Determination of interproton distances from NOESY spectra in the active site of paramagnetic metalloenzymes: cyanide-inhibited horseradish peroxidase

Abstract

Two dimensional (2D) nuclear Overhauser effect (NOE) or NOESY experiments are performed on cyanide inhibited horseradish peroxidase in order to assess the prospects for obtaining quantitative interproton distances for the hyperfine shifted and paramagnetically relaxed active site signals in an intermediate sized (-44 kDa) paramagnetic metalloenzyme. This protein represents an ideal test case for such experiments because a series of structurally defined proton pairs on the heme and axial His 170 have been previously assigned. The relaxation properties of hyperfine shifted signals relevant to the experimental setup of 2D experiments and interpretation of both 1D and 2D NOE data are also investigated. NOESY spectra as a function of mixing time show that quantitative rise curves can be obtained that clearly differentiate between primary and secondary NOES even among the most strongly relaxed protons, but this requires very short mixing times in the range 0.5-3.0 ms. The sensitivity of the weak cross peaks at these short mixing times is improved by the relatively rapid pulse repetition rate and concommitant increase in the number of scans allowed by the rapid relaxation of active site protons. The paramagnetic relaxation influence, as well as the size of the protein, results in rise curves that are linear to only 1.5 ms for geminal protons and to only 3-5 ms for more weakly dipolar coupled proton pairs. However, the cross peak intensities in the linear region are shown to yield cross relaxation rates and internuclear distances for a series of assigned and orientationally invariant proton pairs that are in good agreement with their known distances. The patterns of NOESY rise curves are used both to determine the orientations of one propionate and both vinyl groups relative to the heme and to show that the axial His exhibits an orientation relative to its helix that is similar but not identical to that in crystallographically characterized cytochrome c peroxidase. Selective and nonselective 1D as well as 2D selective relaxation rate measurements for hyperfine shifted signals show that only selective or intrinsic relaxation rates can be used to optimize the setup of NOESY experiments and interpret 1D NOE data. The results of the study indicate that NOESY spectra can be expected to yield valuable quantitative structural information on the hyperfine shifted active site residues in a variety of cyanide-inhibited heme peroxidases.