequences by Co(II) and Cu(II). Protein Sci 2007; 16:1751-61. [PMID: 17600148 PMCID: PMC2203371 DOI: 10.1110/ps.072846407] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Improved ways to cleave peptide chains at engineered sites easily and specifically would form useful tools for biochemical research. Uses of such methods include the activation or inactivation of enzymes or the removal of tags for enhancement of recombinant protein expression or tags used for purification of recombinant proteins. In this work we show by gel electrophoresis and mass spectroscopy that salts of Co(II) and Cu(II) can be used to cleave fusion proteins specifically at sites where sequences of His residues have been introduced by protein engineering. The His residues could be either consecutive or spaced with other amino acids in between. The cleavage reaction required the presence of low concentrations of ascorbate and in the case of Cu(II) also hydrogen peroxide. The amount of metal ions required for cleavage was very low; in the case of Cu(II) only one to two molar equivalents of Cu(II) to protein was required. In the case of Co(II), 10 molar equivalents gave optimal cleavage. The reaction occurred within minutes, at a wide pH range, and efficiently at temperatures ranging from 0 degrees C to 70 degrees C. The work described here can also have implications for understanding protein stability in vitro and in vivo.
Collapse
Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland, Espoo FIN-02044 VTT, Finland
| | | | | | | | | | | | | | | |
Collapse
|
50
|
Iwahara J, Tang C, Marius Clore G. Practical aspects of (1)H transverse paramagnetic relaxation enhancement measurements on macromolecules. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2007; 184:185-95. [PMID: 17084097 PMCID: PMC1994582 DOI: 10.1016/j.jmr.2006.10.003] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 10/06/2006] [Accepted: 10/16/2006] [Indexed: 05/05/2023]
Abstract
The use of (1)H transverse paramagnetic relaxation enhancement (PRE) has seen a resurgence in recent years as method for providing long-range distance information for structural studies and as a probe of large amplitude motions and lowly populated transient intermediates in macromolecular association. In this paper we discuss various practical aspects pertaining to accurate measurement of PRE (1)H transverse relaxation rates (Gamma(2)). We first show that accurate Gamma(2) rates can be obtained from a two time-point measurement without requiring any fitting procedures or complicated error estimations, and no additional accuracy is achieved from multiple time-point measurements recorded in the same experiment time. Optimal setting of the two time-points that minimize experimental errors is also discussed. Next we show that the simplistic single time-point measurement that has been commonly used in the literature, can substantially underestimate the true value of Gamma(2), unless a relatively long repetition delay is employed. We then examine the field dependence of Gamma(2), and show that Gamma(2) exhibits only a very weak field dependence at high magnetic fields typically employed in macromolecular studies. The theoretical basis for this observation is discussed. Finally, we investigate the impact of contamination of the paramagnetic sample by trace amounts (5%) of the corresponding diamagnetic species on the accuracy of Gamma(2) measurements. Errors in Gamma(2) introduced by such diamagnetic contamination are potentially sizeable, but can be significantly reduced by using a relatively short time interval for the two time-point Gamma(2) measurement.
Collapse
Affiliation(s)
- Junji Iwahara
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | | | | |
Collapse
|