Data analysis procedures for pulse ELDOR measurements of broad distance distributions

Abstract

The reliability of procedures for extracting the distance distribution between spins from the dipolar evolution funetion is studied with particular emphasis on broad distributions. A new numerically stable procedure for fitting distance distributions with polynomial interpolation between sampling points is introduced and compared to Tikhonov regulafization in the dipolar frequency and distante domains and to approximate Pake transformation. Distante distributions with only narrow peaks are most reliably extracted by distance-domain Til~aonov regularization, while frequency-domain Tikhonov regularization is favorable for distributions with only broad peaks. For the quantification of distributions by their mean distante and variante, Hermite polynomial interpolation provides the best results. Distributions that contain both broad and narrow peaks are most difficult to analyze. In this case a high signal-to-noise ratio is strietly required and approximate Pake transformation should be applied. A proeedure is given for renormalizing primary expe¡ data from protein preparations with slightly different degrees of spin labeUing, so that they can be compared directly. Performance of all the data analysis procedures is demonstrated on experimental data for a shape-persistent biradical with a label-to-label distante of 5 nm, for a [2]catenane with a broad distante distribution, and fora doubly spin-labelled double mutant of plant light harvesting complex II.

The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and Dynamics

“…All pulsed EPR data were collected with a Bruker EleXsys E580 spectrometer equipped with the ER 4118X-MD-5 dielectric ring resonator at 65 K using a four-pulse DEER sequence (34), described in detail previously (24). The DEER dipolar modulation curves were background-corrected, high pass-filtered, and converted to distance distribution profiles via Tikhonov regularization using DeerAnalysis2008 (35,36). The correct background correction level was determined using a self-consistent analysis procedure, where a series of Gaussian-shaped populations representing the nominal conformations of HIV-1 PR (14, 23) with estimated relative percentage, full width at half-maximum, and most probable distance were summed to reconstruct the distance profile via DeerSim.…”

Mesopores provide an amorphous state suitable for studying biomolecular structures at cryogenic temperatures

“…The determination of interspin distance distribution of the DEER spectroscopy was performed in the time-domain analysis by Tikhonov regularization based on the L-curve method (30,31). The results of the distance distribution were further refined by means of the maximum entropy method (32).…”

“…The baseline slope of DEER signal is strongly correlated with the mean spin concentration (29). The red solid lines represent the best-fit baselines, which are exponential decays, obtained in the Tikhonov analysis (30,31). The corresponding Pake patterns, obtained from Fourier transformation of the time-domain DEER signals, are discussed in Section III in SI Appendix.…”

DEER Distance Measurements on Proteins

“…Comparison of several alternative approaches for computation of the distance distribution (86)(87)(88) revealed that the best transformation method is Tikhonov regularization with an added non-negativity constraint P (r) ≥ 0. The optimum regularization parameter can be estimated from the corner of the L curve (Figure 2e) (88).…”