Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasteurianum ferredoxin as an example.
The possibility of using the relaxation properties of nuclei for solution structure determination of paramagnetic metalloproteins is critically evaluated. First of all, it is theoretically and experimentally demonstrated that magnetization recovery in nonselective inversion recovery experiments can be approximated to an exponential in both diamagnetic and paramagnetic systems. This permits the estimate of the contribution of paramagnetic relaxation when dominant or sizable. Then, it is shown that the averaging of paramagnetic relaxation rates due to cross relaxation is often tolerably small with respect to the use of paramagnetic relaxation rates as constraints for structural determination. Finally, a protocol is proposed to use such paramagnetic relaxation rates, which depend on the sixth power of the metal to resonating nucleus distance, as constraints for solution structure determination of proteins. As an example, the available solution structure of the oxidized ferredoxin from Clostridium pasteurianum has been significantly improved in resolution especially in the proximity of the metal ions by using 69 new constraints based on paramagnetic relaxation.
Bertini
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I
Department of Chemistry, University of Florence, Firenze, Italy. bertini@risc1.lrm.fi.cnr.it
Donaire
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A
Luchinat
C
C
Rosato
A
A
D003013:Clostridium / Q000737:chemistry*; D005288:Ferredoxins / Q000737:chemistry*; D008280:Magnetics; D008432:Mathematical Computing; D011487:Protein Conformation; D012996:Solutions
D005288:Ferredoxins; D012996:Solutions