Name: analyzing protein dynamics using hydrogen exchange mass spectrometry
Uploaded: 2013-11-29T15:30:00
Description: Watch this Scientific Journal Video about Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry at JoVE.com

We thank M. Boysen for comments on the manuscript. This project was funded by the Deutsche Forschungsgemeinschaft (SFB638 and MA 1278/4-1 to M.P.M., and Cluster of Excellence: CellNetworks EXC 81/1). M.P.M. is investigator of the Cluster of Excellence: CellNetworks.

1. Preparation of Buffers and Protein Samples
<ol>
	<li>Prepare H2O buffer. Use Hsp90 standard buffer (40 mM HEPES/KOH, pH 7.5, 50 mM KCl, 5 mM MgCl2, 10% glycerol) as H2O buffer. 
	Note: If the sample was dialyzed before analysis, use the dialysis buffer as H2O buffer. It is essential that the D2O buffer differs from the H2O buffer only in the hydrogen isotope. Volatile buffers like NH4CO3 or NH4-ac...

<ol>
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L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Determination+of+amide+hydrogen+exchange+by+mass+spectrometry:+a+new+tool+for+protein+structure+elucidation.">Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation.</a> Protein Sci. 2 (4), 522-531 (1993).</li><li>Cravello, L., Lascoux, D., Forest, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+different+proteases+working+in+acidic+conditions+to+improve+sequence+coverage+and+resolution+in+hydrogen/deuterium+exchange+of+large+proteins.">Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins.</a> Rapid Commun. Mass Spectrom. : RCM. 17 (21), 2387-2393 (2003).</li><li>Rand, K. D., Zehl, M., Jensen, O. N., J&#248;rgensen, T. J. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+hydrogen+exchange+measured+at+single-residue+resolution+by+electron+transfer+dissociation+mass+spectrometry.">Protein hydrogen exchange measured at single-residue resolution by electron transfer dissociation mass spectrometry.</a> Anal chem. 81 (14), 5577-5584 (2009).</li><li>Pan, J., Han, J., Borchers, C. H., Konermann, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Electron+capture+dissociation+of+electrosprayed+protein+ions+for+spatially+resolved+hydrogen+exchange+measurements.">Electron capture dissociation of electrosprayed protein ions for spatially resolved hydrogen exchange measurements.</a> J. Am. Chem. Soc. 130 (35), 11574-11575 (2008).</li><li>Yamada, N., Suzuki, E. -. I., Hirayama, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+the+interface+of+a+large+protein-protein+complex+using+H/D+exchange+and+Fourier+transform+ion+cyclotron+resonance+mass+spectrometry.">Identification of the interface of a large protein-protein complex using H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry.</a> Rapid Commun. Mass Spectrom. 16 (4), 293-299 (2002).</li><li>Lee, T., Hoofnagle, A. N., 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=Docking+motif+interactions+in+MAP+kinases+revealed+by+hydrogen+exchange+mass+spectrometry.">Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry.</a> Mol. Cell. 14 (1), 43-55 (2004).</li><li>Hasan, A., Smith, D. L., Smith, J. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Alpha-crystallin+regions+affected+by+adenosine+5'-triphosphate+identified+by+hydrogen-deuterium+exchange.">Alpha-crystallin regions affected by adenosine 5'-triphosphate identified by hydrogen-deuterium exchange.</a> Biochem. 41 (52), 15876-15882 (2002).</li><li>Lanman, J., Lam, T. T., Emmett, M. R., Marshall, A. G., Sakalian, M., Prevelige, P. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Key+interactions+in+HIV-1+maturation+identified+by+hydrogen-deuterium+exchange.">Key interactions in HIV-1 maturation identified by hydrogen-deuterium exchange.</a> Nat. Struct. Mol. Biol. 11 (7), 676-677 (2004).</li><li>Wang, L., Lane, L. C., Smith, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detecting+structural+changes+in+viral+capsids+by+hydrogen+exchange+and+mass+spectrometry.">Detecting structural changes in viral capsids by hydrogen exchange and mass spectrometry.</a> Protein Sci. 10 (6), 1234-1243 (2001).</li><li>Pan, H., Raza, A. S., Smith, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Equilibrium+and+kinetic+folding+of+rabbit+muscle+triosephosphate+isomerase+by+hydrogen+exchange+mass+spectrometry.">Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry.</a> J. Mol. Biol. 336 (5), 1251-1263 (2004).</li><li>Mazon, H., Marcillat, O., Forest, E., Smith, D. L., Vial, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+dynamics+of+the+GdmHCl-induced+molten+globule+state+of+creatine+kinase+monitored+by+hydrogen+exchange+and+mass+spectrometry.">Conformational dynamics of the GdmHCl-induced molten globule state of creatine kinase monitored by hydrogen exchange and mass spectrometry.</a> Biochem. 43 (17), 5045-5054 (2004).</li><li>Lanman, J., Lam, T. T., 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=Identification+of+novel+interactions+in+HIV-1+capsid+protein+assembly+by+high-resolution+mass+spectrometry.">Identification of novel interactions in HIV-1 capsid protein assembly by high-resolution mass spectrometry.</a> J. Mol. Biol. 325 (4), 759-772 (2003).</li><li>Rist, W., Graf, C., Bukau, B., Mayer, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Amide+hydrogen+exchange+reveals+conformational+changes+in+hsp70+chaperones+important+for+allosteric+regulation.">Amide hydrogen exchange reveals conformational changes in hsp70 chaperones important for allosteric regulation.</a> J. Biol. chem. 281 (24), 16493-16501 (2006).</li><li>Graf, C., Stankiewicz, M., Kramer, G., Mayer, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spatially+and+kinetically+resolved+changes+in+the+conformational+dynamics+of+the+Hsp90+chaperone+machine.">Spatially and kinetically resolved changes in the conformational dynamics of the Hsp90 chaperone machine.</a> EMBO J. 28 (5), 602-613 (2009).</li><li>Lee, C. -. T., Graf, C., Mayer, F. J., Richter, S. M., Mayer, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamics+of+the+regulation+of+Hsp90+by+the+co-chaperone+Sti1.">Dynamics of the regulation of Hsp90 by the co-chaperone Sti1.</a> EMBO J. 31 (6), 1518-1528 (2012).</li><li>Lou, X., Kirchner, 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=Deuteration+distribution+estimation+with+improved+sequence+coverage+for+HX/MS+experiments.">Deuteration distribution estimation with improved sequence coverage for HX/MS experiments.</a> Bioinformatics. 26 (12), 1535-1541 (2010).</li><li>Kreshuk, A., Stankiewicz, M., Lou, X., Kirchner, M., Hamprecht, F. A., Mayer, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+detection+and+analysis+of+bimodal+isotope+peak+distributions+in+H/D+exchange+mass+spectrometry+using+HeXicon.">Automated detection and analysis of bimodal isotope peak distributions in H/D exchange mass spectrometry using HeXicon.</a> Intl. J. mass spectrom. 302 (1-3), 125-131 (2011).</li><li>Walters, B. T., Ricciuti, A., Mayne, L., Englander, S. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Minimizing+back+exchange+in+the+hydrogen+exchange-mass+spectrometry+experiment.">Minimizing back exchange in the hydrogen exchange-mass spectrometry experiment.</a> J. Am. Soc. Mass Spectrom. 23 (12), 2132-2139 (2012).</li><li>Weis, D. D., Wales, T. E., Engen, J. R., Hotchko, M., Ten Eyck, L. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+and+characterization+of+EX1+kinetics+in+H/D+exchange+mass+spectrometry+by+peak+width+analysis.">Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis.</a> J. Am. Soc. Mass Spectrom. 17 (11), 1498-1509 (2006).</li><li>Fang, J., Rand, K. D., Beuning, P. J., Engen, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=False+EX1+signatures+caused+by+sample+carryover+during+HX+MS+analyses.">False EX1 signatures caused by sample carryover during HX MS analyses.</a> Intl. J. Mass Spectrom. 302 (1-3), 19-25 (2011).</li><li>Deng, Y., Smith, D. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+unfolding+domains+in+large+proteins+by+their+unfolding+rates.">Identification of unfolding domains in large proteins by their unfolding rates.</a> Biochem. 37 (18), 6256-6262 (1998).</li><li>Wales, T. E., Engen, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Partial+unfolding+of+diverse+SH3+domains+on+a+wide+timescale.">Partial unfolding of diverse SH3 domains on a wide timescale.</a> J. Mol. Biol. 357 (5), 1592-1604 (2006).</li><li>Pan, Y., Piyadasa, H., O'Neil, J. D., Konermann, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+dynamics+of+a+membrane+transport+protein+probed+by+h/d+exchange+and+covalent+labeling:+the+glycerol+facilitator.">Conformational dynamics of a membrane transport protein probed by h/d exchange and covalent labeling: the glycerol facilitator.</a> J. Mol. Biol. 416 (3), 400-413 (2012).</li><li>Hebling, C. M., Morgan, C. R., Stafford, D. W., Jorgenson, J. W., Rand, K. D., Engen, J. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Conformational+analysis+of+membrane+proteins+in+phospholipid+bilayer+nanodiscs+by+hydrogen+exchange+mass+spectrometry.">Conformational analysis of membrane proteins in phospholipid bilayer nanodiscs by hydrogen exchange mass spectrometry.</a> Anal chem. 82 (13), 5415-5419 (2010).</li><li>Abzalimov, R. R., Kaplan, D. A., Easterling, M. L., Kaltashov, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+conformations+can+be+probed+in+top-down+HDX+MS+experiments+utilizing+electron+transfer+dissociation+of+protein+ions+without+hydrogen+scrambling.">Protein conformations can be probed in top-down HDX MS experiments utilizing electron transfer dissociation of protein ions without hydrogen scrambling.</a> J. Am. Soc. Mass Spectrom. 20 (8), 1514-1517 (2009).</li></ol>

Binding of an interaction partner to a protein inevitably causes changes in solvent accessibility on the binding site. Additionally, many proteins undergo dynamic conformational changes upon binding, which affect other regions than the actual binding interface. HX-MS is a robust method to monitor these changes and is even capable of revealing conformational changes in proteins on timescales that other methods cannot cover.
To successfully perform HX-MS three points are critical: 1) an optimal ...

The number of crystal structures of proteins and protein complexes increased rapidly in recent years. They present invaluable snapshots of the structural organization of these proteins and provide a basis for structure-function analysis. However, the dynamics of proteins and the conformational changes, which are essential for their functions, are rarely revealed by X-ray crystallography. Cryo-electronmicroscopy, on the other hand, is able to capture protein and protein complexes in different conformations but generally cannot resolve conformational changes down to secondary structure level1. Conformational dynamics of proteins in solution at atomic details can only be resolved by NMR, but this method is still restricted to proteins of relatively small sizes (generally &#8804; 30 kDa) and needs high concentrations of proteins (&#8805; 100 &#956;M), which hampers experiments with oligomerization or aggregation prone proteins2. One method that is able to bridge between high-resolution X-ray crystallography and cryo-electronmicroscopy and which is not limited by protein size or concentration is amide hydrogen-1H/2H-exchange (HX) in combination with mass spectrometry (MS). In recent years this method has developed to a valuable analytical tool for the analysis of protein dynamics, protein folding, protein stability and conformational changes3-5. The molecular basis of this method is the labile nature of backbone amide hydrogens in proteins, which will exchange with deuterium atoms when the protein is placed in a D2O solution. The subsequent increase in protein mass over time is measured with high-resolution MS.
In short unstructured peptides HX only depends on temperature, catalyst concentration (OH-, H3O+ i.e. pH, see Figure 3) and amino acid side chains of adjacent residues due to inductive, catalytic and steric effects. These effects on the intrinsic chemical exchange rate kch have been elegantly quantified by Bai et al.6 and a program is available (courtesy Z. Zhang), which calculates kch for each amino acid within a polypeptide dependent on pH and temperature. At neutral pH and ambient temperatures kch is in the order of 101-103&#160;sec-1. In folded proteins HX can be 2-9 orders of magnitude slower mainly due to hydrogen bonding in the secondary structure and to a minor degree due to restricted access of hydrated OH- ions to the interior of a tightly folded protein. HX in native proteins therefore implicates&#160;partial or global unfolding, chemical exchange and refolding to the native state according to equation (1) and the observed exchange rates kobs depend on the opening rate kop, the closing rate kcl and the intrinsic chemical exchange rate kch according to equation (2).
<img alt="Equations 1-2" src="/files/ftp_upload/50839/50839eq1-2.jpg" /> 
Under native state conditions kop is much smaller than kch and can be neglected in the denominator. There are two extreme exchange regimes called EX1 and EX2. If the kcl is much smaller than kch (EX1) the observed rate is practically equal to the opening rate and HX allows immediate observation of the unfolding of a structural element. Such an exchange regime, where all amide protons exchange at once upon opening of the structural element, is readily observable in MS by a bimodal distribution of the isotope peaks7. If kcl is much greater than kch (EX2) the observed rate is proportional to kch whereby the proportionality constant is equal to the folding-unfolding equilibriums constant Ku = kop/kcl. Under these conditions, many opening and closing events are necessary before all amide protons exchange for deuterons, leading to a gradual increase in average mass while the isotopic distribution remains roughly the same. The EX2 regime allows the determination of the free energy of unfolding &#916;Gu and therefore the stability of a structural element. Under native state condition the EX2 regime is most common. Increase of pH and addition of chaotropic agents can shift the exchange mechanism to EX1. Therefore, HX-MS can be used to explore thermodynamic as well as kinetic parameters of protein folding and conformational changes.
As mentioned above HX is intrinsically pH and temperature dependent and the exchange half-life of a completely solvent exposed proton of the backbone amide group is between 5-400 msec at physiological pH (pH 7.6) and 30 &#176;C, but 10 min to &#62;15 hr with an average of &#62;2 hr at pH 2.9 and 0 &#176;C (except for the proton of the first backbone amide bond of a polypeptide, which exchanges with a half-life of ca. 1-2 min). Under such slow exchanging conditions it is possible to digest the sample using proteases (e.g. pepsin) that are active under these conditions, with out losing all the information contained in the incorporated deuterons. Since the introduction of peptic digestion under slow exchanging conditions, not only the overall HX kinetics of full-length proteins can be analyzed but HX can be localized to specific regions8,9. Spatial resolution is currently limited to the size of the peptic fragments generated, which is in general between 10-30 residues. However, overlapping fragments created due to the nonspecific nature of cleavage by pepsin could lead to an increase in spatial resolution. In addition, several other proteases were found to be active under quench conditions, however, much less efficient than pepsin10. Further increase of spatial resolution can be reached by fragmentation of peptides in the gas phase by methods that preserved the deuteration pattern such as electron capture dissociation (ECD), electron transfer dissociation (ETD) and infrared multiphoton dissociation (IRMPD)11-13. These techniques prevent the loss of spatial resolution due to intramolecular proton migration (&#34;scrambling&#34;), which is observed by collision-induced dissociation (CID) the most commonly used fragmentation technique. However, these methods require optimization for every individual peptide and is thus still quite challenging.
HX-MS has been used to analyze protein-ligand and protein-protein interactions including viral capsid assembly14-17. Protein unfolding and refolding as well as temperature induced conformational changes were investigated7,18,19. Phosphorylation and single amino acid mutation-related conformational changes16,20 and nucleotide-induced changes were analyzed21,22. Therefore, this method seems ideally suitable to analyze assembly and dynamics of molecular machines. One attractive candidate, whose mechanism is of great general interest, is the Hsp90 chaperone complex.

<table border="1">
	<tbody>
		<tr>
			<td>Reagent/Equipment</td>
			<td>Company</td>
			<td>Catalogue number</td>
			<td>Comments (optional)</td>
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		<tr>
			<td>maXis QTOF</td>
			<td>Bruker</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>nanoAcquity UPLC</td>
			<td>Waters Corp.</td>
			<td></td>
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			<td>Shimadzu 10AD-VP</td>
			<td>Shimadzu</td>
			<td></td>
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			<td>6-port Valve EPC6W with microelectric actuator</td>
			<td>Valco</td>
			<td>#EPC6W</td>
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			<td>Injection valve (manual)</td>
			<td>Rheodyne</td>
			<td>#7725</td>
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			<td>Poros AL20 media</td>
			<td>Applied Biosystems</td>
			<td>#1-6029-06</td>
			<td></td>
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			<td>Poros R2</td>
			<td>Applied Biosystems</td>
			<td>#1-1118-02</td>
			<td></td>
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			<td>Pepsin</td>
			<td>Sigma</td>
			<td>#P6887</td>
			<td>use fresh pepsin</td>
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			<td>Microbore (1 mm)</td>
			<td>IDEX</td>
			<td>#C-128</td>
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			<td>Microbore (2 mm)</td>
			<td>IDEX</td>
			<td>#C-130B</td>
			<td></td>
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			<td>Acquity UPLC BEH C8 Column</td>
			<td>Waters Corp.</td>
			<td>#186002876</td>
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			<td>Thermomixer</td>
			<td>Eppendorf</td>
			<td>#5355000.011</td>
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			<td>Tubing (various diameters)</td>
			<td>IDEX</td>
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			<td>Fittings</td>
			<td>IDEX</td>
			<td>#PK-110 with PK-100</td>
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</table>

analyzing protein dynamics using hydrogen exchange mass spectrometry

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique amino acid sequence, it is only realized by the folding of the polypeptide chain into a single defined three-dimensional arrangement or more commonly into an ensemble of interconverting conformations. Investigating the connection between protein conformation and its function is therefore essential for a complete understanding of how proteins are able to fulfill their great variety of tasks. One possibility to study conformational changes a protein undergoes while progressing through its functional cycle is hydrogen-1H/2H-exchange in combination with high-resolution mass spectrometry (HX-MS). HX-MS is a versatile and robust method that adds a new dimension to structural information obtained by e.g. crystallography. It is used to study protein folding and unfolding, binding of small molecule ligands, protein-protein interactions, conformational changes linked to enzyme catalysis, and allostery. In addition, HX-MS is often used when the amount of protein is very limited or crystallization of the protein is not feasible. Here we provide a general protocol for studying protein dynamics with HX-MS and describe as an example how to reveal the interaction interface of two proteins in a complex. &#160;&#160;

Hsp90 is a molecular chaperone in yeast and member of the Hsp90 chaperone family. By going through a complex ATPase cycle it assists late folding steps of many protein clients. Efficient folding requires transfer of clients from Hsp70 and interaction of the co-chaperone Sti1/Hop. Sti1 directly binds to Hsp90 and facilitates client binding by inhibition of Hsp90&#39;s ATPase activity. Interaction of Hsp90 with Sti1 was recently studied using HX-MS23. Here we present representative results of the underlying expe...

Watch this Scientific Journal Video about Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry at JoVE.com

Analyzing Protein Dynamics Using Hydrogen Exchange Mass Spectrometry

Protein conformation and dynamics are key to understanding the relationship between protein structure and function. Hydrogen exchange coupled with high-resolution mass spectrometry is a versatile method to study the conformational dynamics of proteins as well as characterizing protein-ligand and protein-protein interactions, including contact interfaces and allosteric effects.

All cellular processes depend on the functionality of proteins. Although the functionality of a given protein is the direct consequence of its unique ...

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Analytical Chemistry

Chemistry

Unit 1

Mass Spectrometry Fragmentation Methods

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Real-time Breath Analysis by Using Secondary Nanoelectrospray Ionization Coupled to High Resolution Mass Spectrometry

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental exposure in a non-invasive manner. In this work, we present a protocol to characterize the exhaled VOCs in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry (Sec-nanoESI-HRMS). The homemade Sec-nanoESI source was readily set up based on a commercial nanoESI source. Hundreds of peaks were observed in the background-subtracted mass spectra of exhaled breath, and the mass accuracy values are -4.0-13.5 ppm and -20.3-1.3 ppm in the positive and negative ion detection modes, respectively. The peaks were assigned with accurate elemental composition according to the accurate mass and isotopic pattern. Less than 30 s is used for one exhalation measurement, and it takes approximately 7 min for six replicated measurements.

A protocol for characterizing chemical composition of exhaled breath in real time by using secondary nanoelectrospray ionization coupled to high resolution mass spectrometry is demonstrated.

Exhaled volatile organic compounds (VOCs) have aroused considerable interest, since they can serve as biomarkers for disease diagnosis and environmental ...

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.

A protocol is described for the manual synthesis of oligo-peptoids followed by sequence analysis by mass spectrometry.

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have ...

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing metabolic reactions, DNA repair and replication. Therefore, a detailed understanding of these processes provides critical information on how cells function. Integrative structural MS methods offer structural and dynamical information on protein complex assembly, complex connectivity, subunit stoichiometry, protein oligomerization and ligand binding. Recent advances in integrative structural MS have allowed for the characterization of challenging biological systems including large DNA binding proteins and membrane proteins. This protocol describes how to integrate diverse MS data such as native MS and ion mobility-mass spectrometry (IM-MS) with molecular dynamics simulations to gain insights into a helicase-nuclease DNA repair protein complex. The resulting approach provides a framework for detailed studies of ligand binding to other protein complexes involved in important biological processes.

Mass spectrometry (MS) has emerged as an important tool for the investigation of structure and dynamics of macromolecular assemblies. Here, we integrate MS-based approaches to interrogate protein complex formation and ligand binding.

Proteins are an important class of biological macromolecules that play many key roles in cellular functions including gene expression, catalyzing ...

Large-scale Top-down Proteomics Using Capillary Zone Electrophoresis Tandem Mass Spectrometry

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down proteomics that aims to characterize proteoforms in complex proteomes. However, the application of CZE-MS/MS for large-scale top-down proteomics has been impeded by the low sample-loading capacity and narrow separation window of CZE. Here, a protocol is described using CZE-MS/MS with a microliter-scale sample-loading volume and a 90-min separation window for large-scale top-down proteomics. The CZE-MS/MS platform is based on a linear polyacrylamide (LPA)-coated separation capillary with extremely low electroosmotic flow, a dynamic pH-junction-based online sample concentration method with a high efficiency for protein stacking, an electro-kinetically pumped sheath flow CE-MS interface with extremely high sensitivity, and an ion trap mass spectrometer with high mass resolution and scan speed. The platform can be used for the high-resolution characterization of simple intact protein samples and the large-scale characterization of proteoforms in various complex proteomes. As an example, a highly efficient separation of a standard protein mixture and a highly sensitive detection of many impurities using the platform is demonstrated. As another example, this platform can produce over 500 proteoform and 190 protein identifications from an Escherichia coli proteome in a single CZE-MS/MS run.

A detailed protocol is described for the separation, identification, and characterization of proteoforms in protein samples using capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS). The protocol can be used for the high-resolution characterization of proteoforms in simple protein samples and the large-scale identification of proteoforms in complex proteome samples.

Capillary zone electrophoresis-electrospray ionization-tandem mass spectrometry (CZE-ESI-MS/MS) has been recognized as a useful tool for top-down ...

High-throughput and Comprehensive Drug Surveillance Using Multisegment Injection-Capillary Electrophoresis-Mass Spectrometry

New analytical methods are urgently needed to enable high-throughput, yet comprehensive drug screening, given an alarming opioid and prescription drug crisis in public health. Conventional urine drug testing based on a two-tier immunoassay screen followed by a gas chromatography-tandem mass spectrometry (GC-MS/MS) or liquid chromatography-tandem mass spectrometry (LC-MS/MS) method are expensive and prone to bias while being limited to targeted panels of known drugs of abuse (DoA). Herein, we outline an improved method for drug surveillance that allows for the resolution and detection of an expanded panel of DoA and their metabolites when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS). Multiplexed separations of ten urine samples with a quality control by CE (&lt; 3 min/sample) in conjunction with full-scan data acquisition using a time-of-flight mass spectrometer (TOF-MS) under positive ion mode detection allows for the identification and quantification of DoA above recommended cut-off levels. An excellent resolution of drug isomers and isobars, including background interferences, are achieved when using MSI-CE-MS with an electrokinetic spacer between sample segments, where accurate mass/molecular formula together with the comigration of a matching deuterated internal standard and the detection of one or more bio-transformed metabolites facilitate DoA identification over a wider detection window. Additionally, urine samples can be analyzed directly without enzyme deconjugation for the rapid screening without complicated sample workup. MSI-CE-MS enables the surveillance of a broad spectrum of DoA that is required for the treatment monitoring of high-risk patients, including confirming prescribed drug adherence, revealing illicit drug use/substitution, and evaluating optimal dosage regimes as required for new advances in precision medicine.

Here we describe a high-throughput method for comprehensive drug surveillance that allows for the improved resolution and detection of large panels of drugs of abuse and their metabolites, with quality control based on multisegment injection-capillary electrophoresis-mass spectrometry.

New analytical methods are urgently needed to enable high-throughput, yet comprehensive drug screening, given an alarming opioid and prescription drug ...

Imaging Corrosion at the Metal-Paint Interface Using Time-of-Flight Secondary Ion Mass Spectrometry

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass spectrometry (ToF-SIMS), illustrating that SIMS is a suitable technique to study the chemical distribution at a metal-paint interface. The painted Al alloy coupons are immersed in a salt solution or exposed to air only. SIMS provides chemical mapping and 2D molecular imaging of the interface, allowing direct visualization of the morphology of the corrosion products formed at the metal-paint interface and mapping of the chemical after corrosion occurs. The experimental procedure of this method is presented to provide technical details to facilitate similar research and highlight pitfalls that may be encountered during such experiments.

Time-of-flight secondary ion mass spectrometry is applied to demonstrate the chemical mapping and corrosion morphology at the metal-paint interface of an aluminum alloy after being exposed to a salt solution compared with a specimen exposed to air.

Corrosion developed at the paint and aluminum (Al) metal-paint interface of an aluminum alloy is analyzed using time-of-flight secondary ion mass ...

3D Depth Profile Reconstruction of Segregated Impurities Using Secondary Ion Mass Spectrometry

The presented protocol combines excellent detection limits (1 ppm to 1 ppb) using secondary ion mass spectrometry (SIMS) with reasonable spatial resolution (~1 &#181;m). Furthermore, it describes how to obtain realistic three-dimensional (3D) distributions of segregated impurities/dopants in solid state materials. Direct 3D depth profile reconstruction is often difficult to achieve due to SIMS-related measurement artifacts. Presented here is a method to identify and solve this challenge. Three major issues are discussed, including the i) nonuniformity of the detector being compensated by flat-field correction; ii) vacuum background contribution (parasitic oxygen counts from residual gases present in the analysis chamber) being estimated and subtracted; and iii)&#160;performance of all steps within a stable timespan of the primary ion source. Wet chemical etching is used to reveal the position and types of dislocation in a material, then the SIMS result is superimposed on images obtained via scanning electron microscopy (SEM). Thus, the position of agglomerated impurities can be related to the position of certain defects. The method is fast and does not require sophisticated sample preparation stage; however, it requires a high-quality, stable ion source, and the entire measurement must be performed quickly to avoid deterioration of the primary beam parameters.

The presented method describes how to identify and solve measurement artifacts related to secondary ion mass spectrometry as well as obtain realistic 3D distributions of impurities/dopants in solid state materials.

The presented protocol combines excellent detection limits (1 ppm to 1 ppb) using secondary ion mass spectrometry (SIMS) with reasonable spatial ...

Capillary Electrophoresis Mass Spectrometry Approaches for Characterization of the Protein and Metabolite Corona Acquired by Nanomaterials

The adsorption of biomolecules from surrounding biological matrices to the surface of nanomaterials (NMs) to form the corona has been of interest for the past decade. Interest in the bio-nano interface arises from the fact that the biomolecular corona confers a biological identity to NMs and thus causes the body to identify them as &#8220;self&#8221;. For example, previous studies have demonstrated that the proteins in the corona are capable of interacting with membrane receptors to influence cellular uptake and established that the corona is responsible for cellular trafficking of NMs and their eventual toxicity. To date, most research has focused upon the protein corona and overlooked the possible impacts of the metabolites included in the corona or synergistic effects between components in the complete biomolecular corona. As such, this work demonstrates methodologies to characterize both the protein and metabolite components of the biomolecular corona using bottom-up proteomics and metabolomics approaches in parallel. This includes an on-particle digest of the protein corona with a surfactant used to increase protein recovery, and a passive characterization of the metabolite corona by analyzing metabolite matrices before and after NM exposures. This work introduces capillary electrophoresis &#8211; mass spectrometry (CESI-MS) as a new technique for NM corona characterization. The protocols outlined here demonstrate how CESI-MS can be used for the reliable characterization of both the protein and metabolite corona acquired by NMs. The move to CESI-MS greatly decreases the volume of sample required (compared to traditional liquid chromatography &#8211; mass spectrometry (LC-MS) approaches) with multiple injections possible from as little as 5 &#181;L of sample, making it ideal for volume limited samples. Furthermore, the environmental consequences of analysis are reduced with respect to LC-MS due to the low flow rates (&#60;20 nL/min) in CESI-MS, and the use of aqueous electrolytes which eliminates the need for organic solvents.

Here we present a protocol to characterize the complete biomolecular corona, proteins, and metabolites, acquired by nanomaterials from biofluids using a capillary electrophoresis &#8211; mass spectrometry approach.

The adsorption of biomolecules from surrounding biological matrices to the surface of nanomaterials (NMs) to form the corona has been of interest for the ...

Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry

Characterizing a protein&#39;s higher-order structure is essential for understanding its function. Mass spectrometry (MS) has emerged as a powerful tool for this purpose, especially for protein systems that are difficult to study by traditional methods. To study a protein&#39;s structure by MS, specific chemical reactions are performed in solution that encode a protein&#39;s structural information into its mass. One particularly effective approach is to use reagents that covalently modify solvent accessible amino acid side chains. These reactions lead to mass increases that can be localized with residue-level resolution when combined with proteolytic digestion and tandem mass spectrometry. Here, we describe the protocols associated with use of diethylpyrocarbonate (DEPC) as a covalent labeling reagent together with MS detection. DEPC is a highly electrophilic molecule capable of labeling up to 30% of the residues in the average protein, thereby providing excellent structural resolution. DEPC has been successfully used together with MS to obtain structural information for small single-domain proteins, such as &#946;2-microglobulin, to large multi-domain proteins, such as monoclonal antibodies.

The experimental procedures for performing diethylpyrocarbonate-based covalent labeling with mass spectrometric detection are described. Diethylpyrocarbonate is simply mixed with the protein or protein complex of interest, leading to the modification of solvent accessible amino acid residues. The modified residues can be identified after proteolytic digestion and liquid chromatography/mass spectrometry analysis.

Characterizing a protein&#39;s higher-order structure is essential for understanding its function. Mass spectrometry (MS) has emerged as a powerful tool ...

Capillary Electrophoresis-based Hydrogen/Deuterium Exchange for Conformational Characterization of Proteins with Top-down Mass Spectrometry

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of protein therapeutics and the determination of the conformational transition pathways critical for biological functions, ranging from molecular recognition to enzymatic catalysis. Hydrogen/deuterium exchange (HDX) reaction coupled with top-down mass spectrometric (MS) analysis provides a means to characterize protein higher-order structures and dynamics in a conformer-specific manner. The conformational resolving power of this technique is highly dependent on the efficiencies of separating protein states at the intact protein level and minimizing the residual non-deuterated protic content during the HDX reactions. 
Here we describe a capillary electrophoresis (CE)-based variant of the HDX MS approach that aims to improve the conformational resolution. In this approach, proteins undergo HDX reactions while migrating through a deuterated background electrolyte solution (BGE) during the capillary electrophoretic separation. Different protein states or proteoforms that coexist in solution can be efficiently separated based on their differing charge-to-size ratios. The difference in electrophoretic mobility between proteins and protic solvent molecules minimizes the residual non-deuterated solvent, resulting in a nearly complete deuterating environment during the HDX process. The flow-through microvial CE-MS interface allows efficient electrospray ionization of the eluted protein species following a rapid mixing with the quenching and denaturing modifier solution at the outlet of the sprayer. The online top-down MS analysis measures the global deuteration level of the eluted intact protein species, and subsequently, the deuteration of their gas-phase fragments. This paper demonstrates this approach in differential HDX for systems, including the natural protein variants coexisting in milk.

Presented here is a protocol for a capillary electrophoresis-based hydrogen/deuterium exchange (HDX) approach coupled with top-down mass spectrometry. This approach characterizes the difference in higher-order structures between different protein species, including proteins in different states and different proteoforms, by conducting concurrent differential HDX and electrophoretic separation.

Resolving conformational heterogeneity of multiple protein states that coexist in solution remains one of the main obstacles in the characterization of ...