eNORA2 Exact NOE Analysis Program

Abstract

We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from an exact interpretation of NOESY buildup intensities (eNOEs). This enabled us to calculate multistate structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious and required a deep understanding of the underlying spin dynamics. Here, we present a MatLab package that integrates all data processing steps required to convert intensities of assigned peaks in NOESY series into upper and lower distance limits for structure calculation. Those steps include organization of the data in object format, extraction of autorelaxation and cross-relaxation rate constants by fitting of diagonal peak decays and cross peak buildups, validation of the data, correction for spin diffusion, graphical display of the results, and generation of distance limits in CYANA compatible format. The analysis may be carried out using a full relaxation matrix or a simplified "divide and conquer" approach that allows for partial deuteration of protons. As the program does not require expertise beyond that of standard resonance assignment/structure calculation, it is suitable for experts and nonexperts alike.

High-resolution small RNA structures from exact nuclear Overhauser enhancement measurements without additional restraints

“…Cross-relaxation rate constants ( σ ) and auto-relaxation rate constants ( ρ ) were determined using the full-matrix approach 14, 63 , which is a part of the eNORA2 package 64 that has recently been implemented into the CYANA software package 65, 66 . The protein-specific MATLAB code of eNORA2 has been transcribed into the Fortran programing language and generalized for use with DNA/RNA and any other molecules that can be handled by CYANA 67 .…”

NOE‐Derived Methyl Distances from a 360 kDa Proteasome Complex

“…[35] The distances were extracted from the peaks heights in a" tab" file, which contains the peak assignment in NMRpipe, [33] using eNORA 2. [17] The procedure is fully automated and integrates fitting of cross-peak buildup and diagonal-peak decay curves, correction for spin diffusion and deuteration, and conversion into effective distances. The choice of full-matrix or three-spin approach, overall tumbling time, and deuteration levels are set by the user.…”

“…In the next step, we extracted cross-relaxation rates and the effective distances with the eNORA2 package (see table S2 in the Supporting Information). [17] In total, 18 bi-directional buildups, an additional 14 uni-directional buildupsn ormalized to the spin of origin and 29 normalized to the destination spin could be evaluated. [18] Bi-directional buildupsa re those for which both cross-peaks could be fitted and normalized to their respective diagonal peaks.…”

Extending the Applicability of Exact Nuclear Overhauser Enhancements to Large Proteins and RNA

“…The intensities from the cross and diagonal peaks are then fitted to monoexponential buildup and decay curves by using the eNORA2 package, which has been implemented into the most recent version of CYANA (note that the stand‐alone eNORA2 package coded in MATLAB is available for download but cannot handle RNA molecules). eNORA2 fits diagonal peak decays as a function of the mixing time to determine both the autorelaxation rate constant ( ρ ) as well as the initial magnetization at zero mixing time [Δ M (0)].…”