Accuracy of SUPREX (stability of unpurified proteins from rates of H/D exchange) and MALDI mass spectrometry-derived protein unfolding free energies determined under non-EX2 exchange conditions

Dai, Susie Y.; Fitzgerald, Michael C.

doi:10.1016/j.jasms.2006.06.025

Cited by 24 publications

(29 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Collision Complex 5 may transfer a proton or deuteron to the adjacent N-terminus via TS2(6), to form a solvent-stabilized zwitterionic Complex 7, which can transfer a proton or deuteron from the N-terminus back to the C-terminus through TS3 (8) to form a non-zwitterionic Complex 9. Upon completing this reaction channel, a single exchange or no net exchange has occurred, depending on whether ND 3 or ND 2 H is released from Complex 9.…”

Section: Resultsmentioning

confidence: 99%

“…Although H/D exchange reagents can access all labile hydrogen atoms of small peptides, the accessibility of exchange reagents toward labile hydrogen sites of larger peptides and proteins is conformation dependent [1], thus the rate of H/D exchange reactions and the number of hydrogen atoms exchanged can be used as a structural probe [2]. H/D exchange and mass spectrometry can be combined to study both gas-phase and solutionphase H/D exchange reactions [3][4][5][6][7][8][9], and the kinetics of H/D exchange can be utilized to infer the presence of distinct conformations of both solution-phase [10 -12] and gas-phase peptide and protein ions [13]. For example, McLuckey et al studied the gas-phase H/D exchange of bradykinin [M ϩ H] ϩ ions (amino acid sequence RPPGFSPFR) with DI and D 2 O, and they interpreted the observed bimodal distributions of product ions as evidence for two non-interconverting ion conformations having different reactivities toward deuterating reagents [14].…”

mentioning

confidence: 99%

See 1 more Smart Citation

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

The gas-phase H/D exchange reactions of arginine (R) and arginine-containing di-and tri-peptide (gly-arg (GR), arg-gly (RG), gly-gly-arg (GGR), gly-arg-gly (GRG) and arg-gly-gly (RGG)) [M ϩ H] ϩ ions with deuterated ammonia (ND 3 ) were investigated by using Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR), ion mobility-mass spectrometry (IM-MS), ab initio and density functional theory-based molecular orbital calculations and molecular modeling. Three exchanges are observed for arginine and argininecontaining tri-peptide [M ϩ H] [15]. Valentine and Clemmer used ion mobility-mass spectrometry to examine the conformation dependence of H/D exchange reactions, and suggested that ion conformation has a significant effect on H/D exchange [16,17].Compared with the intensive investigations carried out on the conformational characterization of peptides and proteins using solution-phase H/D exchange reaction chemistry, the corresponding gas-phase studies are much less comprehensive. The key question regarding gas-phase H/D exchange is: does the "solvent molecule," i.e., H/D exchange reagent, sample the entire "available surface area" of the peptide/protein ion, or is H/D exchange limited by other factors? For example, are all solution phase labile hydrogen atoms exchangeable in the gas phase and are the reactivities of all exchangeable hydrogen atoms similar? Dookeran and Harrison studied the H/D exchange reactions of 18 naturally occurring amino acids and selected di-and tripeptides with ND 3 , and reported that amino acid [M ϩ H] ϩ ions containing hydroxyl, carboxyl, and amine side chains exchange all labile hydrogen atoms, whereas the side-chain hydrogen atoms of glutamine, asparagine, and histidine [M ϩ H] ϩ ions exchange less readily, and tyrosine and arginine [M ϩ H] ϩ ions do not undergo significant exchange [18]. In a separate study, Lebrilla et al. found that the carboxylic acid group of glycine and aliphatic amino acid [M ϩ H] ϩ ions (alanine, valine, leucine, isoleucine, and proline) undergo H/D exchange three to 10 times faster than the NAddress reprint requests to Dr.

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Huang

Marini

McLean

et al. 2009

J. Am. Soc. Mass Spectrom.

View full text Add to dashboard Cite

show abstract

“…In a typical SUPREX setting, a series of protein or proteinligand complex samples is incubated for a certain time in a deuterated buffer containing increasing amount of a chemical denaturant, for example, guanidinium hydrochloride. Hence, the extent of hydrogen exchange is analyzed as a function of denaturant concentration and yields the free energy of folding DG f and the ligandinduced stabilization of protein structure DDG f , although with some limitations [48,54,59]. Recently, a very similar method in which labile deuterium labeling is substituted with stable oxidative labeling of methionine residues has been proposed -SPROX (stability of proteins from rates of oxidation) [48,[60][61][62].…”

Section: Ion Mobility and Measurement Of Collision Cross Sectionsmentioning

confidence: 99%

Determination of thermodynamic and kinetic properties of biomolecules by mass spectrometry

Gülbakan

Barylyuk

Zenobi

2015

Current Opinion in Biotechnology

View full text Add to dashboard Cite

“…In cases where the global unfolding/refolding reaction of a protein is well modeled by a two-state transition (i.e., partially folded intermediate states of the protein are not populated), SUPREX provides reasonably accurate ⌬G f and m-values for the transition [24,27,31,32]. Such SUPREX-derived ⌬G f and m-values are especially useful for the quantitation of protein-ligand binding affinities.…”

Section: The Informationmentioning

confidence: 99%

Painting proteins with covalent labels: What’s in the picture?

Fitzgerald

West

2009

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

Knowledge about the structural and biophysical properties of proteins when they are free in solution and/or in complexes with other molecules is essential for understanding the biological processes that proteins regulate. Such knowledge is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets. In the last decade a variety of different covalent labeling techniques have been used in combination with mass spectrometry to probe the solution-phase structures and biophysical properties of proteins and protein-ligand complexes. Highlighted here are five different mass spectrometry-based covalent labeling strategies including: continuous hydrogen/deuterium (H/D) exchange labeling, hydroxyl radical-mediated footprinting, SUPREX (stability of unpurified proteins from rates of H/D exchange), PLIMSTEX (protein-ligand interaction by mass spectrometry, titration, and H/D exchange), and SPROX (stability of proteins from rates of oxidation). The basic experimental protocols used in each of the above-cited methods are summarized along with the kind of biophysical information they generate. Also discussed are the relative strengths and weaknesses of the different methods for probing the wide range of conformational states that proteins and proteinligand complexes can adopt when they are in solution. (J Am Soc Mass Spectrom 2009, 20, 1193-1206) © 2009 Published by Elsevier Inc. on behalf of American Society for Mass Spectrometry P roteins fold into elaborate three-dimensional structures and, under native solution conditions, they spend a large fraction of time in highly compact structures. However, the solution-phase structures of proteins are not static. Proteins sample a wide range of conformational states in solution. The conformational changes that proteins undergo in solution can be as dramatic as a global unfolding event in which all higher-order structure is lost or as subtle as a breathing motion in which a specific element of secondary structure is partially unfolded in a more local unfolding event (see Figure 1). Knowledge about the structures, kinetics, and thermodynamics involved in the conformational changes that proteins undergo in solution and as they interact with ligands is crucial for understanding the fundamental biological processes in which proteins participate. It is also important to drug discovery efforts, particularly those focused on the development of therapeutic agents with protein targets.Mass spectrometry (MS) has become an increasingly useful analytical tool for acquiring biophysical information about the conformational properties of proteins in solution. A common strategy that has emerged for acquiring such information is to use matrix-assisted laser desorption/ionization (MALDI) or electrospray ionization (ESI) MS to read out the results of solutionphase reactions that introduce covalent modifications into proteins. Two general types of MS-based covalent labeling strategies have proven useful for probing the biophysical p...

show abstract

Accuracy of SUPREX (stability of unpurified proteins from rates of H/D exchange) and MALDI mass spectrometry-derived protein unfolding free energies determined under non-EX2 exchange conditions

Cited by 24 publications

References 13 publications

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

A mechanistic study of the H/D exchange reactions of protonated arginine and arginine-containing Di- and tripeptides

Determination of thermodynamic and kinetic properties of biomolecules by mass spectrometry

Painting proteins with covalent labels: What’s in the picture?

Contact Info

Product

Resources

About