1
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Spenner JM, Berg JM. Exploring the use of cobalt(II) dipolar shifts in refining the structure of a zinc finger peptide. J Inorg Biochem 2022; 235:111912. [PMID: 35850025 DOI: 10.1016/j.jinorgbio.2022.111912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 06/13/2022] [Accepted: 07/03/2022] [Indexed: 10/17/2022]
Abstract
The uses of dipolar shifts due to cobalt(II) substituted for zinc(II) in a consensus zinc finger peptide for refining the NMR-determined structure were examined. Substantial differences between the calculated and observed chemical shift differences between the cobalt(II) and zinc(II) complexes were observed when these dipolar shifts were not used as constraints in the structure refinement. However, inclusion of these constraints resulted in excellent agreement with minor adjustments in the structure and a slight improvement in the precision of the structure determination. Other calculations revealed that the dipolar shifts were not adequate to determine the overall folded structure by themselves, but were useful in increasing the accuracy and precision of a structure determined based only on nuclear Overhauser effects constraints involving only backbone atoms.
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Affiliation(s)
- Jonathan M Spenner
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeremy M Berg
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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2
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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3
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Lee YS, Mou Z, Opina ACL, Vasalatiy O. Origin of the Isomer Stability of Polymethylated DOTA Chelates Complexed with Ln 3+ ions. Eur J Inorg Chem 2021; 2021:1428-1440. [PMID: 36591318 PMCID: PMC9802879 DOI: 10.1002/ejic.202100019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid)-based chelates that give only a single isomer in solution when complexed with lanthanide (Ln3+) ions is of value for studying protein dynamics and interactions via NMR. Herein, we have investigated the geometries, energetics, and electrostatic potentials of Lu complexed with DOTA (1), ring methylated M4DOTA (2), and arm methylated R-DOTMA (3) and S-DOTMA (4), as well as, both ring and arm methylated 4S-4S-M4DOTMA (5) and 4S-4R-M4DOTMA (6) at the level of M06-L/6-31+G(d)-SDD, to elucidate the origin of the isomer stability. These analyses indicate that the electrostatic repulsion between the arm methyl and the neighboring carboxylate significantly destabilizes the square antiprism (SAP) isomer of Lu-5 and the twisted square antiprism (TSAP) isomer of Lu-6, while the steric repulsion between the ring and arm methyl groups attenuates the stability of both TSAP of Lu-5 and SAP of Lu-6. To rationalize the variable temperature proton NMR spectra, the energy barriers for the inter-conversion in Lu-5 and Lu-6 via arm rotation were also calculated. The modulation of the stability and rigidity of Ln complexes via a modification of DOTA is also discussed. Our investigation will aid to design better chelates for the Ln3+ ions for its use in molecular medicine.
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Affiliation(s)
- Yong-Sok Lee
- Dr. Yong-Sok Lee, Dr. Zhongyu Mou Center for Molecular Modeling, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, United States,Present address: Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Zhongyu Mou
- Dr. Yong-Sok Lee, Dr. Zhongyu Mou Center for Molecular Modeling, Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, United States,Present address: Intramural Research Program, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, United States
| | - Ana Christina L. Opina
- Dr. Ana Christina L. Opina, Dr. Olga Vasalatiy Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850, United States
| | - Olga Vasalatiy
- Dr. Ana Christina L. Opina, Dr. Olga Vasalatiy Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD 20850, United States
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4
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Harnessing the Combined Power of SAXS and NMR. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:171-180. [DOI: 10.1007/978-981-13-2200-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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5
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Eddy NA, Martin MS, Ichalkaranje P, Morton MD. A 13 C NMR method for determining secondary nitroxide-substrate associations. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:1096-1101. [PMID: 28755418 DOI: 10.1002/mrc.4637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Revised: 07/12/2017] [Accepted: 07/23/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Nicholas A Eddy
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | - Michael S Martin
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA
| | | | - Martha D Morton
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
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6
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Schnorr KA, Gophane DB, Helmling C, Cetiner E, Pasemann K, Fürtig B, Wacker A, Qureshi NS, Gränz M, Barthelmes D, Jonker HRA, Stirnal E, Sigurdsson ST, Schwalbe H. Impact of spin label rigidity on extent and accuracy of distance information from PRE data. JOURNAL OF BIOMOLECULAR NMR 2017; 68:53-63. [PMID: 28500543 DOI: 10.1007/s10858-017-0114-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Paramagnetic relaxation enhancement (PRE) is a versatile tool for NMR spectroscopic structural and kinetic studies in biological macromolecules. Here, we compare the quality of PRE data derived from two spin labels with markedly different dynamic properties for large RNAs using the I-A riboswitch aptamer domain (78 nt) from Mesoplamsa florum as model system. We designed two I-A aptamer constructs that were spin-labeled by noncovalent hybridization of short spin-labeled oligomer fragments. As an example of a flexible spin label, UreidoU-TEMPO was incorporated into the 3' terminal end of helix P1 while, the recently developed rigid spin-label Çm was incorporated in the 5' terminal end of helix P1. We determined PRE rates obtained from aromatic 13C bound proton intensities and compared these rates to PREs derived from imino proton intensities in this sizeable RNA (~78 nt). PRE restraints derived from both imino and aromatic protons yielded similar data quality, and hence can both be reliably used for PRE determination. For NMR, the data quality derived from the rigid spin label Çm is slightly better than the data quality for the flexible UreidoTEMPO as judged by comparison of the structural agreement with the I-A aptamer crystal structure (3SKI).
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Affiliation(s)
- K A Schnorr
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D B Gophane
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - C Helmling
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Cetiner
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - K Pasemann
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - B Fürtig
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - A Wacker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - N S Qureshi
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - M Gränz
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - D Barthelmes
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - H R A Jonker
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - E Stirnal
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - S Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, Dunhaga 3, 107, Reykjavik, Iceland
| | - H Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany.
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7
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Pearce BJG, Jabar S, Loh CT, Szabo M, Graham B, Otting G. Structure restraints from heteronuclear pseudocontact shifts generated by lanthanide tags at two different sites. JOURNAL OF BIOMOLECULAR NMR 2017; 68:19-32. [PMID: 28434103 DOI: 10.1007/s10858-017-0111-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/11/2017] [Indexed: 05/14/2023]
Abstract
Pseudocontact shifts (PCS) encode long-range information on 3D structures of protein backbones and side-chains. The level of structural detail that can be obtained increases with the number of different sites tagged with a paramagnetic metal ion to generate PCSs. Here we show that PCSs from two different sites can suffice to determine the structure of polypeptide chains and their location and orientation relative to the magnetic susceptibility tensor χ, provided that PCSs are available for 1H as well as heteronuclear spins. In addition, PCSs from two different sites are shown to provide detailed structural information on the conformation of methyl group-bearing amino-acid side-chains. A previously published ensemble structure of ubiquitin is shown to explain the magnetic susceptibility and alignment tensors slightly better than structures that try to explain the experimental data by a single conformation, illustrating the potential of PCSs as a tool to investigate small conformational changes.
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Affiliation(s)
- Benjamin J G Pearce
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Shereen Jabar
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Choy-Theng Loh
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
| | - Monika Szabo
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Gottfried Otting
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia.
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8
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Seebald LM, DeMott CM, Ranganathan S, Asare Okai PN, Glazunova A, Chen A, Shekhtman A, Royzen M. Cu(II)-Based Paramagnetic Probe to Study RNA-Protein Interactions by NMR. Inorg Chem 2017; 56:3773-3780. [PMID: 28328212 DOI: 10.1021/acs.inorgchem.6b02286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Paramagnetic NMR techniques allow for studying three-dimensional structures of RNA-protein complexes. In particular, paramagnetic relaxation enhancement (PRE) data can provide valuable information about long-range distances between different structural components. For PRE NMR experiments, oligonucleotides are typically spin-labeled using nitroxide reagents. The current work describes an alternative approach involving a Cu(II) cyclen-based probe that can be covalently attached to an RNA strand in the vicinity of the protein's binding site using "click" chemistry. The approach has been applied to study binding of HIV-1 nucleocapsid protein 7 (NCp7) to a model RNA pentanucleotide, 5'-ACGCU-3'. Coordination of the paramagnetic metal to glutamic acid residue of NCp7 reduced flexibility of the probe, thus simplifying interpretation of the PRE data. NMR experiments showed attenuation of signal intensities from protein residues localized in proximity to the paramagnetic probe as the result of RNA-protein interactions. The extent of the attenuation was related to the probe's proximity allowing us to construct the protein's contact surface map.
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Affiliation(s)
- Leah M Seebald
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher M DeMott
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Srivathsan Ranganathan
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Papa Nii Asare Okai
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Anastasia Glazunova
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alan Chen
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Maksim Royzen
- Department of Chemistry, University at Albany, SUNY , 1400 Washington Avenue, Albany, New York 12222, United States
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9
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Nitsche C, Otting G. Pseudocontact shifts in biomolecular NMR using paramagnetic metal tags. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 98-99:20-49. [PMID: 28283085 DOI: 10.1016/j.pnmrs.2016.11.001] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/11/2016] [Accepted: 11/12/2016] [Indexed: 05/14/2023]
Affiliation(s)
- Christoph Nitsche
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia. http://www.rsc.anu.edu.au/~go/index.html
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10
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Gossert AD, Jahnke W. NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:82-125. [PMID: 27888841 DOI: 10.1016/j.pnmrs.2016.09.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/12/2023]
Abstract
Protein-ligand interactions are at the heart of drug discovery research. NMR spectroscopy is an excellent technology to identify and validate protein-ligand interactions. A plethora of NMR methods are available which are powerful, robust and information-rich, but also have pitfalls and limitations. In this review, we will focus on how to choose between different experiments, and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions. Out of scope for this review are methods for subsequent characterization of the interaction such as quantitative KD determination, binding mode analysis, or structure determination.
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Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland.
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland
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11
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Strickland M, Schwieters CD, Göbl C, Opina ACL, Strub MP, Swenson RE, Vasalatiy O, Tjandra N. Characterizing the magnetic susceptibility tensor of lanthanide-containing polymethylated-DOTA complexes. JOURNAL OF BIOMOLECULAR NMR 2016; 66:125-139. [PMID: 27659040 PMCID: PMC6628275 DOI: 10.1007/s10858-016-0061-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 05/16/2023]
Abstract
Lanthanide complexes based on the DOTA (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) cage are commonly used as phase contrast agents in magnetic resonance imaging, but can also be utilized in structural NMR applications due to their ability to induce either paramagnetic relaxation enhancement or a pseudocontact shift (PCS) depending on the choice of the lanthanide. The size and sign of the PCS for any given atom is determined by its coordinates relative to the metal center, and the characteristics of the lanthanide's magnetic susceptibility tensor. Using a polymethylated DOTA tag (Ln-M8-SPy) conjugated to ubiquitin, we calculated the position of the metal center and characterized the susceptibility tensor for a number of lanthanides (dysprosium, thulium, and ytterbium) under a range of pH and temperature conditions. We found that there was a difference in temperature sensitivity for each of the complexes studied, which depended on the size of the lanthanide ion as well as the isomeric state of the cage. Using 17O-NMR, we confirmed that the temperature sensitivity of the compounds was enhanced by the presence of an apically bound water molecule. Since amide-containing lanthanide complexes are known to be pH sensitive and can be used as probes of physiological pH, we also investigated the effect of pH on the Ln-M8-SPy susceptibility tensor, but we found that the changes in this pH range (5.0-7.4) were not significant.
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Affiliation(s)
- Madeleine Strickland
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Charles D Schwieters
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christoph Göbl
- Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Ana C L Opina
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Marie-Paule Strub
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rolf E Swenson
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Olga Vasalatiy
- Imaging Probe Development Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, 20850, USA
| | - Nico Tjandra
- Laboratory of Molecular Biophysics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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12
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Yang Y, Huang F, Huber T, Su XC. Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis. JOURNAL OF BIOMOLECULAR NMR 2016; 64:103-113. [PMID: 26732873 DOI: 10.1007/s10858-016-0011-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/01/2016] [Indexed: 06/05/2023]
Abstract
Design of a paramagnetic metal binding motif in a protein is a valuable way for understanding the function, dynamics and interactions of a protein by paramagnetic NMR spectroscopy. Several strategies have been proposed to site-specifically tag proteins with paramagnetic lanthanide ions. Here we report a simple approach of engineering a transition metal binding motif via site-specific labelling of a protein with 2-vinyl-8-hydroxyquinoline (2V-8HQ). The protein-2V-8HQ adduct forms a stable complex with transition metal ions, Mn(II), Co(II), Ni(II), Cu(II) and Zn(II). The paramagnetic effects generated by these transition metal ions were evaluated by NMR spectroscopy. We show that 2V-8HQ is a rigid and stable transition metal binding tag. The coordination of the metal ion can be assisted by protein sidechains. More importantly, tunable paramagnetic tensors are simply obtained in an α-helix that possesses solvent exposed residues in positions i and i + 3, where i is the residue to be mutated to cysteine, i + 3 is Gln or Glu or i - 4 is His. The coordination of a sidechain carboxylate/amide or imidazole to cobalt(II) results in different structural geometries, leading to different paramagnetic tensors as shown by experimental data.
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Affiliation(s)
- Yin Yang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Feng Huang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT, 0200, Australia
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China.
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13
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Camacho-Zarco AR, Munari F, Wegstroth M, Liu WM, Ubbink M, Becker S, Zweckstetter M. Multiple paramagnetic effects through a tagged reporter protein. Angew Chem Int Ed Engl 2014; 54:336-9. [PMID: 25293958 DOI: 10.1002/anie.201408615] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Indexed: 11/12/2022]
Abstract
Paramagnetic effects provide unique information about the structure and dynamics of biomolecules. We developed a method in which the lanthanoid tag is not directly attached to the protein of interest, but instead to a "reporter" protein, which binds and then transmits paramagnetic information to the target. The designed method allows access to a large number of paramagnetic restraints and residual dipolar couplings produced from independent molecular alignments in high-molecular-weight proteins with unknown 3D structure.
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Affiliation(s)
- Aldo R Camacho-Zarco
- Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen (Germany); German Center for Neurodegenerative Diseases (DZNE), Göttingen (Germany); Center for the Molecular Physiology of the Brain, University Medical Center, Göttingen (Germany)
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14
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Camacho‐Zarco AR, Munari F, Wegstroth M, Liu W, Ubbink M, Becker S, Zweckstetter M. Paramagnetische Effekte mittels eines markierten Reporterproteins. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Aldo R. Camacho‐Zarco
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Francesca Munari
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Melanie Wegstroth
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Wei‐Min Liu
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Niederlande)
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden (Niederlande)
| | - Stefan Becker
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
| | - Markus Zweckstetter
- Max‐Planck‐Institut für Biophysikalische Chemie, Am Fassberg 11, 37077 Göttingen (Deutschland)
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Göttingen (Deutschland)
- Center for the Molecular Physiology of the Brain, Universitätsmedizin, Göttingen (Deutschland)
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15
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Cao C, Chen JL, Yang Y, Huang F, Otting G, Su XC. Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2014; 59:251-61. [PMID: 25002097 DOI: 10.1007/s10858-014-9844-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/01/2014] [Indexed: 05/24/2023]
Abstract
The side-chain amide groups of asparagine and glutamine play important roles in stabilizing the structural fold of proteins, participating in hydrogen-bonding networks and protein interactions. Selective (15)N-labeling of side-chain amides, however, can be a challenge due to enzyme-catalyzed exchange of amide groups during protein synthesis. In the present study, we developed an efficient way of selectively labeling the side chains of asparagine, or asparagine and glutamine residues with (15)NH2. Using the biosynthesis pathway of tryptophan, a protocol was also established for simultaneous selective (15)N-labeling of the side-chain NH groups of asparagine, glutamine, and tryptophan. In combination with site-specific tagging of the target protein with a lanthanide ion, we show that selective detection of (15)N-labeled side-chains of asparagine and glutamine allows determination of magnetic susceptibility anisotropy tensors based exclusively on pseudocontact shifts of amide side-chain protons.
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Affiliation(s)
- Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
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16
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Popik O, Pasternak-Suder M, Leśniak K, Jawiczuk M, Górecki M, Frelek J, Mlynarski J. Amine-catalyzed direct aldol reactions of hydroxy- and dihydroxyacetone: biomimetic synthesis of carbohydrates. J Org Chem 2014; 79:5728-39. [PMID: 24837738 DOI: 10.1021/jo500860g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article presents comprehensive studies on the application of primary, secondary, and tertiary amines as efficient organocatalysts for the de novo synthesis of ketoses and deoxyketoses. Mimicking the actions of aldolase enzymes, the synthesis of selected carbohydrates was accomplished in aqueous media by using proline- and serine-based organocatalysts. The presented methodology also provides direct access to unnatural L-carbohydrates from the (S)-glyceraldehyde precursor. Determination of the absolute configuration of all obtained sugars was feasible using a methodology consisting of concerted ECD and VCD spectroscopy.
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Affiliation(s)
- Oskar Popik
- Institute of Organic Chemistry, Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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17
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Peters F, Maestre-Martinez M, Leonov A, Kovačič L, Becker S, Boelens R, Griesinger C. Cys-Ph-TAHA: a lanthanide binding tag for RDC and PCS enhanced protein NMR. JOURNAL OF BIOMOLECULAR NMR 2011; 51:329-37. [PMID: 21892794 PMCID: PMC3193991 DOI: 10.1007/s10858-011-9560-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 08/11/2011] [Indexed: 05/16/2023]
Abstract
Here we present Cys-Ph-TAHA, a new nonadentate lanthanide tag for the paramagnetic labelling of proteins. The tag can be easily synthesized and is stereochemically homogenous over a wide range of temperatures, yielding NMR spectra with a single set of peaks. Bound to ubiquitin, it induced large residual dipolar couplings and pseudocontact shifts that could be measured easily and agreed very well with the protein structure. We show that Cys-Ph-TAHA can be used to label large proteins that are biochemically challenging such as the Lac repressor in a 90 kDa ternary complex with DNA and inducer.
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Affiliation(s)
- Fabian Peters
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mitcheell Maestre-Martinez
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Andrei Leonov
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Lidija Kovačič
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Stefan Becker
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Christian Griesinger
- Department of NMR-Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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18
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19
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Häussinger D, Huang JR, Grzesiek S. DOTA-M8: An extremely rigid, high-affinity lanthanide chelating tag for PCS NMR spectroscopy. J Am Chem Soc 2010; 131:14761-7. [PMID: 19785413 DOI: 10.1021/ja903233w] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new lanthanide chelating tag (M8) for paramagnetic labeling of biomolecules is presented, which is based on an eight-fold, stereoselectively methyl-substituted DOTA that can be covalently linked to the host molecule by a single disulfide bond. The steric overcrowding of the DOTA scaffold leads to an extremely rigid, kinetically and chemically inert lanthanide chelator. Its steric bulk restricts the motion of the tag relative to the host molecule. These properties result in very large pseudocontact shifts (>5 ppm) and residual dipolar couplings (>20 Hz) for Dy-M8 linked to ubiquitin, which are unprecedented for a small, single-point-attachment tag. Such large pseudocontact shifts should be well detectable even for larger proteins and distances beyond approximately 50 A. Due to its exceptionally high stability and lanthanide affinity M8 can be used under extreme chemical or physical conditions, such as those applied for protein denaturation, or when it is undesirable that buffer or protein react with excess lanthanide ions.
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Affiliation(s)
- Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
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20
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Frelek J, Ruśkowska P, Suszczyńska A, Szewczyk K, Osuch A, Jarosz S, Jagodziński J. Configurational assignment of sugar erythro-1,2-diols from their electronic circular dichroism spectra with dimolybdenum tetraacetate. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.06.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Tartaglia S, Padula D, Scafato P, Chiummiento L, Rosini C. A Chemical/Computational Approach to the Determination of Absolute Configuration of Flexible and Transparent Molecules: Aliphatic Diols As a Case Study. J Org Chem 2008; 73:4865-73. [DOI: 10.1021/jo800516f] [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)
- Sabina Tartaglia
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Daniele Padula
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Patrizia Scafato
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Lucia Chiummiento
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
| | - Carlo Rosini
- Dipartimento di Chimica, Università degli Studi della Basilicata, Via N. Sauro, 85, 85100 Potenza, Italy
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22
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Mlynarski J, Rakiel B, Stodulski M, Suszczyńska A, Frelek J. Chiral Ytterbium Complex-Catalyzed Direct Asymmetric Aldol-Tishchenko Reaction: Synthesis ofanti-1,3-Diols. Chemistry 2006; 12:8158-67. [PMID: 16871507 DOI: 10.1002/chem.200600357] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The asymmetric aldol-Tishchenko reaction of aromatic aldehydes with aliphatic and aromatic ketones has been developed as an efficient strategy for the synthesis of anti-1,3-diols in good yield with high diastereocontrol and good levels of enantioselectivity. This domino-type reaction is catalyzed by a chiral ytterbium complex that promotes both the aldol reaction through enolization of the carbonyl compound and the Evans-Tishchenko reduction of the aldol intermediate. The stereochemistry of the resulting diols is also investigated and finally proved by using CD techniques.
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Affiliation(s)
- Jacek Mlynarski
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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23
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Arnesano F, Banci L, Bertini I, Capozzi F, Ciofi-Baffoni S, Ciurli S, Luchinat C, Mangani S, Rosato A, Turano P, Viezzoli MS. An Italian contribution to structural genomics: Understanding metalloproteins. Coord Chem Rev 2006. [DOI: 10.1016/j.ccr.2006.01.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Jarosz S, Szewczyk K, Gaweł A, Luboradzki R. Reaction of sugar allyltins with aldehydes under high pressure. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.04.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Frelek J, Klimek A, Ruśkowska P. Optical activity of vic-amino alcohols in the presence of dimolybdenum tetracetate. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0957-4166(02)00647-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Battistuzzi G, Borsari M, Cowan JA, Ranieri A, Sola M. Control of cytochrome C redox potential: axial ligation and protein environment effects. J Am Chem Soc 2002; 124:5315-24. [PMID: 11996572 DOI: 10.1021/ja017479v] [Citation(s) in RCA: 145] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Axial iron ligation and protein encapsulation of the heme cofactor have been investigated as effectors of the reduction potential (E degrees ') of cytochrome c through direct electrochemistry experiments. Our approach was that of partitioning the E degrees ' changes resulting from binding of imidazole, 2-methyl-imidazole, ammonia, and azide to both cytochrome c and microperoxidase-11 (MP11), into the enthalpic and entropic contributions. N-Acetylmethionine binding to MP11 was also investigated. These ligands replace Met80 and a water molecule axially coordinated to the heme iron in cytochrome c and MP11, respectively. This factorization was achieved through variable temperature E degrees ' measurements. In this way, we have found that (i) the decrease in E degrees ' of cytochrome c due to Met80 substitution by a nitrogen-donor ligand is almost totally enthalpic in origin, as a result of the stronger electron donor properties of the exogenous ligand which selectively stabilize the ferric state; (ii) on the contrary, the binding of the same ligands and N-acetylmethionine to MP11 results in an enthalpic stabilization of the reduced state, whereas the entropic effect invariably decreases E degrees ' (the former effect prevails for the methionine ligand and the latter for the nitrogenous ligands). A comparison of the reduction thermodynamics of cytochrome c and the MP11 adducts offers insight on the effect of changing axial heme ligation and heme insertion into the folded polypeptide chain. Principally, we have found that the overall E degrees ' increase of approximately 400 mV, comparing MP11 and native cytochrome c, consists of two opposite enthalpic and entropic terms of approximately +680 and -280 mV, respectively. The enthalpic term includes contributions from both axial methionine binding (+300 mV) and protein encapsulation of the heme (+380 mV), whereas the entropic term is almost entirely manifest at the stage of axial ligand binding. Both terms are dominated by the effects of water exclusion from the heme environment.
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Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
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27
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Affiliation(s)
- A Lombardi
- Department of Chemistry, University of Napoli Federico II, Complesso Universitario Monte S. Angelo, Via Cynthia 45, I-80126 Napoli, Italy.
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28
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Stepowska H, Zamojski A. From methyl mannosides to methyl octosides by a stepwise homologation with Grignard C(1) reagents. Carbohydr Res 2001; 332:429-38. [PMID: 11438099 DOI: 10.1016/s0008-6215(01)00103-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A four-step procedure for homologation of methyl alpha-D-mannofuranoside and alpha-D-mannopyranoside was examined. The reactions consisted in (i) oxidation of the terminal hydroxymethyl group in a protected sugar derivative to an aldehyde; (ii) reaction with allyloxymethylmagnesium chloride (or (phenyldimethyl)silylmethyl-magnesium chloride); (iii) protection of the newly formed secondary alcohol group; (iv) deprotection of the terminal CH(2)OR (or oxidation of the CH(2)SiMe(2)Ph) group. From methyl alpha-D-mannosides, stereoisomeric DalphaD and LalphaD methyl heptosides and from them, methyl octosides of D-threo- and L-erythro-alpha-D-manno configuration were obtained.
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Affiliation(s)
- H Stepowska
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44, PL-01224, Warsaw, Poland
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29
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Grzeszczyk B, Zamojski A. Homologation of methyl 2-azido- and 2-acetamido-3,4-di-O-benzyl-2-deoxy-D-hexopyranosides with allyloxymethylmagnesium chloride. Carbohydr Res 2001; 332:225-34. [PMID: 11434382 DOI: 10.1016/s0008-6215(01)00078-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Methyl 2-azido-2-deoxy-hexodialdo-1,5-pyranosides of the alpha-, beta-D-gluco and alpha-D-manno configuration as well as methyl 2-acetamido-2-deoxy-hexodialdo-1,5-pyranosides of the alpha- and beta-D-gluco configuration, protected at positions 3 and 4 with O-benzyl groups were reacted with an excess of allyloxymethylmagnesium or (phenyldimethylsilyl)methylmagnesium chlorides to afford mixtures of C-6 stereoisomeric heptopyranosides. Configuration of the products separated by column chromatography was assigned by 1H NMR data.
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Affiliation(s)
- B Grzeszczyk
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw
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30
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Iwasaki T, Watanabe E, Ohmori D, Imai T, Urushiyama A, Akiyama M, Hayashi-Iwasaki Y, Cosper NJ, Scott RA. Spectroscopic investigation of selective cluster conversion of archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7. J Biol Chem 2000; 275:25391-401. [PMID: 10827091 DOI: 10.1074/jbc.m909243199] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Archaeal zinc-containing ferredoxin from Sulfolobus sp. strain 7 contains one [3Fe-4S] cluster (cluster I), one [4Fe-4S] cluster (cluster II), and one isolated zinc center. Oxidative degradation of this ferredoxin led to the formation of a stable intermediate with 1 zinc and approximately 6 iron atoms. The metal centers of this intermediate were analyzed by electron paramagnetic resonance (EPR), low temperature resonance Raman, x-ray absorption, and (1)H NMR spectroscopies. The spectroscopic data suggest that (i) cluster II was selectively converted to a cubane [3Fe-4S](1+) cluster in the intermediate, without forming a stable radical species, and that (ii) the local metric environments of cluster I and the isolated zinc site did not change significantly in the intermediate. It is concluded that the initial step of oxidative degradation of the archaeal zinc-containing ferredoxin is selective conversion of cluster II, generating a novel intermediate containing two [3Fe-4S] clusters and an isolated zinc center. At this stage, significant structural rearrangement of the protein does not occur. We propose a new scheme for oxidative degradation of dicluster ferredoxins in which each cluster converts in a stepwise manner, prior to apoprotein formation, and discuss its structural and evolutionary implications.
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Affiliation(s)
- T Iwasaki
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Sendagi, Tokyo, Japan. iwasaki/
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