15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale

Summary

Here, a detailed description of the protocol implemented in the laboratory for acquisition and analysis of ¹⁵N relaxation dispersion profiles by solution NMR spectroscopy is provided.

Abstract

Protein conformational dynamics play fundamental roles in regulation of enzymatic catalysis, ligand binding, allostery, and signaling, which are important biological processes. Understanding how the balance between structure and dynamics governs biological function is a new frontier in modern structural biology and has ignited several technical and methodological developments. Among these, CPMG relaxation dispersion solution NMR methods provide unique, atomic-resolution information on the structure, kinetics, and thermodynamics of protein conformational equilibria occurring on the µs-ms timescale. Here, the study presents detailed protocols for acquisition and analysis of a ¹⁵N relaxation dispersion experiment. As an example, the pipeline for the analysis of the µs-ms dynamics in the C-terminal domain of bacteria Enzyme I is shown.

Introduction

Carr-Purcell Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments are used on a routine base to characterize conformational equilibria occurring on the µs-ms timescale by solution NMR spectroscopy^1,2,3,4,5. Compared to other methods for investigation of conformational dynamics, CPMG techniques are relatively easy to implement on modern NMR spectrometers, do not require specialized sample preparation steps (i.e., crystallization, sample freezing or alignment, and/or covalent conjugation with a fluorescent or paramagnetic tag), and provide a comprehensive characterization of conformational equilibria returning structural, kinetic, and thermodynamic information on exchange processes. In order for a CPMG experiment to report on a conformational equilibrium, two conditions must apply: (i) the observed NMR spins must possess different chemical shifts in the states undergoing conformational exchange (microstates) and (ii) the exchange has to occur at a time scale ranging from ~50 µs to ~10 ms. Under these conditions, the observed transverse relaxation rate () is the sum of the intrinsic R₂ (the R₂ measured in the absence of µs-ms dynamics, ) and the exchange contribution to the transverse relaxation (R_ex). The R_ex contribution to R₂^obs can be progressively quenched by reducing the spacing between the 180° pulses constituting the CPMG block of the pulse sequence, and the resulting RD curves can be modeled using the Bloch-McConnell theory to obtain the chemical shift difference among microstates, the fractional population of each microstate, and the rates of exchange among microstates (Figure 1)^1,2,3.

Several different pulse sequences and analysis protocols have been reported in the literature for ¹⁵N CPMG experiments. Herein, the protocol implemented in the laboratory is described. In particular, the crucial steps for preparation of the NMR sample, set up and acquisition of the NMR experiments, and processing and analysis of the NMR data will be introduced (Figure 2). To facilitate transfer of the protocol to other laboratories, the pulse program, processing and analysis scripts, and one example dataset are provided as Supplemental Files and are available for download at (https://group.chem.iastate.edu/Venditti/downloads.html). The provided pulse sequence incorporates a four-step phase cycle in the CPMG block for suppression of offset-dependent artifacts⁶ and it is coded for acquisition of several interleaved experiments. These interleaved experiments have an identical relaxation period but different numbers of refocusing pulses in order to achieve different CPMG fields⁷. It is also important to notice that the described pulse program measures the ¹⁵N R₂ of the TROSY component of the NMR signal⁸. Overall, the protocol has been successfully applied for the characterization of conformational exchange in medium and large-sized proteins^4,5,9,10. For smaller systems (<20 kDa), the use of an Heteronuclear Single Quantum Coherence (HSQC)-based pulse sequence^11,12 is advisable.

Protocol

1. Preparation of the NMR sample

1. Express and purify a ²H,¹⁵N-labled sample of the protein of interest.
   NOTE: While a ¹⁵N-labeled protein sample can be used for acquisition of the CPMG RD experiment, perdeuteration (where possible) dramatically increases the quality of the obtained data. Protocols for the production of perdeuterated proteins are available in the literature¹³.
2. Buffer exchange the purified protein sample into a degassed NMR buffer.
3. Transfer the NMR sample into the NMR tube.
   NOTE: The concentration of the NMR sample needs to be carefully optimized in order to maximize the signal-to-noise ratio and minimize the occurrence of protein-protein interactions. In general, the typical concentration range for CPMG experiments is 0.1-1.0 mM.

2. First time set-up of the NMR experiment

1. Download and unzip the Supplemental Files.
2. Copy the files bits.vv and trosy_15N_cpmg.vv (located the in the folder named pulseprogram) into the pulse program directory (<path>/exp/stan/nmr/lists/pp/user).
   NOTE: Make sure the path to bits.vv listed on the first line of the trosy_15N_cpmg.vv file is correct.
3. Open acquisition software and copy a previously run ¹H-¹⁵N HSQC experiment into a new experiment using the command edc.
4. Using the command pulprog, load the pulse program trosy_15N_cpmg.vv into the newly created experiment.
5. Set up the CPMG experiment using the instructions provided at the end of the pulse program file (trosy_15N_cpmg.vv).

3. Routine set-up of the NMR experiment

1. Introduce the sample in the magnet and perform all the basic steps for acquisition of any NMR experiment: lock and shim the sample; match and tune the ¹H and ¹⁵N channels.
2. Set p1 and p7 to the duration of the ¹H and ¹⁵N hard 90° pulses, respectively.
   NOTE: For optimal results, it is important to calibrate the ¹⁵N 90° pulse with great care. Calibration is usually accomplished using a 100 mM sample of ¹⁵N-labeled urea in DMSO as described in the spectrometer manual. In addition, it is possible to double-check the calibration directly on the working NMR sample by acquiring the first increment of a ¹H-¹⁵N HSQC spectrum in which the ¹⁵N 90° pulse of the first INEPT block is switched to a 180° pulse. If the calibration is correct, a null should be obtained.
3. In the acquisition window, set the center and spectral width for the ¹H and ¹⁵N dimensions.
   NOTE: Center the ¹H spectrum at the frequency of the water signal for optimal water suppression.
4. Set the relaxation delay (d30) equal to 0.7 T₂, where T₂ is the expected ¹⁵N transverse relaxation time of your protein.
   NOTE: The value of d30 can be optimized empirically to obtain the best results.
5. Use the command vclist to create a list of integer numbers corresponding to the parameter n in Figure 1A and Figure 1B. Ensure that each entry in the list corresponds to a different CPMG field (ν_cpmg) according to ν_cpmg = 4 x n / d30. Make sure that the first number in the list is 0 (this corresponds to the reference experiment for which the CPMG block is skipped and d30 = 0 s) and not to use numbers larger than 1,000 x d30 / 4. Numbers larger than this threshold result in ν_cpmg > 1 kHz and might damage the probe.
6. Set l8 to the number of entries in the vclist, l3 to the number of real points for the indirect dimension (usually a range of 64-200 is set for l3), and 1 td equal to l8 x l3 x 2.
   NOTE: Perform the steps 3.7-3.11 to optimize the water suppression.
7. Set the receiver gain (rg) to 1; open the pulse program file (edcpul), go to line 91, remove the semicolon preceding goto 999, and save the file.
8. Using the command gs adjust the parameters spdb0 (or spdw0) in order to minimize the intensity of the FID signal.
9. Reintroduce the semicolon at line 91 of the pulse program file and save the file.
10. Repeat the steps 3.7-3.9 to optimize spdb11 (line 168 of the pulse program file), spdb2 (line 179 of the pulse program file), and pldb2 (line 184 of the pulse program file).
11. Run the command rga to optimize the receiver gain.
12. Set the number of scans (ns) to a multiple of 8.
13. Run the command zg to start the experiment.

4. Processing and analysis of the NMR data

1. Copy the folder named Process (Supplemental Files) into the directory containing the ser file.
2. Use the files sep_fid.com and ft2D.com to process the NMR data.
   NOTE: Instruction as to how to edit the processing scripts is provided within the sep_fid.com and ft2D.com files.
3. Open the ucsf files contained in the directory CPMG_Sparky_files in Sparky.
   NOTE: The ucsf files are created by the processing scripts. There is one ucsf file for each entry in the vclist. The first ucsf file (test_1.ucsf) contains the reference experiment. The subsequent ucsf files (test_2.ucsf, test_3.ucsf,… test_n.ucsf) are ordered from the lowest to the largest value of ν_cpmg.
4. Pick the NMR cross-peaks on the reference NMR spectrum (test_1.ucsf).
5. Select all the picked cross-peaks using the Sparky command pa.
6. Run the Sparky command rh. This command opens a dialogue window. Select the option heights at the same position in each spectrum. Click on Setup and check all the NMR spectra. Click on Update and save the output file in the working directory. The output file contains the matrix of the signal intensities over all opened NMR spectra.
   NOTE: More accurate protocols that use lineshape fitting for recovering intensities from interleaved pseudo-3D experiments have been described in the literature¹⁴. Freely available software for lineshape fitting is available at https://pint-nmr.github.io/PINT/ (PINT), https://www.ucl.ac.uk/hansen-lab/fuda/ (FUDA), and within NMRPipe (nLinLS module) and SPARKY (it module).
7. For each CPMG field, convert the signal intensities to R₂ rates using the formula , where I₀ and I_d30 are the intensity of the reference (vc = 0) and relaxed (vc > 0) NMR spectra, respectively.
   NOTE: In the Supplemental Files, a template of the spreadsheet file (R2_calc.xls) used to convert the signal intensities to R₂ rates and to visualize the RD profiles is provided.
8. Read the noise level in the reference spectrum using the Sparky command st and propagate the error on the R₂ rates.
   NOTE: In the Supplemental Files, a template of the spreadsheet file (R2_calc.xls) used to propagate the error on the measured R₂ rates is provided.

5. Fitting RD curves

1. Copy the folder named RD_fitting (Supplemental Files) into the working directory.
2. For each assigned NMR peak, estimate R_ex by calculating the . and are the R₂ rates measured at the lowest and highest ν_cpmg in the vclist.
3. Visually inspect the RD curves with R_ex larger than two times the estimated error and discard all the RD curves that are too noisy to be modeled accurately.
   NOTE: Noise on R_ex can be propagated from the errors on and .
4. Prepare an input file for the fitting script using all RD curves with R_ex larger than two times the estimated error.
   NOTE: Detailed instruction on the preparation of the input files are provided within the fitting scripts. Example input files are provided as Supplemental Files. Commonly, RD data are measured at two different static fields and fitted simultaneously. In this protocol, two different input files are required (Supplemental Files).
5. Fit the RD data using the scripts provided in Supplemental Files.
   NOTE: Two different scripts are provided to perform a residue-based or a global fit of the RD curves, respectively. Both scripts fit the RD curves using a two-site exchange model and the Carver-Richards equation. More detailed instructions are provided within the fitting scripts. Additional software packages such as Chemex (https://github.com/gbouvignies/ChemEx) and CATIA (https://www.ucl.ac.uk/hansen-lab/catia/ ) are available to carry out data fitting using the Block-McConnell equations.
6. Test the reliability of the fitted parameters estimating the reduced χ² as a function of p_b and k_ex.
   NOTE: The reduced χ² is provided in the output file. p_b and k_ex can be restrained to specific values using lower and upper bounds in the fitting procedures. In our scripts, the lower and upper bounds for p_b are lb(2) and ub(2), respectively. The lower and upper bounds for k_ex are lb(3) and ub(3), respectively.
7. Estimate the error on the fitted parameters. This can be done by setting the value of MC_fac in the script to 1 and repeating the fitting multiple times (typically >20 repeats). The error on each parameter is estimated as the standard deviation of the distribution.
   NOTE: Setting MC_fac to 1 generates a synthetic dataset in which a Gaussian distributed error (calculated based on the experimental error) is added to the experimental data.

Results

The protocol described here results in acquisition of RD profiles for each peak in the ¹H-¹⁵N TROSY spectrum (Figure 3A). From the acquired RD profiles, it is possible to estimate the exchange contribution to the ¹⁵N transverse relaxation of each backbone amide group (Figure 3A,3B). By plotting the R_ex on the 3D structure of the protein under investigation, it is possible to identify the structural reg...

Discussion

This manuscript describes the protocol implemented in the laboratory for acquisition and analysis of ¹⁵N RD data on proteins. In particular, the crucial steps for preparation of the NMR sample, measurement of the NMR data, and analysis of the RD profiles are covered. Below some important aspects regarding the acquisition and analysis of RD experiments are discussed. However, for a more in-depth description of the experiment and data analysis, careful studying of the original literature is highly recommended

Materials

Name	Company	Catalog Number	Comments
Cryoprobe	Bruker	5mm TCI 800 H-C/N-D cryoprobe	Improve sensitivity
Deuterium Oxide	Sigma Aldrich	756822-1	>99.8% pure, utilised in preparing NMR samples and deuterated cultures
Hand driven centrifuge	United Scientific supply	CENTFG1	Used to remove any air bubbles or residual liquid stuck on the walls of NMR tube.
High Field NMR spectrometer	Bruker	Bruker Avance II 600, Bruker Avance 800	acquisition of the NMR data
MATLAB	MathWorks	https://www.mathworks.com/products/get-matlab.html	Modeling of the NMR data
NMR pasteur Pipette	Corning Incorporation	7095D-NMR	Pyrex glass pastuer pipette to transfer liquid sample in NMR tube
NMR tube	Willmad Precision	535-PP-7	5mm thin wall 7'' cylinderical glass tube
NMRPipe	Institute of Biosciences and Biotechnology research	https://www.ibbr.umd.edu/nmrpipe/install.html	NMR data processing
SPARKY	University of California, San Francisco	https://www.cgl.ucsf.edu/home/sparky/	Analysis of the NMR data
Tospin 3.2 (or newer)	Bruker	https://www.bruker.com/protected/en/services/software-downloads/nmr/pc/pc-topspin.html	acquisition software