Characterization of histone (H1B) oxalate binding protein in experimental urolithiasis and bioinformatics approach to study its oxalate interaction

Latha, P. G.; Kalaiselvi, Periandavan; Varalakshmi, P.; Rameshkumar, G.

doi:10.1016/j.bbrc.2006.04.086

Cited by 7 publications

(4 citation statements)

References 26 publications

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“…Homology model building of the identified proteins: ethanolamine-phosphate cytidylyltransferase and macrophage-capping protein was done using molecular operating environment (MOE) [28], [29]. The template used for model building of ethanolamine-phosphate cytidylyltransferase was the crystal structure of human CTP: Phosphoethanolamine Cytidylyltransferase in complex with CMP [PDB ID: 3ELB_A] with a query coverage of 85% and sequence identity of 98%.…”

Section: Methodsmentioning

confidence: 99%

Peeping into Human Renal Calcium Oxalate Stone Matrix: Characterization of Novel Proteins Involved in the Intricate Mechanism of Urolithiasis

et al. 2013

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BackgroundThe increasing number of patients suffering from urolithiasis represents one of the major challenges which nephrologists face worldwide today. For enhancing therapeutic outcomes of this disease, the pathogenic basis for the formation of renal stones is the need of hour. Proteins are found as major component in human renal stone matrix and are considered to have a potential role in crystal–membrane interaction, crystal growth and stone formation but their role in urolithiasis still remains obscure.MethodsProteins were isolated from the matrix of human CaOx containing kidney stones. Proteins having MW>3 kDa were subjected to anion exchange chromatography followed by molecular-sieve chromatography. The effect of these purified proteins was tested against CaOx nucleation and growth and on oxalate injured Madin–Darby Canine Kidney (MDCK) renal epithelial cells for their activity. Proteins were identified by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF MS) followed by database search with MASCOT server. In silico molecular interaction studies with CaOx crystals were also investigated.ResultsFive proteins were identified from the matrix of calcium oxalate kidney stones by MALDI-TOF MS followed by database search with MASCOT server with the competence to control the stone formation process. Out of which two proteins were promoters, two were inhibitors and one protein had a dual activity of both inhibition and promotion towards CaOx nucleation and growth. Further molecular modelling calculations revealed the mode of interaction of these proteins with CaOx at the molecular level.ConclusionsWe identified and characterized Ethanolamine-phosphate cytidylyltransferase, Ras GTPase-activating-like protein, UDP-glucose:glycoprotein glucosyltransferase 2, RIMS-binding protein 3A, Macrophage-capping protein as novel proteins from the matrix of human calcium oxalate stone which play a critical role in kidney stone formation. Thus, these proteins having potential to modulate calcium oxalate crystallization will throw light on understanding and controlling urolithiasis in humans.

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Section: Methodsmentioning

confidence: 99%

Peeping into Human Renal Calcium Oxalate Stone Matrix: Characterization of Novel Proteins Involved in the Intricate Mechanism of Urolithiasis

et al. 2013

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“…In addition, angiotensin and proteins belonging to the renin-angiotensin system were found (e.g., Cathepsin G, Kallikrein, Lysosomal Pro-X carboxypeptidase, aminopeptidase N), which via NADPH-oxidase and reactive oxygen species (ROS) activate P38, MAPK and JUNK. These mediators, in turn, increase the expression of OPN, BK, HS and PG among others [32][33][34].…”

Section: Inorganic Compositionmentioning

confidence: 99%

A comprehensive analysis of sialolith proteins and the clinical implications

et al. 2020

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Background: Sialolithiasis or salivary gland stones are associated with high clinical morbidity. The advances in the treatment of sialolithiasis has been limited, however, by our understanding of their composition. More specifically, there is little information regarding the formation and composition of the protein matrix, the role of mineralogical deposition, or the contributions of cell epithelium and secretions from the salivary glands. A better understanding of these stone characteristics could pave the way for future non-invasive treatment strategies. Methods: Twenty-nine high-quality ductal stone samples were analyzed. The preparation included successive washings to avoid contamination from saliva and blood. The sialoliths were macerated in liquid nitrogen and the maceration was subjected to a sequential, four-step, protein extraction. The four fractions were pooled together, and a standardized aliquot was subjected to tandem liquid chromatography mass spectrometry (LCMS). The data output was subjected to a basic descriptive statistical analysis for parametric confirmation and a subsequent G.O.-KEGG data base functional analysis and classification for biological interpretation. Results: The LC-MS output detected 6934 proteins, 824 of which were unique for individual stones. An example of our sialolith protein data is available via ProteomeXchange with the identifier PXD012422. More important, the sialoliths averaged 53% homology with bone-forming proteins that served as a standard comparison, which favorably compared with 62% homology identified among all sialolith sample proteins. The non-homologous protein fraction had a highly variable protein identity. The G.O.-KEGG functional analysis indicated that extracellular exosomes are a primary cellular component in sialolithiasis. Light and electron microscopy also confirmed the presence of exosomallike features and the presence of intracellular microcrystals. Conclusion: Sialolith formation presents similarities with the hyperoxaluria that forms kidney stones, which suggests the possibility of a common origin. Further verification of a common origin could fundamentally change the way in which lithiasis is studied and treated.

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“…histone-H1B. 7 Two-thirds of proteins with oxalate-binding ability found in rat kidney and liver homogenates are localized in nucleus, whereas the other onethird are present in mitochondria. 7 The binding between nuclear proteins and oxalate has been proposed to mediate through a basic amino acid residue; i.e.…”

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confidence: 99%

“…In addition, the oxalatebinding bond can be disrupted by a lysine modifier, 4,4 0 -diisothiocyanostilbene 2,2 0 -disulfonic acid (DIDS). 7 Because of their roles in CaOx crystal modulation, oxalatebinding proteins should be investigated more extensively, and isolation as well as purification of oxalate-binding proteins derived from renal tubular epithelial cells are crucial. Previously, oxalate-binding proteins were labeled by 14 C-oxalate, which was used to bind with them, and were then purified by isolation of radioisotopic protein fractions using Sephadex and/or diethylaminoethyl (DEAE) columns.…”

mentioning

confidence: 99%

Development of an oxalate-affinity chromatographic column to isolate oxalate-binding proteins

Roop-ngam

Thongboonkerd

2010

Anal. Methods

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Calcium oxalate (CaOx) is the major crystalline component in kidney stones. Many previous studies on stone modulation have focused mainly to calcium-binding proteins, whereas oxalate-binding proteins remain under-investigated due to a lack of a simple method to purify oxalate-binding proteins. Therefore, we have developed an affinity chromatographic column to isolate or purify oxalate-binding proteins. The oxalate-affinity column developed contained EAH-Sepharose 4B beads conjugated with oxalic acid by carbodiimide reaction using 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) as an activator. The coupling efficacy of coupled beads (oxalic acid-EAH Sepharose 4B) was determined by a competitive ninhydrin assay to quantify the remaining amino group on EAH-Sepharose 4B. In addition, the oxalate-affinity column showed high specific binding to a known oxalate-binding protein (p62) but not to an irrelevant protein (carbonic anhydrase). In conclusion, we have established the oxalate-affinity chromatographic column, which showed the high efficiency to isolate oxalate-binding proteins. This novel chromatographic column will be very useful for future stone research, particularly in the area of stone modulation by oxalate-binding proteins.

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Characterization of histone (H1B) oxalate binding protein in experimental urolithiasis and bioinformatics approach to study its oxalate interaction

Cited by 7 publications

References 26 publications

Peeping into Human Renal Calcium Oxalate Stone Matrix: Characterization of Novel Proteins Involved in the Intricate Mechanism of Urolithiasis

Peeping into Human Renal Calcium Oxalate Stone Matrix: Characterization of Novel Proteins Involved in the Intricate Mechanism of Urolithiasis

A comprehensive analysis of sialolith proteins and the clinical implications

Development of an oxalate-affinity chromatographic column to isolate oxalate-binding proteins

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