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Shamir Y, Goldbourt A. Atomic-Resolution Structure of the Protein Encoded by Gene V of fd Bacteriophage in Complex with Viral ssDNA Determined by Magic-Angle Spinning Solid-State NMR. J Am Chem Soc 2022; 145:300-310. [PMID: 36542094 PMCID: PMC9837838 DOI: 10.1021/jacs.2c09957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
F-specific filamentous phages, elongated particles with circular single-stranded DNA encased in a symmetric protein capsid, undergo an intermediate step, where thousands of homodimers of a non-structural protein, gVp, bind to newly synthesized strands of DNA, preventing further DNA replication and preparing the circular genome in an elongated conformation for assembly of a new virion structure at the membrane. While the structure of the free homodimer is known, the ssDNA-bound conformation has yet to be determined. We report an atomic-resolution structure of the gVp monomer bound to ssDNA of fd phage in the nucleoprotein complex elucidated via magic-angle spinning solid-state NMR. The model presents significant conformational changes with respect to the free form. These modifications facilitate the binding mechanism and possibly promote cooperative binding in the assembly of the gVp-ssDNA complex.
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2
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Abstract
Computational modeling of proteins using evolutionary or de novo approaches offers rapid structural characterization, but often suffers from low success rates in generating high quality models comparable to the accuracy of structures observed in X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. A computational/experimental hybrid approach incorporating sparse experimental restraints in computational modeling algorithms drastically improves reliability and accuracy of 3D models. This chapter discusses the use of structural information obtained from various paramagnetic NMR measurements and demonstrates computational algorithms implementing pseudocontact shifts as restraints to determine the structure of proteins at atomic resolution.
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3
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Yu M, Liu SL, Sun PB, Pan H, Tian CL, Zhang LH. Peptide toxins and small-molecule blockers of BK channels. Acta Pharmacol Sin 2016; 37:56-66. [PMID: 26725735 DOI: 10.1038/aps.2015.139] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/13/2015] [Indexed: 12/21/2022] Open
Abstract
Large conductance, Ca(2+)-activated potassium (BK) channels play important roles in the regulation of neuronal excitability and the control of smooth muscle contractions. BK channels can be activated by changes in both the membrane potential and intracellular Ca(2+) concentrations. Here, we provide an overview of the structural and pharmacological properties of BK channel blockers. First, the properties of different venom peptide toxins from scorpions and snakes are described, with a focus on their characteristic structural motifs, including their disulfide bond formation pattern, the binding interface between the toxin and BK channel, and the functional consequence of the blockage of BK channels by these toxins. Then, some representative non-peptide blockers of BK channels are also described, including their molecular formula and pharmacological effects on BK channels. The detailed categorization and descriptions of these BK channel blockers will provide mechanistic insights into the blockade of BK channels. The structures of peptide toxins and non-peptide compounds could provide templates for the design of new channel blockers, and facilitate the optimization of lead compounds for further therapeutic applications in neurological disorders or cardiovascular diseases.
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Sumowski CV, Hanni M, Schweizer S, Ochsenfeld C. Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides. J Chem Theory Comput 2015; 10:122-33. [PMID: 26579896 DOI: 10.1021/ct400713t] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.
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Affiliation(s)
- Chris Vanessa Sumowski
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Matti Hanni
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Sabine Schweizer
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU) , Butenandtstr. 7, D-81377 Munich, Germany and Center for Integrated Protein Science (CIPSM) at the Department of Chemistry, University of Munich (LMU) , Butenandtstr. 5-13, D-81377 Munich, Germany
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5
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Nikouee A, Khabiri M, Cwiklik L. Scorpion toxins prefer salt solutions. J Mol Model 2015; 21:287. [PMID: 26475740 DOI: 10.1007/s00894-015-2822-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 09/15/2015] [Indexed: 11/26/2022]
Abstract
There is a wide variety of ion channel types with various types of blockers, making research in this field very complicated. To reduce this complexity, it is essential to study ion channels and their blockers independently. Scorpion toxins, a major class of blockers, are charged short peptides with high affinities for potassium channels. Their high selectivity and inhibitory properties make them an important pharmacological tool for treating autoimmune or nervous system disorders. Scorpion toxins typically have highly charged surfaces and-like other proteins-an intrinsic ability to bind ions (Friedman J Phys Chem B 115(29):9213-9223, 1996; Baldwin Biophys J 71(4):2056-2063, 1996; Vrbka et al. Proc Natl Acad Sci USA 103(42):15440-15444, 2006a; Vrbka et al. J Phys Chem B 110(13):7036-43, 2006b). Thus, their effects on potassium channels are usually investigated in various ionic solutions. In this work, computer simulations of protein structures were performed to analyze the structural properties of the key residues (i.e., those that are presumably involved in contact with the surfaces of the ion channels) of 12 scorpion toxins. The presence of the two most physiologically abundant cations, Na(+) and K(+), was considered. The results indicated that the ion-binding properties of the toxin residues vary. Overall, all of the investigated toxins had more stable structures in ionic solutions than in water. We found that both the number and length of elements in the secondary structure varied depending on the ionic solution used (i.e., in the presence of NaCl or KCl). This study revealed that the ionic solution should be chosen carefully before performing experiments on these toxins. Similarly, the influence of these ions should be taken into consideration in the design of toxin-based pharmaceuticals.
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Affiliation(s)
- Azadeh Nikouee
- Institute of Applied Physiology, Ulm University, Ulm, Germany
| | - Morteza Khabiri
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Lukasz Cwiklik
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
- J. Heyrovský Institute of Physical Chemistry Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223, Prague 8, Czech Republic
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6
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Li J, Pilla KB, Li Q, Zhang Z, Su X, Huber T, Yang J. Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts. J Am Chem Soc 2013; 135:8294-303. [DOI: 10.1021/ja4021149] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jianping Li
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Kala Bharath Pilla
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Qingfeng Li
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Xuncheng Su
- State Key Laboratory of Elemento-Organic
Chemistry, Nankai University, Tianjin300071,
PR China
| | - Thomas Huber
- Research School
of Chemistry, Australian National University, Canberra, ACT 0200,
Australia
| | - Jun Yang
- Key Laboratory of Magnetic Resonance
in Biological Systems, State Key Laboratory of Magnetic Resonance
and Atomic and Molecular Physics, Wuhan Centre for Magnetic Resonance,
Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, PR China
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7
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G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy. Biochem J 2013; 450:443-57. [DOI: 10.1042/bj20121644] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.
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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.
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Affiliation(s)
- Ishita Sengupta
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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9
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Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH. A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination. Chemphyschem 2011; 12:915-8. [DOI: 10.1002/cphc.201100062] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Indexed: 11/07/2022]
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10
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Shewmaker F. The application of NMR techniques to bacterial adhesins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 715:241-56. [PMID: 21557068 DOI: 10.1007/978-94-007-0940-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular adhesins frequently compose large, highly-ordered structural assemblies that project away from the bacterial surface. These assemblies, known as pili or fimbriae, are rod-like polymeric structures that in some cases can extend up to several micrometers from the cell surface. Because these adhesin structures are critical to bacterial colonization of host cell surfaces, there is an incentive to understand their structure, assembly and mechanism of host cell attachment. Various methods in Nuclear Magnetic Resonance (NMR) spectroscopy have been used to address these topics, yielding structural information at the atomic level. Also, new methods in solid-state NMR spectroscopy have thus far been under-utilized in the study of large adhesin structures and offer a powerful approach to overcoming problems with crystallization to better understand the structures of these complexes. The following is a brief overview of the contributions of NMR to the study of bacterial adhesins with an emphasis on the future potential of solid-state NMR.
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Affiliation(s)
- Frank Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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11
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12
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Tycko R, Hu KN. A Monte Carlo/simulated annealing algorithm for sequential resonance assignment in solid state NMR of uniformly labeled proteins with magic-angle spinning. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2010; 205:304-14. [PMID: 20547467 PMCID: PMC2902575 DOI: 10.1016/j.jmr.2010.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Revised: 05/19/2010] [Accepted: 05/21/2010] [Indexed: 05/05/2023]
Abstract
We describe a computational approach to sequential resonance assignment in solid state NMR studies of uniformly (15)N,(13)C-labeled proteins with magic-angle spinning. As input, the algorithm uses only the protein sequence and lists of (15)N/(13)C(alpha) crosspeaks from 2D NCACX and NCOCX spectra that include possible residue-type assignments of each crosspeak. Assignment of crosspeaks to specific residues is carried out by a Monte Carlo/simulated annealing algorithm, implemented in the program MC_ASSIGN1. The algorithm tolerates substantial ambiguity in residue-type assignments and coexistence of visible and invisible segments in the protein sequence. We use MC_ASSIGN1 and our own 2D spectra to replicate and extend the sequential assignments for uniformly-labeled HET-s(218-289) fibrils previously determined manually by Siemer et al. (J. Biomol. NMR, 34 (2006) 75-87) from a more extensive set of 2D and 3D spectra. Accurate assignments by MC_ASSIGN1 do not require data that are of exceptionally high quality. Use of MC_ASSIGN1 (and its extensions to other types of 2D and 3D data) is likely to alleviate many of the difficulties and uncertainties associated with manual resonance assignments in solid state NMR studies of uniformly labeled proteins, where spectral resolution and signal-to-noise are often sub-optimal.
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Affiliation(s)
- Robert Tycko
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA.
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13
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Abstract
The prion hypothesis states that the prion and non-prion form of a protein differ only in their 3D conformation and that different strains of a prion differ by their 3D structure. Recent technical developments have enabled solid-state NMR to address the atomic-resolution structures of full-length prions, and a first comparative study of two of them, HET-s and Ure2p, in fibrillar form, has recently appeared as a pair of companion papers. Interestingly, the two structures are rather different: HET-s features an exceedingly well-ordered prion domain and a partially disordered globular domain. Ure2p in contrast features a very well ordered globular domain with a conserved fold, and-most probably-a partially ordered prion domain. For HET-s, the structure of the prion domain is characterized at atomic-resolution. For Ure2p, structure determination is under way, but the highly resolved spectra clearly show that information at atomic resolution should be achievable.
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Affiliation(s)
- Anja Böckmann
- IBCP UMR 5086 CNRS/Université de Lyon, Lyon, France.
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14
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Loquet A, Gardiennet C, Böckmann A. Protein 3D structure determination by high-resolution solid-state NMR. CR CHIM 2010. [DOI: 10.1016/j.crci.2010.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Bertini I, Bhaumik A, De Paëpe G, Griffin RG, Lelli M, Lewandowski JR, Luchinat C. High-resolution solid-state NMR structure of a 17.6 kDa protein. J Am Chem Soc 2010; 132:1032-40. [PMID: 20041641 DOI: 10.1021/ja906426p] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.
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Affiliation(s)
- Ivano Bertini
- Magnetic Resonance Center, CERM, University of Florence, Via L. Sacconi, 6-50019 Sesto Fiorentino, Italy.
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16
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Pentelute BL, Mandal K, Gates ZP, Sawaya MR, Yeates TO, Kent SBH. Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography. Chem Commun (Camb) 2010; 46:8174-6. [DOI: 10.1039/c0cc03148h] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Schneider R, Seidel K, Etzkorn M, Lange A, Becker S, Baldus M. Probing Molecular Motion by Double-Quantum (13C,13C) Solid-State NMR Spectroscopy: Application to Ubiquitin. J Am Chem Soc 2009; 132:223-33. [DOI: 10.1021/ja906283h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Robert Schneider
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Karsten Seidel
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Manuel Etzkorn
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Adam Lange
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Stefan Becker
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Marc Baldus
- Department for NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany, and Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Kim HJ, Howell SC, Van Horn WD, Jeon YH, Sanders CR. Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2009; 55:335-360. [PMID: 20161395 PMCID: PMC2782866 DOI: 10.1016/j.pnmrs.2009.07.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Affiliation(s)
- Hak Jun Kim
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, 406-840, Korea
| | - Stanley C. Howell
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Wade D. Van Horn
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
| | - Young Ho Jeon
- Center for Magnetic Resonance, Korea Basic Research Institute, Daejon, 305-333, Korea
| | - Charles R. Sanders
- Department of Biochemistry, Center for Structural Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232-8725, USA
- Corresponding Author: ; phone: 615-936-3756; fax: 615-936-2211
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19
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McDermott A. Structure and dynamics of membrane proteins by magic angle spinning solid-state NMR. Annu Rev Biophys 2009; 38:385-403. [PMID: 19245337 DOI: 10.1146/annurev.biophys.050708.133719] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins remain difficult to study by traditional methods. Magic angle spinning solid-state NMR (MAS SSNMR) methods present an important approach for studying membrane proteins of moderate size. Emerging MAS SSNMR methods are based on extensive assignments of the nuclei as a basis for structure determination and characterization of function. These methods have already been used to characterize fibrils and globular proteins and are being increasingly used to study membrane proteins embedded in lipids. This review highlights recent applications to intrinsic membrane proteins and summarizes recent technical advances that will enable these methods to be utilized for more complex membrane protein systems in the near future.
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Affiliation(s)
- Ann McDermott
- Department of Chemistry, Columbia University, New York, NY 10027, USA.
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20
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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
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Renault M, Saurel O, Czaplicki J, Demange P, Gervais V, Löhr F, Réat V, Piotto M, Milon A. Solution State NMR Structure and Dynamics of KpOmpA, a 210 Residue Transmembrane Domain Possessing a High Potential for Immunological Applications. J Mol Biol 2009; 385:117-30. [DOI: 10.1016/j.jmb.2008.10.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 09/16/2008] [Accepted: 10/04/2008] [Indexed: 10/21/2022]
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22
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Paramagnetic shifts in solid-state NMR of proteins to elicit structural information. Proc Natl Acad Sci U S A 2008; 105:17284-9. [PMID: 18988744 DOI: 10.1073/pnas.0708460105] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The recent observation of pseudocontact shifts (pcs) in (13)C high-resolution solid-state NMR of paramagnetic proteins opens the way to their application as structural restraints. Here, by investigating a microcrystalline sample of cobalt(II)-substituted matrix metalloproteinase 12 [CoMMP-12 (159 AA, 17.5 kDa)], it is shown that a combined strategy of protein labeling and dilution of the paramagnetic species (i.e., (13)C-,(15)N-labeled CoMMP-12 diluted in unlabeled ZnMMP-12, and (13)C-,(15)N-labeled ZnMMP-12 diluted in unlabeled CoMMP-12) allows one to easily separate the pcs contributions originated from the protein internal metal (intramolecular pcs) from those due to the metals in neighboring proteins in the crystal lattice (intermolecular pcs) and that both can be used for structural purposes. It is demonstrated that intramolecular pcs are significant structural restraints helpful in increasing both precision and accuracy of the structure, which is a need in solid-state structural biology nowadays. Furthermore, intermolecular pcs provide unique information on positions and orientations of neighboring protein molecules in the solid phase.
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23
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Abbas N, Belghazi M, Abdel-Mottaleb Y, Tytgat J, Bougis PE, Martin-Eauclaire MF. A new Kaliotoxin selective towards Kv1.3 and Kv1.2 but not Kv1.1 channels expressed in oocytes. Biochem Biophys Res Commun 2008; 376:525-30. [DOI: 10.1016/j.bbrc.2008.09.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 09/05/2008] [Indexed: 01/02/2023]
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