This work was supported by funds from NIGMS R35GM133488 and from the Roy J. Carver Charitable Trust to V.V.

1. Preparation of the NMR sample
<ol>
	<li>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.</li>
	<li>Buffer exchange the purified protein sample into a degassed NM...

<ol>
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E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=New+tools+provide+new+insights+in+NMR+studies+of+protein+dynamics.">New tools provide new insights in NMR studies of protein dynamics.</a> Science. 312 (5771), 224-228 (2006).</li><li>Venditti, V., Clore, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+selection+and+substrate+binding+regulate+the+monomer/dimer+equilibrium+of+the+C-terminal+domain+of+Escherichia+coli+enzyme+I.">Conformational selection and substrate binding regulate the monomer/dimer equilibrium of the C-terminal domain of Escherichia coli enzyme I.</a> Journal of Biological Chemistry. 287 (32), 26989-26998 (2012).</li><li>Venditti, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large+interdomain+rearrangement+triggered+by+suppression+of+micro-+to+millisecond+dynamics+in+bacterial+Enzyme+I.">Large interdomain rearrangement triggered by suppression of micro- to millisecond dynamics in bacterial Enzyme I.</a> Nature Communications. 6, 5960 (2015).</li><li>Yip, G. N., Zuiderweg, E. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+phase+cycle+scheme+that+significantly+suppresses+offset-dependent+artifacts+in+the+R2-CPMG+15N+relaxation+experiment.">A phase cycle scheme that significantly suppresses offset-dependent artifacts in the R2-CPMG 15N relaxation experiment.</a> Journal of Magnetic Resonance. 171 (1), 25-36 (2004).</li><li>Mulder, F. A., Skrynnikov, N. R., Hon, B., Dahlquist, F. W., Kay, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+slow+(micros-ms)+time+scale+dynamics+in+protein+side+chains+by+(15)N+relaxation+dispersion+NMR+spectroscopy:+application+to+Asn+and+Gln+residues+in+a+cavity+mutant+of+T4+lysozyme.">Measurement of slow (micros-ms) time scale dynamics in protein side chains by (15)N relaxation dispersion NMR spectroscopy: application to Asn and Gln residues in a cavity mutant of T4 lysozyme.</a> Journal of the American Chemical Society. 123 (5), 967-975 (2001).</li><li>Loria, J. P., Rance, M., Palmer, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+TROSY+CPMG+sequence+for+characterizing+chemical+exchange+in+large+proteins.">A TROSY CPMG sequence for characterizing chemical exchange in large proteins.</a> Journal of Biomolecular NMR. 15 (2), 151-155 (1999).</li><li>Dotas, R. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Hybrid+thermophilic/mesophilic+enzymes+reveal+a+role+for+conformational+disorder+in+regulation+of+bacterial+Enzyme+I.">Hybrid thermophilic/mesophilic enzymes reveal a role for conformational disorder in regulation of bacterial Enzyme I.</a> Journal of Molecular Biology. 432 (16), 4481-4498 (2020).</li><li>Purslow, J. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Active+site+breathing+of+human+Alkbh5+revealed+by+solution+NMR+and+accelerated+molecular+dynamics.">Active site breathing of human Alkbh5 revealed by solution NMR and accelerated molecular dynamics.</a> Biophysical Journal. 115, 1895-1905 (2018).</li><li>Loria, J. P., Rance, M., Palmer, A. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+relaxation-compensated+Carr&#8722;Purcell&#8722;Meiboom&#8722;Gill+sequence+for+characterizing+chemical+exchange+by+NMR+Spectroscopy.">A relaxation-compensated Carr&#8722;Purcell&#8722;Meiboom&#8722;Gill sequence for characterizing chemical exchange by NMR Spectroscopy.</a> Journal of the American Chemical Society. 121 (10), 2331-2332 (1999).</li><li>Hansen, D. F., Vallurupalli, P., Kay, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+improved+15N+relaxation+dispersion+experiment+for+the+measurement+of+millisecond+time-scale+dynamics+in+proteins.">An improved 15N relaxation dispersion experiment for the measurement of millisecond time-scale dynamics in proteins.</a> Journal of Physical Chemistry B. 112 (19), 5898-5904 (2008).</li><li>Tugarinov, V., Kanelis, V., Kay, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isotope+labeling+strategies+for+the+study+of+high-molecular-weight+proteins+by+solution+NMR+spectroscopy.">Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy.</a> Nature Protocols. 1 (2), 749-754 (2006).</li><li>Niklasson, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive+analysis+of+NMR+data+using+advanced+line+shape+fitting.">Comprehensive analysis of NMR data using advanced line shape fitting.</a> Journal of Biomolecular NMR. 69, 93-99 (2017).</li><li>Palmer, A. G., Kroenke, C. D., Loria, J. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclear+magnetic+resonance+methods+for+quantifying+microsecond-to-millisecond+motions+in+biological+macromolecules.">Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules.</a> Methods in Enzymology. 339, 204-238 (2001).</li><li>Tollinger, M., Skrynnikov, N. R., Mulder, F. A., Forman-Kay, J. D., Kay, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Slow+dynamics+in+folded+and+unfolded+states+of+an+SH3+domain.">Slow dynamics in folded and unfolded states of an SH3 domain.</a> Journal of the American Chemical Society. 123, 11341-11352 (2001).</li><li>Carver, J. P., Richards, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+general+two-site+solution+for+the+chemical+exchange+produced+dependence+of+T2+upon+the+Carr-Purcell+pulse+separation.">A general two-site solution for the chemical exchange produced dependence of T2 upon the Carr-Purcell pulse separation.</a> Journal of Magnetic Resonance. 6 (1), 89-105 (1972).</li><li>Egner, T. K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Surface+Contrast'+NMR+Reveals+Non-innocent+Role+of+Support+in+Pd/CeO2+Catalyzed+Phenol+Hydrogenation.">Surface Contrast' NMR Reveals Non-innocent Role of Support in Pd/CeO2 Catalyzed Phenol Hydrogenation.</a> ChemCatChem. 12 (6), 4160-4166 (2020).</li><li>Egner, T. K., Naik, P., Nelson, N. C., Slowing, I. I., Venditti, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanistic+Insight+into+Nanoparticle+Surface+Adsorption+by+Solution+NMR+Spectroscopy+in+an+Aqueous+Gel.">Mechanistic Insight into Nanoparticle Surface Adsorption by Solution NMR Spectroscopy in an Aqueous Gel.</a> Angewandte Chemie (International Edition in English). 56, 9802-9806 (2017).</li><li>Tugarinov, V., Libich, D. S., Meyer, V., Roche, J., Clore, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+energetics+of+a+three-state+protein+folding+system+probed+by+high-pressure+relaxation+dispersion+NMR+spectroscopy.">The energetics of a three-state protein folding system probed by high-pressure relaxation dispersion NMR spectroscopy.</a> Angewandte Chemie (International Edition in English). 54, 11157-11161 (2015).</li><li>Korzhnev, D. M., Kloiber, K., Kanelis, V., Tugarinov, V., Kay, L. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+slow+dynamics+in+high+molecular+weight+proteins+by+methyl-TROSY+NMR+spectroscopy:+application+to+a+723-residue+enzyme.">Probing slow dynamics in high molecular weight proteins by methyl-TROSY NMR spectroscopy: application to a 723-residue enzyme.</a> Journal of the American Chemical Society. 126 (12), 3964-3973 (2004).</li><li>Mayzel, M., Ahlner, A., Lundstrom, P., Orekhov, V. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Measurement+of+protein+backbone+(13)CO+and+(15)N+relaxation+dispersion+at+high+resolution.">Measurement of protein backbone (13)CO and (15)N relaxation dispersion at high resolution.</a> Journal of Biomolecular NMR. 69, 1-12 (2017).</li><li>Pritchard, R. B., Hansen, D. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterising+side+chains+in+large+proteins+by+protonless+(13)C-detected+NMR+spectroscopy.">Characterising side chains in large proteins by protonless (13)C-detected NMR spectroscopy.</a> Nature Communications. 10, 1747 (2019).</li></ol>

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<su...

Carr-Purcell Meiboom-Gill (CPMG) relaxation dispersion (RD) experiments are used on a routine base to characterize conformational equilibria occurring on the &#181;s-ms timescale by solution NMR spectroscopy1,2,3,4,5. 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 &#181;s to ~10 ms. Under these conditions, the observed transverse relaxation rate (<img alt="Equation 1" src="/files/ftp_upload/62395/62395eq01v2.jpg" />) is the sum of the intrinsic R2 (the R2 measured in the absence of &#181;s-ms dynamics, <img alt="Equation 2" src="/files/ftp_upload/62395/62395eq02v3.jpg" />) and the exchange contribution to the transverse relaxation (Rex). The Rex contribution to R2obs can be progressively quenched by reducing the spacing between the 180&#176; 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 proteins4,5,9,10. For smaller systems (&#60;20 kDa), the use of an Heteronuclear Single Quantum Coherence (HSQC)-based pulse sequence11,12 is advisable.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Cryoprobe</td>
			<td>Bruker</td>
			<td>5mm TCI 800 H-C/N-D cryoprobe</td>
			<td>Improve sensitivity</td>
		</tr>
		<tr>
			<td>Deuterium Oxide</td>
			<td>Sigma Aldrich</td>
			<td>756822-1</td>
			<td>&#62;99.8% pure, utilised in preparing NMR samples and deuterated cultures</td>
		</tr>
		<tr>
			<td>Hand driven centrifuge</td>
			<td>United Scientific supply</td>
			<td>CENTFG1</td>
			<td>Used to remove any air bubbles or residual liquid stuck on the walls of NMR tube.</td>
		</tr>
		<tr>
			<td>High Field NMR spectrometer</td>
			<td>Bruker</td>
			<td>Bruker Avance II 600, Bruker Avance 800</td>
			<td>acquisition of the NMR data</td>
		</tr>
		<tr>
			<td>MATLAB</td>
			<td>MathWorks</td>
			<td>https://www.mathworks.com/products/get-matlab.html</td>
			<td>Modeling of the NMR data</td>
		</tr>
		<tr>
			<td>NMR pasteur Pipette</td>
			<td>Corning Incorporation</td>
			<td>7095D-NMR</td>
			<td>Pyrex glass pastuer pipette to transfer liquid sample in NMR tube</td>
		</tr>
		<tr>
			<td>NMR tube</td>
			<td>Willmad Precision</td>
			<td>535-PP-7</td>
			<td>5mm thin wall 7&#39;&#39; cylinderical glass tube</td>
		</tr>
		<tr>
			<td>NMRPipe</td>
			<td>Institute of Biosciences and Biotechnology research</td>
			<td>https://www.ibbr.umd.edu/nmrpipe/install.html</td>
			<td>NMR data processing</td>
		</tr>
		<tr>
			<td>SPARKY</td>
			<td>University of California, San Francisco</td>
			<td>https://www.cgl.ucsf.edu/home/sparky/</td>
			<td>Analysis of the NMR data</td>
		</tr>
		<tr>
			<td>Tospin 3.2 (or newer)</td>
			<td>Bruker</td>
			<td>https://www.bruker.com/protected/en/services/software-downloads/nmr/pc/pc-topspin.html</td>
			<td>acquisition software</td>
		</tr>
	</tbody>
</table>

15n cpmg relaxation dispersion for the investigation of protein conformational dynamics on the &#181;s-ms timescale

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 &#181;s-ms timescale. Here, the study presents detailed protocols for acquisition and analysis of a&#160;15N relaxation dispersion experiment. As an example, the pipeline for the analysis of the &#181;s-ms dynamics in the C-terminal domain of bacteria Enzyme I is shown.

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 Rex on the 3D structure of the protein under investigation, it is possible to identify the structural reg...

Watch this Scientific Journal Video about 15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the Âµs-ms Timescale at JoVE.com

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the  &amp;#181;s-ms Timescale

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.

15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the &#181;s-ms Timescale

Protein conformational dynamics play fundamental roles in regulation of enzymatic catalysis, ligand binding, allostery, and signaling, which are important ...

This protocol can be used for detection and characterization of protein conformational dynamics, which are essential for understanding a large variety of cellular processes. Compared to other methods, this method does not require specialized sample preparation steps and provides in comprehensive characterization of the kinetics, thermodynamics, and structural aspects of confirmational equilibrium. CPMG relaxation dispersion can be applied more widely for the characterization of confirmational dynamics in nucleic acids and other biomolecules, as well as for the characterization of ligand nanoparticle interactions.Our protocol is aimed at first-time CPMG users. So it is a good starting point. However, we do expect users to know the basic steps for running conventional NMR experiments.To set up an NMR experiment for the first time, first download and unzip these supplemental files. Copy the Bits. vv and trosy_15N_CPMG.vv files in the pulse program folder to the pulse program directory. Open the acquisition software and use the EDC command to copy a previously run hydrogen nitrogen 15 HSQC experiment into a new experiment. Use the pulse program command to load the trosy_15N_CPMG.vv pulse program file into the newly created experiment. Then use the instructions from the end of the pulse program file to set up the CPMG experiment. To set up a routine NMR experiment, introduce the sample to the magnet and perform all of the basic NMR acquisition steps.Set P1 to the duration of the hydrogen hard 90 degree pulses and P7 to the duration nitrogen 15 hard 90 degree pulses. In the acquisition window, set the center and spectral width for the hydrogen and nitrogen 15 dimensions. Set the relaxation delay to 0.7 T2 and use the VC list command to create a list of integer numbers corresponding to N.After confirming that each entry in the list corresponds to a different CPMG field according to CPMG filed equals times 4N divided by D30, check that the first number in the list is zero.Set L8 to the number of entries in the VC list, L3 to the number of real points for the indirect dimension, and 1TD to L8 times L3 times two. To optimize the water suppression, set the receiver gain to one and type EDC pull to open the pulse program file. On line 91, remove the semi-colon preceding goto 999, and save the file.Using the GS command, adjust the SPDB0 parameters to minimize the intensity of the FID signal. When the signal intensity has been modified, reintroduce a semi-colon at line 91 of the pulse program file and save the file. To optimize SPDB11, set the receiver gain to one and the type EDC pull to open the pulse program file.On line 168, remove the semi-colon preceding goto 999, and save the file. Using the GS command, adjust the SPDB11 parameters to minimize the intensity of the FID signal. When the signal intensity has been modified, reintroduce the semi-colon at line 168 and save the file.To optimize SPDB2, set the receiver gain to one and enter EDC pull to open the pulse program file. On line 179, remove the semi-colon preceding goto 999, and save the file. Using the GS command, adjust the SPDB2 parameters to minimize the intensity of the FID signal.When the signal intensity has been modified, re-introduce the semi-colon at line 179 of the pulse program file and save the file. To optimize PLDB2, set the receiver gain to one and enter EDC pull to open the pulse program file. On line 184, remove the semi-colon preceding goto 999, and save the file.Using the GS command, adjust the PLDB2 parameters to minimize the intensity of the FID signal. When the signal intensity has been modified, reintroduce the semi-colon at line 184 of the pulse program file and save the file. Run the RGA command to optimize the receiver gain.Then run the ZG command to start the experiment. In this figure, the results of the relaxation dispersion profiles acquired for each peak in the hydrogen nitrogen 15 Trosy spectrum can be observed. From the acquired relaxation dispersion profiles, it's possible to estimate the exchange contribution to the nitrogen 15 transverse relaxation of each backbone AMI group.By plotting the transverse relaxation on the 3D structure of the protein under investigation it's possible to identify the structural regions undergoing confirmational exchange on the microsecond millisecond timescale. Modeling of the relaxation dispersion curves using the Carver-Richards equations returns the thermodynamic and kinetic parameters on the exchange process, such as the fractional populations of the states in equilibrium and the rate of exchange among these states. The temperature dependence of these thermodynamic and kinetic parameters can then be modeled using the van't Hoff and I-ring equations, respectively, to obtain detailed information on the energetics of the confirmational exchange.It is crucial to carefully optimize all of the acquisition parameters, in particular P7.It is also important to produce highly pure and homogenous samples to avoid spurious dispersions. The kinetic, thermodynamic, and chemical chip parameters obtained using this protocol can be used to derive energetic and structural information about the species undergoing the confirmational exchange. Characterization of the protein confirmational dynamics obtained by CPMG methods provides crucial information towards understanding signaling and enzymatic activity, as well as new perspectives for drug design.

15n-cpmg-relaxation-dispersion-for-investigation-protein

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Biochemistry

4.8K vistas.  Iowa State University. Este protocolo se puede utilizar para la detección y caracterización de la dinámica conformacional de proteínas, que son esenciales para la comprensión de una gran variedad de procesos celulares. En comparación con otros métodos, este método no requiere pasos especializados en la preparación de muestras y proporciona una caracterización exhaustiva de la cinética, la termodinámica y los aspectos estructurales del equilibrio de confirmación. La dispersión de relajación cpmg se pu...