NMR Spectroscopy of Paramagnetic Metalloproteins

Bertini, Ivano; Luchinat, Claudio; Parigi, Giacomo; Pierattelli, Roberta

doi:10.1002/cbic.200500124

Cited by 305 publications

(307 citation statements)

References 148 publications

(169 reference statements)

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“…In the absence of preexisting structural knowledge, the anisotropy and the orientation of the magnetic-susceptibility tensor can be determined and iteratively refined within the procedure for the determination of the NMR structure (46). The anisotropy values of the magnetic-susceptibility tensor can be also approximated by literature values (47), as is done in the following section. ‡ For the sake of clarity, only the 231 values that are common in the spectra of the 3 samples (fully labeled CoMMP-12, diluted CoMMP-12, and diluted ZnMMP-12) are reported in the plot.…”

Section: Resultsmentioning

confidence: 99%

“…The use of pcs in the protein structural calculations followed the well-described protocols for solution structure determinations (22,46,47), and average values reported in the literature for the paramagnetic tensor parameters ⌬ ax and ⌬ rh in cobalt(II) ions (Eq. 1) were used (47).…”

Section: Fig 2 13 C Pcs Observed (Blue Lines) For Fully Labeled Commentioning

confidence: 99%

“…1) were used (47). ¶ Such calculations also show that some distance restraints are always needed, otherwise pcs alone hardly converge to a correct folding (22,48).…”

Section: Fig 2 13 C Pcs Observed (Blue Lines) For Fully Labeled Commentioning

confidence: 99%

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Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

Balayssac

Bertini

Bhaumik

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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141

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The recent observation of pseudocontact shifts (pcs) in 13 C highresolution 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.S olid-state NMR (SSNMR) on biomolecules is a rapidly growing technique, with an increased interest based on its ability to determine protein structures in the solid phase (1, 2) and to permit the study of noncrystalline biomolecular systems such as membrane proteins (3) and fibrils (4, 5).Limitations in biomolecular structural determination through SSNMR are due to the difficulties in obtaining a large number of restraints to be used for structural purposes (4, 6-9). Most of the structural information is obtained through distance restraints, analogous to nuclear Overhauser effects (NOE) in solution NMR, which in the solid state are obtained through experiments such as proton-driven spin diffusion (PDSD) (1, 6, 10), and CHHC (11), whereas specifically designed sequences can be applied on short peptides (4,(12)(13)(14). The ability to obtain a large number of distance restraints is hampered by the reduced resolution of SSNMR spectra, which increases the amount of ambiguities in the assigned restraints (15), whereas relayed transfer (10, 16) and the effects of the dipolar truncation (17) affect the accuracy of these restraints. These problems have been tackled by working on samples prepared with selective labeling schemes (1, 6) and, more recently, on uniformly labeled proteins with the help of software able to provide automated PDSD/ CHHC assignment and on dealing with a large number of ambiguous restraints (10,15,18). However, even when additional dihedral angle restraints from backbone chemical shiftsthrough Chemical Shift Index (CSI) (19) or TALOS (20) programs-are used, the size of the affordable proteins has been, up to now, limited to small systems (Ͻ100 aa) (10,15,18). In this work, we show how SSNMR paramagnetic restraints such as pseudocontact shifts (pcs) can be used as additional sources of restraints for protein structural determination, even providing information abou...

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Section: Resultsmentioning

confidence: 99%

Section: Fig 2 13 C Pcs Observed (Blue Lines) For Fully Labeled Commentioning

confidence: 99%

See 1 more Smart Citation

Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

Balayssac

Bertini

Bhaumik

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

141

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“…In terms of activity, the unliganded and NO-bound forms of SO2144 would be the targets for structural studies to correlate activity with ligand binding. However, the heme is paramagnetic in both the Fe(II) WT (S ϭ 2) and the Fe(II)-NO WT (S ϭ 1/2) complexes that limit observation in the vicinity of the heme because electron-nuclear spin relaxation broadens resonance lines beyond the limit of detection for protons within a Ϸ10-Å radius around the heme iron (12).…”

Section: Identification Of Active and Inactive Diamagnetic States Of mentioning

confidence: 99%

A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation

Erbil¹,

Price

Wemmer

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

112

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“…If a paramagnetic metal ion is present in a protein, the NMR signals of the nuclei in a shell around it will be affected [34] by several effects, including contact and pseudocontact shifts, relaxation rate enhancements, and cross-correlation effects.…”

Section: Paramagnetic Restraintsmentioning

confidence: 99%

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

Fuentes

Dijk

Bonvin

2008

Methods in Molecular Biology

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Summary Nuclear magnetic resonance (NMR) has become a well-established AQ: Please provide first name for all the authors. method to characterize the structures of biomolecules in solution. High-quality structures are now produced, thanks to both experimental and computational developments, allowing the use of new NMR parameters and improved protocols and force fields in structure calculation and refinement. In this chapter, we give a short overview of the various types of NMR data that can provide structural information, and then focus on the structure calculation methodology itself. We discuss and illustrate with tutorial examples both "classical" structure calculation and refinement approaches as well as more recently developed protocols for modeling biomolecular complexes.

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NMR Spectroscopy of Paramagnetic Metalloproteins

Cited by 305 publications

References 148 publications

Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

Paramagnetic shifts in solid-state NMR of proteins to elicit structural information

A structural basis for H-NOX signaling in Shewanella oneidensis by trapping a histidine kinase inhibitory conformation

Nuclear Magnetic Resonance-Based Modeling and Refinement of Protein Three-Dimensional Structures and Their Complexes

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