Standard procedures for using nuclear Overhauser enhancements (NOE) between protons to generate structures for diamagnetic proteins in solution from NMR data may be supplemented by using dipolar shifts if the protein is paramagnetic. This is advantageous since the electron -nuclear dipolar coupling provides relatively long-range geometric information with respect to the paramagnetic centre which complements the short-range distance constraints NOEs. Several different strategies have been developed to date, but none of these attempts to combine data from NOEs and dipolar shifts in the initial stages of structure calculation or to determine three dimensional protein structures together with their magnetic properties. This work shows that the magnetic and atomic structures are highly correlated and that it is important to have additional constraints both to provide starting parameters for the magnetic properties and to improve the definition of the best fit. Useful parameters can be obtained for haem proteins from Fermi contact shifts; this approach is compared with a new method based on the analysis of dipolar shifts in haem methyl groups with respect to data from horse and tuna ferricytochromes c. The methods developed for using data from NOEs and dipolar shifts have been incorporated in a new computer program, PARADYANA, which is demonstrated in application to a model data set for the sequence of the haem octapeptide known as microperoxidase-8.
[NMR paper] NMR structures of paramagnetic metalloproteins.
NMR structures of paramagnetic metalloproteins.
Related Articles NMR structures of paramagnetic metalloproteins.
Q Rev Biophys. 2005 May;38(2):167-219
Authors: Arnesano F, Banci L, Piccioli M
Metalloproteins represent a large share of the proteome and many of them contain paramagnetic metal ions. The knowledge, at atomic resolution, of their structure in solution is important to understand processes in which they are involved, such as electron transfer mechanisms, enzymatic reactions, metal homeostasis and metal trafficking, as well as...
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11-25-2010 08:21 PM
[NMR paper] Determination of the electron relaxation rates in paramagnetic metal complexes: appli
Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods.
Related Articles Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods.
J Magn Reson. 2004 Apr;167(2):169-77
Authors: Jensen MR, Led JJ
Four different approaches for determining the electron relaxation rates in paramagnetic metallo-proteins are investigated, using a paramagnetic Ni2+ complex of a protein as an example. All four approaches rely on the...
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11-24-2010 09:51 PM
[NMR paper] Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures
Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures tell us.
Related Articles Fatty acid interactions with proteins: what X-ray crystal and NMR solution structures tell us.
Prog Lipid Res. 2004 May;43(3):177-99
Authors: Hamilton JA
The interactions of fatty acids with proteins have been studied by a variety of conventional approaches for decades. However, only limited aspects of fatty acid-protein interactions have been elucidated, even with the integration of information gleaned from the many techniques....
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11-24-2010 09:51 PM
[NMR paper] NMR solution structure determination of membrane proteins reconstituted in detergent
NMR solution structure determination of membrane proteins reconstituted in detergent micelles.
Related Articles NMR solution structure determination of membrane proteins reconstituted in detergent micelles.
FEBS Lett. 2003 Nov 27;555(1):144-50
Authors: Fernández C, Wüthrich K
As an alternative to X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy in solution can be used for three-dimensional structure determination of small membrane proteins, preferably proteins with beta-barrel fold. This paper reviews recent achievements as...
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11-24-2010 09:16 PM
[NMR paper] Structures of larger proteins in solution: three- and four-dimensional heteronuclear
Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.
Related Articles Structures of larger proteins in solution: three- and four-dimensional heteronuclear NMR spectroscopy.
Science. 1991 Jun 7;252(5011):1390-9
Authors: Clore GM, Gronenborn AM
Three- and four-dimensional heteronuclear nuclear magnetic resonance (NMR) spectroscopy offers dramatic improvements in spectral resolution by spreading through-bond and through-space correlations in three and four orthogonal frequency axes....
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08-21-2010 11:16 PM
Structure determination of proteins in 2H2O solution aided by a deuterium-decoupled 3
Abstract We developed an NMR pulse sequence, 3D HCA(N)CO, to correlate the chemical shifts of protein backbone 1Hα and 13Cα to those of 13C� in the preceding residue. By applying 2H decoupling, the experiment was accomplished with high sensitivity comparable to that of HCA(CO)N. When combined with HCACO, HCAN and HCA(CO)N, the HCA(N)CO sequence allows the sequential assignment using backbone 13C� and amide 15N chemical shifts without resort to backbone amide protons. This assignment strategy was demonstrated for 13C/15N-labeled GB1 dissolved in 2H2O. The quality of the GB1 structure...
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08-14-2010 04:19 AM
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Michael John, Guido Pintacuda, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting
J. Am. Chem. Soc.; 2006; 128(39) pp 12910 - 12916; (Article)
Abstract:
Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small...
Determination of solution structures of paramagnetic proteins by NMR.
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