1
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Cunningham TF, Pornsuwan S, Horne WS, Saxena S. Rotameric preferences of a protein spin label at edge-strand β-sheet sites. Protein Sci 2016; 25:1049-60. [PMID: 26948069 DOI: 10.1002/pro.2918] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/01/2016] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Protein spin labeling to yield the nitroxide-based R1 side chain is a powerful method to measure protein dynamics and structure by electron spin resonance. However, R1 measurements are complicated by the flexibility of the side chain. While analysis approaches for solvent-exposed α-helical environment have been developed to partially account for flexibility, similar work in β-sheets is lacking. The goal of this study is to provide the first essential steps for understanding the conformational preferences of R1 within edge β-strands using X-ray crystallography and double electron electron resonance (DEER) distance measurements. Crystal structures yielded seven rotamers for a non-hydrogen-bonded site and three rotamers for a hydrogen-bonded site. The observed rotamers indicate contextual differences in R1 conformational preferences compared to other solvent-exposed environments. For the DEER measurements, each strand site was paired with the same α-helical site elsewhere on the protein. The most probable distance observed by DEER is rationalized based on the rotamers observed in the crystal structure. Additionally, the appropriateness of common molecular modeling methods that account for R1 conformational preferences are assessed for the β-sheet environment. These results show that interpretation of R1 behavior in β-sheets is difficult and indicate further development is needed for these computational methods to correctly relate DEER distances to protein structure at edge β-strand sites.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Soraya Pornsuwan
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave, Pittsburgh, Pennsylvania, 15260
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2
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van Son M, Lindhoud S, van der Wild M, van Mierlo CPM, Huber M. Double Electron-Electron Spin Resonance Tracks Flavodoxin Folding. J Phys Chem B 2015; 119:13507-14. [PMID: 26101942 DOI: 10.1021/acs.jpcb.5b00856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein folding is one of the important challenges in biochemistry. Understanding the folding process requires mapping of protein structure as it folds. Here we test the potential of distance determination between paramagnetic spin-labels by a pulsed electron paramagnetic resonance method. We use double electron-electron spin resonance (DEER) to study the denaturant-dependent equilibrium folding of flavodoxin. This flavoprotein is spin-labeled with MTSL ((1-oxy-,2,2,5,5-tetramethyl-d-pyrroline-3-methyl)-methanethiosulfonate) at positions 69 and 131. We find that nativelike spin-label separation dominates the distance distributions up to 0.8 M guanidine hydrochloride. At 2.3 M denaturant, the distance distributions show an additional component, which we attribute to a folding intermediate. Upon further increase of denaturant concentration, the protein expands and evidence for a larger number of conformations than in the native state is found. We thus demonstrate that DEER is a versatile technique to expand the arsenal of methods for investigating how proteins fold.
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Affiliation(s)
- Martin van Son
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University , 6700 ET Wageningen, The Netherlands
| | - Matthijs van der Wild
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Carlo P M van Mierlo
- Laboratory of Biochemistry, Wageningen University , 6700 ET Wageningen, The Netherlands
| | - Martina Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University , PO Box 9504, 2300 RA Leiden, The Netherlands
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3
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The double-histidine Cu²⁺-binding motif: a highly rigid, site-specific spin probe for electron spin resonance distance measurements. Angew Chem Int Ed Engl 2015; 54:6330-4. [PMID: 25821033 DOI: 10.1002/anie.201501968] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/07/2022]
Abstract
The development of ESR methods that measure long-range distance distributions has advanced biophysical research. However, the spin labels commonly employed are highly flexible, which leads to ambiguity in relating ESR measurements to protein-backbone structure. Herein we present the double-histidine (dHis) Cu(2+)-binding motif as a rigid spin probe for double electron-electron resonance (DEER) distance measurements. The spin label is assembled in situ from natural amino acid residues and a metal salt, requires no postexpression synthetic modification, and provides distance distributions that are dramatically narrower than those found with the commonly used protein spin label. Simple molecular modeling based on an X-ray crystal structure of an unlabeled protein led to a predicted most probable distance within 0.5 Å of the experimental value. Cu(2+) DEER with the dHis motif shows great promise for the resolution of precise, unambiguous distance constraints that relate directly to protein-backbone structure and flexibility.
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Affiliation(s)
- Timothy F Cunningham
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Miriam R Putterman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - Astha Desai
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA)
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA).
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, PA 15260 (USA).
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4
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Cunningham TF, Putterman MR, Desai A, Horne WS, Saxena S. The Double-Histidine Cu2+-Binding Motif: A Highly Rigid, Site-Specific Spin Probe for Electron Spin Resonance Distance Measurements. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201501968] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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5
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Shabestari MH, Wolfs CJAM, Spruijt RB, van Amerongen H, Huber M. Exploring the structure of the 100 amino-acid residue long N-terminus of the plant antenna protein CP29. Biophys J 2014; 106:1349-58. [PMID: 24655510 DOI: 10.1016/j.bpj.2013.11.4506] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 11/14/2013] [Accepted: 11/27/2013] [Indexed: 12/01/2022] Open
Abstract
The structure of the unusually long (∼100 amino-acid residues) N-terminal domain of the light-harvesting protein CP29 of plants is not defined in the crystal structure of this membrane protein. We studied the N-terminus using two electron paramagnetic resonance (EPR) approaches: the rotational diffusion of spin labels at 55 residues with continuous-wave EPR, and three sets of distances with a pulsed EPR method. The N-terminus is relatively structured. Five regions that differ considerably in their dynamics are identified. Two regions have low rotational diffusion, one of which shows α-helical character suggesting contact with the protein surface. This immobile part is flanked by two highly dynamic, unstructured regions (loops) that cover residues 10-22 and 82-91. These loops may be important for the interaction with other light-harvesting proteins. The region around residue 4 also has low rotational diffusion, presumably because it attaches noncovalently to the protein. This section is close to a phosphorylation site (Thr-6) in related proteins, such as those encoded by the Lhcb4.2 gene. Phosphorylation might influence the interaction with other antenna complexes, thereby regulating the supramolecular organization in the thylakoid membrane.
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Affiliation(s)
| | - Cor J A M Wolfs
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | - Ruud B Spruijt
- Laboratory of Biophysics, Wageningen University, Wageningen, The Netherlands
| | | | - Martina Huber
- Department of Molecular Physics, Leiden University, Leiden, The Netherlands.
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6
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Jean-Francois FL, Dai J, Yu L, Myrick A, Rubin E, Fajer PG, Song L, Zhou HX, Cross TA. Binding of MgtR, a Salmonella transmembrane regulatory peptide, to MgtC, a Mycobacterium tuberculosis virulence factor: a structural study. J Mol Biol 2013; 426:436-46. [PMID: 24140750 DOI: 10.1016/j.jmb.2013.10.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/10/2013] [Accepted: 10/11/2013] [Indexed: 01/28/2023]
Abstract
MgtR, a highly hydrophobic peptide expressed in Salmonella enterica serovar Typhimurium, inhibits growth in macrophages through binding to the membrane protein MgtC that has been identified as essential for replication in macrophages. While the Mycobacterium tuberculosis MgtC is highly homologous to its S. Typhi analogue, there does not appear to be an Mtb homologue for MgtR, raising significant pharmacological interest in this system. Here, solid-state NMR and EPR spectroscopy in lipid bilayer preparations were used to demonstrate the formation of a heterodimer between S. Typhi MgtR and the transmembrane helix 4 of Mtb MgtC. Based on the experimental restraints, a structural model of this heterodimer was developed using computational techniques. The result is that MgtR appears to be ideally situated in the membrane to influence the functionality of MgtC.
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Affiliation(s)
- Frantz L Jean-Francois
- National High Magnetic Field Laboratory, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Jian Dai
- Department of Physics, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Lu Yu
- University of Science and Technology of China, Hefei 230031, China
| | - Alissa Myrick
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02138, USA
| | - Eric Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02138, USA
| | - Piotr G Fajer
- National High Magnetic Field Laboratory, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Likai Song
- National High Magnetic Field Laboratory, Tallahassee, FL 32306, USA
| | - Huan-Xiang Zhou
- Department of Physics, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
| | - Timothy A Cross
- National High Magnetic Field Laboratory, Tallahassee, FL 32306, USA; Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.
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7
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de Vera IMS, Smith AN, Dancel MCA, Huang X, Dunn BM, Fanucci GE. Elucidating a relationship between conformational sampling and drug resistance in HIV-1 protease. Biochemistry 2013; 52:3278-88. [PMID: 23566104 DOI: 10.1021/bi400109d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Enzyme targets in rapidly replicating systems, such as retroviruses, commonly respond to drug-selective pressure with mutations arising in the active site pocket that limit inhibitor effectiveness by introducing steric hindrance or by eliminating essential molecular interactions. However, these primary mutations are disposed to compromising pathogenic fitness. Emerging secondary mutations, which are often found outside of the binding cavity, may or can restore fitness while maintaining drug resistance. The accumulated drug pressure selected mutations could have an indirect effect in the development of resistance, such as altering protein flexibility or the dynamics of protein-ligand interactions. Here, we show that accumulation of mutations in a drug-resistant HIV-1 protease (HIV-1 PR) variant, D30N/M36I/A71V, changes the fractional occupancy of the equilibrium conformational sampling ensemble. Correlations are made among populations of the conformational states, namely, closed-like, semiopen, and open-like, with inhibition constants, as well as kinetic parameters. Mutations that stabilize a closed-like conformation correlate with enzymes of lowered activity and with higher affinity for inhibitors, which is corroborated by a further increase in the fractional occupancy of the closed state upon addition of inhibitor or substrate-mimic. Cross-resistance is found to correlate with combinations of mutations that increase the population of the open-like conformations at the expense of the closed-like state while retaining native-like occupancy of the semiopen population. These correlations suggest that at least three states are required in the conformational sampling model to establish the emergence of drug resistance in HIV-1 PR. More importantly, these results shed light on a possible mechanism whereby mutations combine to impart drug resistance while maintaining catalytic activity.
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Affiliation(s)
- Ian Mitchelle S de Vera
- Department of Chemistry, P.O. Box 117200, University of Florida , Gainesville, Florida 32611-7200, United States
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8
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Abstract
Distance distributions between paramagnetic centers in the range of 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed, and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The present scope and limitations of the technique are illustrated.
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Affiliation(s)
- Gunnar Jeschke
- Laboratory of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, Switzerland.
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9
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Song Y, Meade TJ, Astashkin A, Klein E, Enemark J, Raitsimring A. Pulsed dipolar spectroscopy distance measurements in biomacromolecules labeled with Gd(III) markers. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 210:59-68. [PMID: 21388847 PMCID: PMC3081411 DOI: 10.1016/j.jmr.2011.02.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 02/03/2011] [Accepted: 02/08/2011] [Indexed: 05/11/2023]
Abstract
This work demonstrates the feasibility of using Gd(III) tags for long-range Double Electron Electron Resonance (DEER) distance measurements in biomacromolecules. Double-stranded 14- base pair Gd(III)-DNA conjugates were synthesized and investigated at K(a) band. For the longest Gd(III) tag the average distance and average deviation between Gd(III) ions determined from the DEER time domains was about 59±12Å. This result demonstrates that DEER measurements with Gd(III) tags can be routinely carried out for distances of at least 60Å, and analysis indicates that distance measurements up to 100Å are possible. Compared with commonly used nitroxide labels, Gd(III)-based labels will be most beneficial for the detection of distance variations in large biomacromolecules, with an emphasis on large scale changes in shape or distance. Tracking the folding/unfolding and domain interactions of proteins and the conformational changes in DNA are examples of such applications.
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Affiliation(s)
- Y. Song
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - T. J. Meade
- Departments of Chemistry; Molecular Biosciences; Neurobiology & Physiology; and Radiology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - A.V. Astashkin
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - E.L. Klein
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - J.H. Enemark
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
| | - A. Raitsimring
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA
- Corresponding Author: Arnold Raitsimring, Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721-0041, USA.
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10
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Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Combining NMR and EPR methods for homodimer protein structure determination. J Am Chem Soc 2010; 132:11910-3. [PMID: 20698532 PMCID: PMC3057626 DOI: 10.1021/ja105080h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - Robert M. McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Erik A. Feldmann
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - John R. Cort
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Huang Wang
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Colleen Ciccosanti
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Mei Jiang
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Haleema Janjua
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Thomas B. Acton
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Rong Xiao
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - John K. Everett
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
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Milikisyants S, Scarpelli F, Finiguerra MG, Ubbink M, Huber M. A pulsed EPR method to determine distances between paramagnetic centers with strong spectral anisotropy and radicals: the dead-time free RIDME sequence. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 201:48-56. [PMID: 19758831 DOI: 10.1016/j.jmr.2009.08.008] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 07/15/2009] [Accepted: 08/07/2009] [Indexed: 05/09/2023]
Abstract
Methods to determine distances between paramagnetic metal centers and radicals are scarce. This is unfortunate because paramagnetic metal centers are frequent in biological systems and so far have not been employed much as distance markers. Successful pulse sequences that directly target the dipolar interactions cannot be applied to paramagnetic metal centers with fast relaxation rates and large g-anisotropy, if no echos can be detected and the excitation bandwidth is not sufficient to cover a sufficiently large part of the spectrum. The RIDME method Kulik et al. (2002) [20] circumvents this problem by making use of the T(1)-induced spin-flip of the transition-metal ion. Designed to measure distance between such a fast relaxing metal center and a radical, it suffers from a dead time problem. We show that this is severe because the anisotropy of the metal center broadens the dipolar curves, which therefore, only can be analyzed if the full curve is known. Here, we introduce five-pulse RIDME (5p-RIDME) that is intrinsically dead-time free. Proper functioning of the sequence is demonstrated on a nitroxide biradical. The distance between a low-spin Fe(III) center and a spin label in spin-labeled cytochrome f shows the complete dipolar trace of a transition-metal ion center and a spin label, yielding the distance expected from the structure.
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Affiliation(s)
- Sergey Milikisyants
- Department of Molecular Physics, Huygens Laboratory, Leiden University, 2300 RA Leiden, The Netherlands
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12
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Ward R, Zoltner M, Beer L, El Mkami H, Henderson I, Palmer T, Norman D. The Orientation of a Tandem POTRA Domain Pair, of the Beta-Barrel Assembly Protein BamA, Determined by PELDOR Spectroscopy. Structure 2009; 17:1187-94. [DOI: 10.1016/j.str.2009.07.011] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 07/23/2009] [Accepted: 07/24/2009] [Indexed: 11/29/2022]
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