Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine

Xu, Hua; Zhang, Liwen; Freitas, Michael A.

doi:10.1021/pr070363z

Cited by 126 publications

(151 citation statements)

References 37 publications

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“…1). Exogenous pungent chemicals and endogenous inflammatory mediators, such as allicin, cinnamaldehyde, allyl isothiocyanate, iodoacetamide (IA), 3 N-methylmaleimide (NMM), nitric oxide (NO), hydrogen peroxide (H 2 O 2 ), 4-hydroxynonenal, and 15-deoxy-␦ 12,14 -prostaglandin J 2 (1)(2)(3)(4)(5)(6), are sensed by and activate the channel. The resulting cation influx through the central pore depolarizes the neuron, producing an action potential that ultimately leads to the perception of pain in mammal organisms (7).…”

Section: Trpa1 (Transient Receptor Potential Ankyrin 1)mentioning

confidence: 99%

Identification of in Vivo Disulfide Conformation of TRPA1 Ion Channel

Wang

Cvetkov

Chance

et al. 2012

Journal of Biological Chemistry

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Background:The TRPA1 ion channel is activated by electrophilic compounds and plays a role in chemical nociception. Results: Four in vivo disulfide bonds were detected following electrophilic treatment. Conclusion: Channel activation by electrophiles could involve the formation of disulfide bonds in the N terminus of TRPA1. Significance: Understanding the activation mechanism of TRPA1 is important for elucidating its role in chemical nociception.

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Section: Trpa1 (Transient Receptor Potential Ankyrin 1)mentioning

confidence: 99%

Identification of in Vivo Disulfide Conformation of TRPA1 Ion Channel

Wang

Cvetkov

Chance

et al. 2012

Journal of Biological Chemistry

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“…The eluent was injected into an LTQ-FT ultra mass spectrometer (Thermo Scientific). MS data were analyzed with the aid of Mascot Deamon software version 2.2.0 (Matrix Science Ltd., Boston) and the Massmatrix data base search engine (22,23).…”

Section: Purification Of Cross-linked Products and Identification Of mentioning

confidence: 99%

Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

Golczak

Kiser

Lodowski

et al. 2010

Journal of Biological Chemistry

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Regeneration of visual chromophore in the vertebrate visual cycle involves the retinal pigment epithelium-specific protein RPE65, the key enzyme catalyzing the cleavage and isomerization of all-trans-retinyl fatty acid esters to 11-cis-retinol. Although RPE65 has no predicted membrane spanning domains, this protein predominantly associates with microsomal fractions isolated from bovine retinal pigment epithelium (RPE). We have re-examined the nature of RPE65 interactions with native microsomal membranes by using extraction and phase separation experiments. We observe that hydrophobic interactions are the dominant forces that promote RPE65 association with these membranes. These results are consistent with the crystallographic model of RPE65, which features a large lipophilic surface that surrounds the entrance to the catalytic site of this enzyme and likely interacts with the hydrophobic core of the endoplasmic reticulum membrane. Moreover, we report a critical role for phospholipid membranes in preserving the retinoid isomerization activity and physical properties of RPE65. Isomerase activity measured in bovine RPE was highly sensitive to phospholipase A 2 treatment, but the observed decline in 11-cis-retinol production did not directly reflect inhibition by products of lipid hydrolysis. Instead, a direct correlation between the kinetics of phospholipid hydrolysis and retinoid isomerization suggests that the lipid membrane structure is critical for RPE65 enzymatic activity. We also provide evidence that RPE65 operates in a multiprotein complex with retinol dehydrogenase 5 and retinal G protein-coupled receptor in RPE microsomes. Modifications in the phospholipid environment affecting interactions with these protein components may be responsible for the alterations in retinoid metabolism observed in phospholipid-depleted RPE microsomes. Thus, our results indicate that the enzymatic activity of native RPE65 strongly depends on its membrane binding and phospholipid environment.In vertebrates, the perception of light is preceded by a quantum event in which a photon of light hits the 11-cis-retinylidene chromophore of rhodopsin in the retina. Photoisomerization of this chromophore to its all-trans isomer results in activation of rhodopsin triggering a cascade of signal transduction events (summarized in Ref. 1). This process simultaneously leads to loss of photoreceptor light sensitivity making continuous regeneration of 11-cis-retinal a requirement to sustain vision. The visual (retinoid) cycle is the fundamental series of reactions responsible for regeneration of the visual chromophore that occurs in photoreceptors and the retinal pigment epithelium (RPE) 4 (summarized in Ref.2). The key component of this enzymatic cycle is the RPE-specific microsomal membrane protein known as RPE65 (3-5). The importance of RPE65 in the retinoid cycle is underscored by the metabolic dysfunction found in Rpe65 Ϫ/Ϫ mice, which is characterized by complete lack of 11-cis-retinoid production accompanied by accumulation of the all-tr...

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“…Dual protease digestion (trypsin followed by chymotrypsin) of RNase A was performed using previously described methods [15,21]. Briefly, RNase A was dissolved at 1 mg mL −1 in a 25 mM ammonium acetate buffer adjusted to pH 6.0 with 10 mM formic acid.…”

Section: Ribonuclease a Proteolytic Digestionmentioning

confidence: 99%

Effect of Cysteic Acid Position on the Negative Ion Fragmentation of Proteolytic Derived Peptides

Williams

Kmiec

Russell

et al. 2011

J. Am. Soc. Mass Spectrom.

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A study on the effect of cysteic acid position on the types of fragment ions formed by collisioninduced dissociation (CID) of [M -H] − ions is presented. Of particular note is the observation of d-type fragment ions for peptides that contain an N-terminal cysteic acid (fixed negative charge) and cleavable amino acid side chains possessing a β-γ carbon-carbon bond. For example, the CID mass spectrum of oxidized cys-kemptide (C ox LRRASLG) [M -H + O 3 ] − ions contains abundant series of d-type fragment ions, and similar results are observed for oxidized cysteinecontaining ribonuclease A proteolytic peptides. The d i fragment ions are assumed to arise by a charge-remote and/or charge-assisted fragmentation mechanism, which both occur at high collision energies and involve consecutive reactions (i.e., the formation of a i ions followed by the elimination of the side chain to form d i ions).

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Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine

Cited by 126 publications

References 37 publications

Identification of in Vivo Disulfide Conformation of TRPA1 Ion Channel

Identification of in Vivo Disulfide Conformation of TRPA1 Ion Channel

Importance of Membrane Structural Integrity for RPE65 Retinoid Isomerization Activity

Effect of Cysteic Acid Position on the Negative Ion Fragmentation of Proteolytic Derived Peptides

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