Name: millisecond hydrogen/deuterium-exchange mass spectrometry for the study of alpha-synuclein structural dynamics under physiological conditions
Uploaded: 2022-06-23T14:30:00
Description: Watch this Scientific Journal Video about Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions at JoVE.com

NS is funded by the University Council Diamond Jubilee Scholarship. JJP is supported by a UKRI Future Leaders Fellowship [Grant number: MR/T02223X/1].

1. Protein expression and purification of aSyn
<ol>
	<li>Prepare aSyn following a previously published report9.</li>
	<li>Dialyze into a safe storage buffer (e.g., Tris, pH 7.2 ).</li>
	<li>If required, concentrate the sample (e.g., spin filter microcentrifuge tubes using 3 kDa MWCO, 14,000 x g for approximately 10-30 min, see Table of Materials). 
	NOTE: It is advised not to concentrate excessively. The integrity of the monomer ensemble has not be...

In the present article, the following procedures are described: (1) performing peptide mapping experiments on monomeric aSyn to obtain the highest sequence coverage, (2) acquiring millisecond HDX-MS data on monomeric aSyn under physiological conditions, and (3) performing data analysis and interpretation of the resulting HDX-MS data. The provided procedures are generally simple to execute, each labeling experiment typically lasts only around 8 h for three replicates and eight timepoints, and the mapping experiment lasts ...

Parkinson&#39;s disease (PD) is a neurodegenerative illness affecting millions of people worldwide1. It is characterized by the formation of cytoplasmic inclusions known as Lewy bodies and Lewy neurites in the brain&#39;s substantia nigra pars compacta region. These cytoplasmic inclusions have been found to contain aggregates of the intrinsically disordered protein aSyn2. In PD and other synucleinopathies, aSyn transforms from a soluble disordered state into an insoluble, highly structured diseased state. In its native form, monomeric aSyn adopts a wide range of conformations stabilized by long-range electrostatic interactions between its N- and C-termini and hydrophobic interactions between its C-terminus and non-amyloid beta component (NAC) region3,4,5,6. Any disruptions in those stabilizing interactions, such as mutations, post-translational modifications, and changes in the local environment, can lead to the misfolding of the monomer, thus triggering the process of aggregation7.
While a vast amount of research exists on the oligomeric and fibrillar forms of aSyn8,9,10,11, there is a crucial need to study the monomeric form of the protein and better understand which conformers are functional (and how) and which are prone to aggregate8,9,10,11. Being intrinsically disordered, only 14 kDa in size, and difficult to crystallize, the aSyn monomer is not amenable to most structural biological techniques. However, one technique capable of measuring the conformational dynamics of monomeric aSyn is millisecond HDX-MS, which has recently generated important structural observations that would be challenging or impossible to obtain otherwise12,13,14. Millisecond HDX-MS sensitively measures the average of the protein conformational ensemble by monitoring the isotopic exchange at amide hydrogens, indicating solvent accessibility and hydrogen-bonding network participation of a particular protein region on the millisecond timescale. It is necessary to stress the millisecond aspect of the HDX-MS as, due to its natively unfolded, meta-stable nature, aSyn exhibits very fast hydrogen-exchange kinetics that manifest well below the lower limit of conventional HDX-MS systems. For example, most of the aSyn molecule has completely exchanged hydrogen for deuterium under intracellular conditions in less than 1 s. Several laboratories have now built fast-mixing instrumentation; in this case, a prototype fast-mixing quench-flow instrument capable of performing HDX-MS with a dead-time of 50 ms and a temporal resolution of 1 ms is used15. While millisecond HDX-MS has recently been acutely important in the study of aSyn, it stands to be valuable in studying intrinsically disordered proteins/regions more widely and a large number of proteins with loops/regions that are only weakly stable. For example, peptide drugs (e.g., insulin; GLP-1/glucagon; tirzepatide) and peptide-fusion proteins (e.g., the HIV inhibitor FN3-L35-T1144) are major drug formats where solution-phase structural and stability information can be a critical input for drug development decisions, and, yet, the peptide moiety is often only weakly stable and intractable by HDX-MS at the seconds timescale16,17,18,19,20. Emergent HDX-MS methods with labeling in the seconds/minutes domains have been shown to derive structural information for DNA G-quadruplexes, but it should be possible to extend this to more diverse oligonucleotide structures by the application of millisecond HDX-MS21.
HDX-MS experiments can be performed at three different levels: (1) bottom-up (whereby the labeled protein is digested proteolytically), (2) middle-down (whereby the labeled protein is digested proteolytically, and the resulting peptides are fragmented further by soft-fragmentation techniques), and (3) top-down (whereby soft-fragmentation techniques directly fragment the labeled protein)22. Thus, sub-molecular HDX-MS data allow us to localize the exchange behavior to specific regions of a protein, making it critical to have adequate sequence coverage for such experiments. The structural resolution of any HDX-MS experiment relies on the number of proteolytic peptides or fragments derived from the protein upon digestion or soft-fragmentation, respectively. In each of the three experiment types outlined above, the change in amide exchange at each peptide/fragment is mapped back onto the protein&#39;s primary structure to indicate the behavior of localized regions of the protein. While the highest structural resolution is achieved through soft-fragmentation, the description of these experiments is out of the scope of the current study, which focuses on the measurement of aSyn monomer conformations. Excellent results can be obtained with the commonly applied &#34;bottom-up&#34; workflow described here.
Here, procedures are provided on (1) how to prepare and handle aSyn samples and HDX-MS buffers, (2) how to perform peptide mapping for a bottom-up HDX-MS experiment, (3) how to acquire HDX-MS data on monomeric aSyn under physiological conditions, specifically in the millisecond time domain (using a custom-built instrument; alternative instruments for millisecond labeling have also been described), and (4) how to process and analyze the HDX-MS data. Methods using monomeric aSyn at physiological pH (7.40) in two solution conditions are exemplified here. While critically useful in the study of aSyn, these procedures can be applied to any protein and are not limited to intrinsically disordered proteins.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 &#215; 100 mm ACQUITY BEH 1.7 &#956;m C18 column&#160;</td>
			<td>Waters Corporation</td>
			<td>186002346</td>
			<td>Analytical column</td>
		</tr>
		<tr>
			<td>Acetonitrile HPLC grade &#62;99.9% HiPerSolv</td>
			<td>VWR</td>
			<td>20060.420</td>
			<td>For LC mobile phases</td>
		</tr>
		<tr>
			<td>CaCl2</td>
			<td>Sigma Aldrich</td>
			<td>C5670</td>
			<td>Salt for HDX buffers</td>
		</tr>
		<tr>
			<td>Chronos</td>
			<td>Axel Semrau (Purchased from Waters Corporation)</td>
			<td>667006090</td>
			<td>Scheduling software to enable multiple HDX-MS sample injections automatically. Alternative software is available from other vendors e.g. HDXDirector or LEAP Shell</td>
		</tr>
		<tr>
			<td>Deuterium chloride</td>
			<td>Goss Scientific (Cambridge Isotope Laboratories)</td>
			<td>DLM-2-50</td>
			<td>For HDX labelling buffers</td>
		</tr>
		<tr>
			<td>Deuterium oxide (99.9% D2O)</td>
			<td>Goss Scientific (Cambridge Isotope Laboratories)</td>
			<td>DLM-4</td>
			<td>Deuterated water</td>
		</tr>
		<tr>
			<td>DynamX 3.0</td>
			<td>Waters Corporation</td>
			<td>176016027</td>
			<td>Isotopic assignment and deuterium incorporation calculation</td>
		</tr>
		<tr>
			<td>Enzymate BEH Pepsin Column</td>
			<td>Waters Corporation</td>
			<td>186007233</td>
			<td>Pepsin digestion column</td>
		</tr>
		<tr>
			<td>Formic Acid, 99.0% LC/MS Grade</td>
			<td>Fisher Scientific</td>
			<td>10596814</td>
			<td>For LC mobile phases</td>
		</tr>
		<tr>
			<td>Guanidinium hydrochloride</td>
			<td>Sigma Aldrich</td>
			<td>RDD001-500G</td>
			<td>Chaotrope/Denaturant</td>
		</tr>
		<tr>
			<td>HDfleX</td>
			<td>University of Exeter</td>
			<td>N/A</td>
			<td>https://ore.exeter.ac.uk/repository/handle/10871/127982</td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Sigma Aldrich</td>
			<td>P3911</td>
			<td>Salt for HDX buffers</td>
		</tr>
		<tr>
			<td>LEAP HDX-2 CTC PAL sampling robot</td>
			<td>Waters Corporation</td>
			<td>725000637</td>
			<td>Autosampler robot</td>
		</tr>
		<tr>
			<td>Leucine enkephalin</td>
			<td>Waters Corporation</td>
			<td>186006013</td>
			<td>For mass spectrometry lockspray calibration.</td>
		</tr>
		<tr>
			<td>MassLynx</td>
			<td>Waters Corporation</td>
			<td>667004007</td>
			<td>Software controlling inlet methods and mass spectrometer</td>
		</tr>
		<tr>
			<td>Maximum recovery vials</td>
			<td>Waters Corporation</td>
			<td>600000670CV</td>
			<td>100 pack including caps - used for quench tray in LEAP HDX-2</td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma Aldrich</td>
			<td>M8266</td>
			<td>Salt for HDX buffers</td>
		</tr>
		<tr>
			<td>Millipore 0.22 &#181;m syringe filters</td>
			<td>Millipore</td>
			<td>N9CA7069B</td>
			<td>Syringe filters</td>
		</tr>
		<tr>
			<td>ms2min</td>
			<td>Applied Photophysics Ltd</td>
			<td>N/A</td>
			<td>fast-mix quench-flow millisecond hdx instrument</td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma Aldrich</td>
			<td>S9888</td>
			<td>Salt for HDX buffers</td>
		</tr>
		<tr>
			<td>Peltier temperature controller</td>
			<td>LEAP Technologies Inc.</td>
			<td>HP115-COOL/D</td>
			<td>Peltier controller to set precise temperature of chambers in the LEAP robot.</td>
		</tr>
		<tr>
			<td>ProteinLynx Global Server 3.0</td>
			<td>Waters Corporation</td>
			<td>715001030</td>
			<td>Peptide identification software. Alternative software is available from other vendors.</td>
		</tr>
		<tr>
			<td>Reagent pot caps</td>
			<td>Waters Corporation</td>
			<td>186004632</td>
			<td>100 pack</td>
		</tr>
		<tr>
			<td>Reagent pots for LEAP HDX-2</td>
			<td>Waters Corporation</td>
			<td>186001420</td>
			<td>100 pack excluding caps - used for buffers in LEAP HDX-2</td>
		</tr>
		<tr>
			<td>Sodium deuteroxide (99.5% in D2O)</td>
			<td>Goss Scientific (Cambridge Isotope Laboratories)</td>
			<td>DLM-57</td>
			<td>For HDX labelling buffers</td>
		</tr>
		<tr>
			<td>Spin filter microcentrifuge tubes (3 kDa MWCO)</td>
			<td>Amicon (Merck Sigma Aldrich)</td>
			<td>UFC5003</td>
			<td>Micro centrifuge tubes to concentrate protein. This facilitates buffer exchange and accurate sample loading for HDX-MS experiments.</td>
		</tr>
		<tr>
			<td>Synapt G2-Si mass spectrometer</td>
			<td>Waters Corporation</td>
			<td>176850035</td>
			<td>Mass spectrometer</td>
		</tr>
		<tr>
			<td>Total recovery vials</td>
			<td>Waters Corporation</td>
			<td>600000671CV</td>
			<td>100 pack including caps - used for labelling tray in LEAP HDX-2</td>
		</tr>
		<tr>
			<td>Tris-HCl</td>
			<td>Sigma Aldrich</td>
			<td>T3253-250G</td>
			<td>Buffer</td>
		</tr>
		<tr>
			<td>Trizma base</td>
			<td>Sigma Aldrich</td>
			<td>T60040-B2005</td>
			<td>Buffer</td>
		</tr>
		<tr>
			<td>Urea</td>
			<td>Sigma Aldrich</td>
			<td>U5378-1KG</td>
			<td>Chaotrope/Denaturant</td>
		</tr>
		<tr>
			<td>VanGuard 2.1 x 5 mm ACQUITY BEH C18 column&#160;</td>
			<td>Waters Corporation</td>
			<td>186004623</td>
			<td>Trap desalting column</td>
		</tr>
	</tbody>
</table>

millisecond hydrogen/deuterium-exchange mass spectrometry for the study of alpha-synuclein structural dynamics under physiological conditions

Alpha-synuclein (aSyn) is an intrinsically disordered protein whose fibrillar aggregates are abundant in Lewy bodies and neurites, which are the hallmarks of Parkinson's disease. Yet, much of its biological activity, as well as its aggregation, centrally involves the soluble monomer form of the protein. Elucidation of the molecular mechanisms of aSyn biology and pathophysiology requires structurally highly resolved methods and is sensitive to biological conditions. Its natively unfolded, meta-stable structures make monomeric aSyn intractable to many structural biology techniques. Here, the application of one such approach is described: hydrogen/deuterium-exchange mass spectrometry (HDX-MS) on the millisecond timescale for the study of proteins with low thermodynamic stability and weak protection factors, such as aSyn. At the millisecond timescale, HDX-MS data contain information on the solvent accessibility and hydrogen-bonded structure of aSyn, which are lost at longer labeling times, ultimately yielding structural resolution up to the amino acid level. Therefore, HDX-MS can provide information at high structural and temporal resolutions on conformational dynamics and thermodynamics, intra- and inter-molecular interactions, and the structural impact of mutations or alterations to environmental conditions. While broadly applicable, it is demonstrated how to acquire, analyze, and interpret millisecond HDX-MS measurements in monomeric aSyn.

Due to its intrinsically disordered nature, it is difficult to capture the intricate structural changes in aSyn at physiological pH. HDX-MS monitors isotopic exchange at backbone amide hydrogens, probing the protein conformational dynamics and interactions. It is one of the few techniques to acquire this information at high structural and temporal resolutions. This protocol is broadly applicable to a wide range of proteins and buffer conditions, and this is exemplified by the measurement of the exchange kinetics of aSyn ...

Watch this Scientific Journal Video about Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions at JoVE.com

Millisecond Hydrogen/Deuterium-Exchange Mass Spectrometry for the Study of Alpha-Synuclein Structural Dynamics Under Physiological Conditions

The structural ensemble of monomeric alpha-synuclein affects its physiological function and physicochemical properties. The present protocol describes how to perform millisecond hydrogen/deuterium-exchange mass spectrometry and subsequent data analyses to determine conformational information on the monomer of this intrinsically disordered protein under physiological conditions.

Alpha-synuclein (aSyn) is an intrinsically disordered protein whose fibrillar aggregates are abundant in Lewy bodies and neurites, which are the hallmarks ...

All organisms have disorder in their proteome, estimated up to 33%These regions are observable by hydrogen/deuterium exchange mass spectrometry, but only in the millisecond time range. Our protocol will show you how to do this successfully. This is a fully automated analytical technique.You just set everything up, program the desired time measurements, hit go and walk away. This technique opens up the exciting opportunity of screening for compounds that stabilize specific confirmations of intrinsically disordered proteins such alpha-synuclein. To begin sample preparation for peptide mapping, first take a vial of stored alpha-synuclein protein stock from the minus 80 degrees Celsius freezer.And once it is thawed, filter using a 0.22 micrometer syringe filter. Then measure the absorbance of the solution at 218 nanometers to determine the protein concentration using Beer-Lambert's law, and dilute the protein with equilibrium buffer to a final concentration of five micromolar. Next, to set up the autosampler robot, add 50 microliters of the five micromolar protein solution to a total recovery vial, and place the vial in the sample position in the right chamber of the hydrogen/deuterium exchange, or HDX, robotics in line with the mass spectrometer.Then put one vial of equilibrium buffer and two vials of pepsin wash buffer to reagent positions one, four, and five of the left chambers and one vial of quench buffer to reagent position one in the HDX right chamber and set the temperature at 20 degrees Celsius using the Peltier temperature controller. Then add an equal number of total recovery vials and maximum recovery vials in the same reaction positions of the HDX left chamber and HDX right chamber respectively. Next, set up a sample list with appropriate LC and MS methods in the scheduling software and start the schedule.To obtain the final peptide coverage map, manually curate the isotopic assignments in the DynamX HDX data analysis software. After cleaning the Fast HDX prototype instrument, open the graphical user interface of the compatible HDX software to initialize the system. Enter 20 degrees Celsius and 0.5 degrees Celsius as the sample chamber and quench chamber temperatures respectively, followed by clicking set to apply the new temperatures.To clean and prepare the instrument, set up the centrifuge tubes with LC/MS grade water at all inlets, then check both left and right syringes in the titrator plumbing delivery tab and continue clicking prime until all latent air bubbles in the tubes are gone. To check all the boxes for syringes, first go to the macros tab and click on calibrate syringes home position, then first click wash syringe load loop, followed by wash all mixing loop volumes. If there is any bubble in a buffer syringe, disconnect the syringe and degas it by vertically ejecting the bubble.Before recalibrating to the zero position, replace the syringe. For setting up the Fast HDX prototype instrument for HDX experiments, first insert the left titration inlet tube into the total recovery vial. To prevent temperature-induced oligomerization and aggregation, place the tube in a tabletop fridge.Next, add 50 milliliters of equilibrium, labeling, quench, and pepsin wash buffers to the respective buffer inlets in the right and left chambers of the instrument, followed by adding 50 milliliters of column wash buffer to the pepsin wash inlet. For priming the protein and column wash lines, check the right and left syringes in the titrator plumbing delivery tab and click prime once. After checking all the boxes for syringes as demonstrated earlier, go to the manual quench flow tab to enter the required settings.For a time course experiment, use the symbolic dot button to enter the times in milliseconds. Then set the trap time to three and the wait for HPLC to trap time plus run time plus 1.5 minutes. If blank experiments are run between sample runs, click on the run blank box after ensuring an entry in the acquisition software for the blank run after each sample run.Once the sample list is ready and the appropriate entries have been highlighted, start the run by clicking play and Fast HDX in the software. For data processing, open the file menu of the file of spectrally assigned peptides from the peptide mapping experiments and click open in the DynamX software, then import the raw files to the DynamX software. After opening the data menu, click on MS Files.To create states for each protein condition being studied, click on new state. To add each HDX time point, click on new exposure, then click new raw. To import raw files, drag each file to the correct position and click OK when finished.After automatically assigning isotopes, manually curate the isotopic assignment to ensure high data quality. Export the cluster data in csv file with the column order as described in the manuscript. Open the data menu in the mass measurement software and click on export cluster data.For data analysis, first load the exported clustered data into the HDX analysis software HDfleX. To fit the experimental data for all experiments and states, select the appropriate back exchange correction methods to get the observed rate constants for the HDX reaction. Then calculate a global significance threshold using a preferred method in HDfleX and perform hybrid significance testing to determine the significant differences across the states compared.The mapping experiment on alpha-synuclein generated a peptide coverage map that covered 100%of the protein sequence with an average redundancy of 3.79. Moreover, this protocol enabled the generation of deuterium uptake curves for different peptides of alpha-synuclein, which were then expressed as fitted and back exchange corrected graphs. It was evident that most hydrogen/deuterium exchange in alpha-synuclein was done by one second.The conformational difference between states A and B of alpha-synuclein was also evident from the higher deuterium uptake by state B both at the peptide and amino acid levels. For such a sensitive technique, it is important to use robust statistical significance tests when comparing data. Here, we used our software HDfleX.

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