Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry

Guan, Jing Qu; Chance, Mark R.

doi:10.1016/j.tibs.2005.08.007

Cited by 110 publications

(149 citation statements)

References 61 publications

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“…This percentage was obtained by dividing the total number of product ions with similar relative abundances (i.e., within 10%) by the total number of product ions observed in the spectra; this was done for all the unoxidized and oxidized peptides. As an°example°of°this°evaluation,°Figure°6°shows°that°the z 3 , z 4 , z 5 , z 6 , and c 6 product ions have relative abundances that are very similar (i.e., within 10% relative abundance) in both spectra, whereas the relative abundances of the z 2 product ion are 14 and 27%, respectively, in the spectra of the unoxidized and oxidized peptides. By this analysis, the z 3 , z 4 , z 5 , z 6 , and c 6 product ions are established as similar in both spectra, but the z 2 product ion is considered dissimilar.…”

Section: Etd Is Relatively Insensitive To Side-chain Chemistrymentioning

confidence: 95%

“…As an°example°of°this°evaluation,°Figure°6°shows°that°the z 3 , z 4 , z 5 , z 6 , and c 6 product ions have relative abundances that are very similar (i.e., within 10% relative abundance) in both spectra, whereas the relative abundances of the z 2 product ion are 14 and 27%, respectively, in the spectra of the unoxidized and oxidized peptides. By this analysis, the z 3 , z 4 , z 5 , z 6 , and c 6 product ions are established as similar in both spectra, but the z 2 product ion is considered dissimilar. For comparison, if the same analysis is done for the CID spectra of all the unoxidized and oxidized peptides, the percentage of product ions that have similar relative abundances is 3%.…”

Section: Etd Is Relatively Insensitive To Side-chain Chemistrymentioning

confidence: 95%

“…To get more sequence information, an ETD spectrum of the doubly oxidized C*LRRASLG peptide ion [M°ϩ°2O°ϩ°2H] 2°ϩ°w as°obtained°(Figure°1c).°The presence of unoxidized z 5 , z 6 , and z 7 product ions, and oxidized c 4 , c 5 , c 6 , and c 7 product ions allows the sequence to be determined and the site of oxidation to be identified. Clearly, oxidized cysteine does not limit the amount of sequence information obtainable from the ETD spectrum of this peptide like it does the CID spectrum.…”

Section: Peptides With Cysteine Sulfinic Acid Residuesmentioning

confidence: 99%

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Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Rapole

Wilson

Bridgewater

et al. 2007

J. Am. Soc. Mass Spectrom.

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Oxidative modifications to the side chains of sulfur-containing amino acids often limit the number of product ions formed during collision-induced dissociation (CID) and thus make it difficult to obtain sequence information for oxidized peptides. In this work, we demonstrate that electron-transfer dissociation (ETD) can be used to improve the sequence information obtained from peptides with oxidized cysteine and methionine residues. In contrast to CID, ETD is found to be much less sensitive to the side-chain chemistry, enabling extensive sequence information to be obtained in cases where CID fails to provide this information. These results indicate that ETD is a valuable technique for studying oxidatively modified peptides and proteins. In addition, we report a unique and very abundant product ion that is formed in the CID spectra of peptides having N-terminal cysteine sulfinic acid residues. The mechanism for this unique dissociation pathway involves a six-membered cyclic intermediate and leads to the facile loss of NH 3 and SO 2 , which corresponds to a mass loss of 81 Da. While the facile nature of this dissociation pathway limits the sequence information present in CID spectra of peptides with N-terminal cysteine sulfinic acid residues, extensive sequence information for these peptides can be obtained with ETD. M ass spectrometry (MS) is widely used for sequencing and identifying amino acid modifications in peptides and proteins. Identifying modifications to proteins is important for a variety of reasons. Post-translational modifications (PTMs) of proteins are necessary for a wide range of cellular functions such as protein trafficking, protein-protein interactions, and transcription. Identifying and pinpointing these modification sites are important for more deeply understanding protein function, both normal and abnormal. In this context, PTMs such as phosphorylation, acetylation, glycosylation, sulfonation, and methylation are important to characterize. Oxidation is another important protein modification that is typically associated with oxidative stress [1-4], but recent work has also shown that protein oxidation can play a regulatory role as well [5]. Furthermore, an increasing number of techniques make use of oxidative labeling to study protein structure. These methods use radicals (e.g., · OH) to modify solvent-exposed [6 -9] or metal-bound amino acids [10 -17], and MS n to identify oxidatively modified residues, typically in conjunction with proteolytic digestion.Very often side-chain modifications to peptides can make sequencing by collision-induced dissociation (CID) difficult. Perhaps the most well known example is the effect of phosphorylation on peptide ion dissociation. The CID spectra of phosphorylated peptides are commonly dominated by a neutral loss of H 3 PO 4 , often with little other sequence information present. Similarly, side-chain oxidation can dramatically affect peptide dissociation patterns and limit sequence information that is available by CID. For example, oxidation of cysteine ...

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Section: Etd Is Relatively Insensitive To Side-chain Chemistrymentioning

confidence: 95%

Section: Etd Is Relatively Insensitive To Side-chain Chemistrymentioning

confidence: 95%

Section: Peptides With Cysteine Sulfinic Acid Residuesmentioning

confidence: 99%

See 1 more Smart Citation

Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Rapole

Wilson

Bridgewater

et al. 2007

J. Am. Soc. Mass Spectrom.

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“…Other covalent labeling approaches rely on reagents that irreversibly modify either specific amino acids [7][8][9] or most amino acids (e.g. hydroxyl radicals 10,11 ). These reagents provide information about protein structure by identifying amino acids that are exposed to solvent.…”

Section: Introductionmentioning

confidence: 99%

Protein Surface Mapping Using Diethylpyrocarbonate with Mass Spectrometric Detection

2008

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The reliability and information content of diethylpyrocarbonate (DEPC) as a covalent probe of protein surface structure has been improved when used appropriately with mass spectrometric detection. Using myoglobin, cytochrome c, and β-2-microglobulin as model protein systems, we demonstrate for the first time that DEPC can modify Ser and Thr residues in addition to His and Tyr residues. This result expands the capability of DEPC as a structural probe because about 25% of the sequence of the average protein can now be covered using this covalent labeling reagent. In addition, we establish a new approach based on mass spectrometry to ensure the structural integrity of proteins during amino acid-specific covalent labeling reactions. This approach involves monitoring the extent of modification as a function of reagent concentration and allows any small-scale or local perturbations caused by the covalent label to be readily identified and avoided. Results indicate that these dose-response plots are much more reliable and generally applicable probes of possible protein structural changes than fluorescence or circular dichroism spectroscopies. These dose-response plots also provide a means of quantitatively comparing the reactivity of each modified residue. Based on comparisons to known X-ray crystal structures, we find that the solvent accessibility of the reactive atom in the side chain and the presence of a nearby charged residue most affect modification rates. Finally, this improved surface mapping method has been used to determine the effect of Cu(II) binding on the structure of β-2-microglobulin. Results confirm that Cu(II) binds His31, but not any of the other three His residues, and changes the solvent accessibility of residues near His31 and near the N-terminus.

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“…Structural probing; structure determination; bifunctional crosslinking; bis-(1,2-dicarbonyls); Argspecific labels; ESI-FTICR mass spectrometry Chemical labeling techniques and mass spectrometric analysis constitute an ideal combination for investigating the structure and dynamics of biomolecules that exceed the size accessible by nuclear magnetic resonance, or afford inadequate crystallization [1][2][3][4]. Monofunctional footprinting targeted to specific functional groups provides valuable information about *Corresponding author: University of Maryland Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21228 USA, Tel.…”

Section: Introductionmentioning

confidence: 99%

Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies

Zhang

Crosland

Fabris

2008

Analytica Chimica Acta

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The combination of chemical probing and high-resolution mass spectrometry constitutes a powerful alternative for the structural elucidation of biomolecules possessing unfavorable size, solubility, and flexibility. We have developed nested Arg-specific bifunctional crosslinkers to obtain complementary information to typical Cys-and Lys-specific reagents available on the market. The structures of 1,4-phenyl-diglyoxal (PDG) and 4,4′-biphenyl-diglyoxal (BDG) include two identical 1,2-dicarbonyl functions capable of reacting with the guanido group of Arg residues in proteins, as well as the base-pairing face of guanine in nucleic acids. The reactive functions are separated by modular spacers consisting of one or two benzene rings, which confer greater rigidity to the crosslinker structure than it is afforded by typical aliphatic spacers. Analysis by electrospray ionization (ESI) Fourier transform ion cyclotron resonance (FTICR) mass spectrometry has shown that the probes provide both mono-and bifunctional products with model protein substrates, which are stabilized by the formation of diester derivatives in the presence of borate buffer. The identification of crosslinked sites was accomplished by employing complementary proteolytic procedures and peptide mapping by ESI-FTICR. The results showed excellent correlation with the solvent accessibility and structural context of susceptible residues, and highlighted the significance of possible dynamic effects in determining the outcome of crosslinking reactions. The application of nested reagents with different spacing has provided a new tool for experimentally recognizing flexible regions that may be involved in prominent dynamics in solution. The development of new bifunctional crosslinkers with diverse target specificity and different bridging spans is expected to facilitate the structure elucidation of progressively larger biomolecular assemblies by increasing the number and diversity of spatial constraints available for triangulating the position of crosslinked structures in the three dimensions. KeywordsStructural probing; structure determination; bifunctional crosslinking; bis-(1,2-dicarbonyls); Argspecific labels; ESI-FTICR mass spectrometry Chemical labeling techniques and mass spectrometric analysis constitute an ideal combination for investigating the structure and dynamics of biomolecules that exceed the size accessible by nuclear magnetic resonance, or afford inadequate crystallization [1][2][3][4]. Monofunctional footprinting targeted to specific functional groups provides valuable information about *Corresponding author: University of Maryland Baltimore County, Department of Chemistry and Biochemistry, 1000 Hilltop Circle, Baltimore, MD 21228 USA, Tel. (410) Fax (410) 455-2608. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resu...

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Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry

Cited by 110 publications

References 61 publications

Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation

Protein Surface Mapping Using Diethylpyrocarbonate with Mass Spectrometric Detection

Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies

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