Solution Structure Calculations through Self-Orientation in a Magnetic Field of a Cerium(III) Substituted Calcium-Binding Protein

Bertini, Ivano; Janik, Matthias; Liu, Gaohua; Luchinat, Claudio; Rosato, Antonio

doi:10.1006/jmre.2000.2218

Cited by 45 publications

(34 citation statements)

References 42 publications

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“…From 1823 NOEs, 191 dihedral angles, 15 hydrogen bonds, 1738 d pcs values related to 11 lanthanides, 64 self-orientation rdc values, 26 R 1 values, and 47 paramagnetic ccr values, a family with a backbone root mean square deviation (RMSD) from the mean of less than 0.3 was obtained. [23,90,110,111] The backbone RMSD from the mean of the family obtained with the diamagnetic restraints was 0.7 . Figure 9 shows the two families (30 structures) calculated without and with the inclusion of the paramagnetism-based restraints.…”

Section: Residual Dipolar Couplingsmentioning

confidence: 99%

NMR Spectroscopy of Paramagnetic Metalloproteins

et al. 2005

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This article deals with the solution structure determination of paramagnetic metalloproteins by NMR spectroscopy. These proteins were believed not to be suitable for NMR investigations for structure determination until a decade ago, but eventually novel experiments and software protocols were developed, with the aim of making the approach suitable for the goal and as user-friendly and safe as possible. In the article, we also give hints for the optimization of experiments with respect to each particular metal ion, with the aim of also providing a handy tool for nonspecialists. Finally, a section is dedicated to the significant progress made on 13C direct detection, which reduces the negative effects of paramagnetism and may constitute a new chapter in the whole field of NMR spectroscopy.

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Section: Residual Dipolar Couplingsmentioning

confidence: 99%

NMR Spectroscopy of Paramagnetic Metalloproteins

et al. 2005

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“…Calbindin D 9k , a 75 amino acid calcium-binding protein, in which one of the two calcium ions can easily be substituted by a lanthanide ion, [1,2] was used as the test protein. Previous work has shown that all known paramagnetism-based constraints (relaxation rates (R 1 and R 2 ), [3,4] pseudocontact shifts (PCSs), [3±5] residual dipolar couplings (RDCs), [3,6,7] dipole-Curie cross-correlations (CCRs), [8] and even contact shifts [9] ) can be obtained for derivatives of calbindin D 9k with paramagnetic lanthanides, and that they can be used to substantially refine the NMR structure.…”

Section: Introductionmentioning

confidence: 99%

“…A list of upper distance and lower distance constraints was thus obtained from the measured values of the paramagnetic enhancements to the longitudinal relaxation rates R 1M by using Equation (6) and adding and subtracting 1 ä to the distances so obtained, respectively. The constant k CCR for the CCR constraints was calculated to be À1900 ä 3 s À1 at 800 MHz from Equation (5).…”

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confidence: 99%

Backbone‐Only Protein Solution Structures with a Combination of Classical and Paramagnetism‐Based Constraints: A Method that Can Be Scaled to Large Molecules

2004

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Herein, it is shown that a medium-resolution solution structure of a protein can be obtained with the sole assignment of the protein backbone and backbone-related constriants if a derivative with a firmly bound paramagnetic metal is available. The proof-of-concept is provided on calbindin D9k, a calcium binding protein in which one of the two calcium ions can be selectively substituted by a paramagnetic lanthanide ion. The constraints used are HN (and Ha) nuclear Overhauser effects (NOEs), hydrogen bonds, dihedral angle constriants from chemical shifts, and the following paramagnetism-based constraints: 1) pseudocontact shifts, acquired by substituting one (or more) lanthanide(s) in the C-terminal calcium binding site; 2) N-HN residual dipolar couplings due to self-orientation induced by the paramagnetic lanthanide(s); 3) cross-correlations between the Curie and internuclear dipole-dipole interactions; and 4) paramagnetism-induced relaxation rate enhancements. An upper distance limit for internuclear distances between any two backbone atoms was also given according to the molecular weight of the protein. For this purpose, the paramagnetism-based constraints were collectively implemented in the program CYANA for solution structure determinations, similarly to what was previously done for the program DYANA. The method is intrinsically suitable for large molecular weight proteins.

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“…They arise from not complete averaging of dipolar interactions in solution and carry a great deal of structural information. Despite this effect was known since the early days of NMR [3], only a few years ago NMR experiments were introduced to actively exploit DrdcÕs for solution structure determination [4][5][6][7]. Several approaches to increase the partial alignment of macromolecules in solution have been proposed including liquid crystals [4,8,9], purple membrane fragments [10], filamentous phages [11], mineral liquid crystals [12], and other media [13][14][15].…”

Section: Introductionmentioning

confidence: 99%