Backbone-only restraints for fast determination of the protein fold: the role of paramagnetism-based restraints. Cytochrome b562 as an example.
CH(alpha) residual dipolar couplings (Deltardc's) were measured for the oxidized cytochrome b562 from Escherichia coli as a result of its partial self-orientation in high magnetic fields due to the anisotropy of the overall magnetic susceptibility tensor. Both the low spin iron (III) heme and the four-helix bundle fold contribute to the magnetic anisotropy tensor. CH(alpha) Deltardc's, which span a larger range than the analogous NH values (already available in the literature) sample large space variations at variance with NH Deltardc's, which are largely isooriented within alpha helices. The whole structure is now significantly refined with the chemical shift index and CH(alpha) Deltardc's. The latter are particularly useful also in defining the molecular magnetic anisotropy parameters. It is shown here that the backbone folding can be conveniently and accurately determined using backbone restraints only, which include NOEs, hydrogen bonds, residual dipolar couplings, pseudocontact shifts, and chemical shift index. All these restraints are easily and quickly determined from the backbone assignment. The calculated backbone structure is comparable to that obtained by using also side chain restraint. Furthermore, the structure obtained with backbone only restraints is, in its whole, very similar to that obtained with the complete set of restraints. The paramagnetism based restraints are shown to be absolutely relevant, especially for Deltardc's.
Banci
Lucia
L
CERM and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
Bertini
Ivano
I
Felli
Isabella C
IC
Sarrou
Josephine
J
D016880:Anisotropy; D001426:Bacterial Proteins / Q000737:chemistry; D003573:Cytochrome b Group / Q000737:chemistry*; D029968:Escherichia coli Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D017510:Protein Folding
D001426:Bacterial Proteins; D003573:Cytochrome b Group; D029968:Escherichia coli Proteins; C017850:cytochrome b562, E coli