Detection of protein Z in a renal calculus composed of calcium oxalate monohydrate with the use of liquid chromatography–mass spectrometry/mass spectrometry following two-dimensional polyacrylamide gel electrophoresis separation

Kaneko, Kiyoko; Yamanobe, Tomoyo; Nakagomi, Kazuya; Mawatari, Ken‐ichi; Onoda, Maki; Fujimori, Shin

doi:10.1016/j.ab.2003.09.018

Cited by 22 publications

(29 citation statements)

References 17 publications

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“…[11][12][13][14][15] Briefly, the powdered stone samples were extracted in sequence with 0.6 M KCl, 10% formic acid, 4 M guanidine hydrochloride in 50 mM Tris/HCl buffer (pH 7.4) containing 1 mM phenyl methyl sulfonyl fluoride, and 0.5 M EDTA in 50 mM Tris/HCl buffer (pH 7.4) for 24 h at 4 C. At each step, the sediment was washed 3 times with the same solvent used for extraction, and the supernatant was collected after centrifugation at 15000 rpm for 10 min at 4 C. Fractions of the supernatant at each extraction step were dialyzed 8 times against 40 L of 0.005% Brij-35/10 mM NH4CO3 for 4 days and concentrated by lyophilization. Lyophilized samples were kept at -80 C until electrophoresis.…”

Section: Protein Extraction From Urinary Stonesmentioning

confidence: 99%

“…Several proteomic studies on proteins in urinary stones have identified inflammatory proteins and cellular defense proteins. [7][8][9][10][11][12][13][14][15] In this study, 13 urinary stones were meticulously analyzed using micro-area X-ray diffractometry and IR analysis. Matrix proteins from 16 parts of the urinary stones were then individually extracted using 4 different sequential solutions.…”

Section: Proteins Identified In Stones Using Lc-ms/msmentioning

confidence: 99%

“…A micro-area X-ray diffractometer (JEOL JDX-8030, DX-MAP2, Tokyo, Japan) with a microscope was used according to previously reported methods. [11][12][13][14][15] The analytical conditions were as follows: target, Cu; filter, Ni; voltage, 40 kV; current, 40 μA; collimator diameter, 100 μm. The diffraction pattern obtained was compared with the data registered in the Joint Committee on Powder Diffraction Standards (JCPDS) database.…”

Section: Micro-area X-ray Diffractometrymentioning

confidence: 99%

“…[11][12][13] Protein Z, a vitamin K-dependent calcium-binding protein, has been identified in urinary stones composed of CaOx by our work. 14,15 In this study, X-ray diffraction and IR analysis were used to determine the precise crystal components of CaOx stones, and the matrix proteins in 13 calculi composed of COM or COD were extracted sequentially via 4 different solutions. Proteins obtained from each fraction were digested with trypsin following SDS-polyacrylamide gel electrophoresis (SDS-PAGE), and the peptide mixtures were analyzed by nano-flow liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS).…”

Section: Introductionmentioning

confidence: 99%

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Proteomic Analysis after Sequential Extraction of Matrix Proteins in Urinary Stones Composed of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate

et al. 2015

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In this study, we performed proteomic analysis following sequential protein extraction on calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) urinary stones to determine the specific matrix proteins according to the crystal components of the stones. After X-ray and IR analysis of 13 urinary stones, matrix proteins were sequentially extracted with KCl, formic acid, guanidine-HCl, and EDTA, before SDS-electrophoresis followed by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). The electrophoretic patterns of the extracted proteins differed from that of COM and COD stones. LC-MS/MS identified 65 proteins, of which many were cellular plasma proteins, and were frequently detected regardless of the crystal components. However, 6 proteins (protein Z, protein S, prothrombin, osteopontin, fatty acid binding protein 5, and ubiquitin) were detected in the final EDTA fractions of COM stones. These proteins are involved in the coagulation process or osteometabolism, and thus the roles they play are of particular interest.

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Section: Protein Extraction From Urinary Stonesmentioning

confidence: 99%

Section: Proteins Identified In Stones Using Lc-ms/msmentioning

confidence: 99%

Section: Micro-area X-ray Diffractometrymentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Proteomic Analysis after Sequential Extraction of Matrix Proteins in Urinary Stones Composed of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate

et al. 2015

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“…Stone proteins were similar to urine proteins and characteristic of the type of stones present (53). LC/MS has also been used on proteins extracted from stones (55). Recently, an elegant approach was used to identify an inhibitor of crystal formation in urine (23).…”

Section: Nephrolithiasismentioning

confidence: 99%

Proteomics in renal research

Janech¹,

Raymond²,

Arthur³

2007

American Journal of Physiology-Renal Physiology

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Proteomic technologies are used with increasing frequency in the renal community. In this review, we highlight the use in renal research of a number of available techniques including two-dimensional gel electrophoresis, liquid chromatography/mass spectrometry, surface-enhanced laser desorption/ionization, capillary electrophoresis/mass spectrometry, and antibody and tissue arrays. These techniques have been used to identify proteins or changes in proteins specific to regions of the kidney or associated with renal diseases or toxicity. They have also been used to examine protein expression changes and posttranslational modifications of proteins during signaling. A number of studies have used proteomic methodologies to look for diagnostic biomarkers in body fluids. The rapid rate of development of the technologies along with the combination of classic physiological and biochemical techniques with proteomics will enable new discoveries.

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Detection of coexisting protein conformations in capillary zone electrophoresis subsequent to transient contact with sodium dodecyl sulfate solutions

et al. 2005

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Non-native conformations of proteins were generated by temporary contact with aqueous solutions of sodium dodecyl sulfate (SDS) and separated from the native state with capillary zone electrophoresis (CZE) in alkaline borate buffer deficient of SDS. Nine proteins at concentrations of 2.0 or 3.0 mg.L(-1) were compared in terms of their susceptibility to SDS. For superoxide dismutase and ferritin the tendency of unfolding was modest with < 25% of the protein being transformed to the non-native state at 10 mmol.L(-1) SDS. Highest susceptibility was observed for albumin, myoglobin (Mb), and hemoglobin with > 75% in the non-native state even at 2.0 mmol.L(-1) SDS. The influence of varying SDS concentrations on the conformational state of Mb was tested. Increasing the SDS concentration, circular dichroism revealed a reduction in alpha-helix, an increase in random coil, and an introduction of beta-sheet, which is absent in native structure. Modifications in the secondary structure were in agreement with distinct changes in the shape of the non-native Mb peak in CZE and make a gradual unfolding/refolding process with several coexisting molten globules instead of two-state transition of conformations most plausible for Mb. CZE was found to contribute to a further understanding of holo-Mb transformation towards a population of non-native conformations (i) by means of calculated peak area ratios of native to non-native states, which showed sigmoid transition, (ii) by detecting the release of the prosthetic heme group, and (iii) by changes in the effective electrophoretic mobility of the Mb-SDS peaks. Reconstituted holo-Mb forms differed in the Soret band around 410 nm, indicating diversity in the conformation of the heme pocket.

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Detection of protein Z in a renal calculus composed of calcium oxalate monohydrate with the use of liquid chromatography–mass spectrometry/mass spectrometry following two-dimensional polyacrylamide gel electrophoresis separation

Cited by 22 publications

References 17 publications

Proteomic Analysis after Sequential Extraction of Matrix Proteins in Urinary Stones Composed of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate

Proteomic Analysis after Sequential Extraction of Matrix Proteins in Urinary Stones Composed of Calcium Oxalate Monohydrate and Calcium Oxalate Dihydrate

Proteomics in renal research

Detection of coexisting protein conformations in capillary zone electrophoresis subsequent to transient contact with sodium dodecyl sulfate solutions

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