Proteomics Study in Urolithiasis

2020 ◽  
Vol 17 (2) ◽  
pp. 88-94
Author(s):  
Manavi Jain ◽  
Paramveer Yadav ◽  
Priyadarshini
Keyword(s):  
Protein Interactions ◽  
Kidney Diseases ◽  
Stone Formation ◽  
Protein Composition ◽  
Protein Crystal ◽  
World Population ◽  
Protein Protein Interactions ◽  
Bioinformatic Tools ◽  
Proteomic Study ◽  
Stone Matrix

Urolithiasis, which is the presence of stones in the urinary tract, has long been linked with a higher risk of causing chronic kidney diseases and associated illnesses, such as diabetes-affecting 12% of the world population. This clinical condition arises due to the supersaturation of urine and alterations in the expression of cellular and urinary proteins. The renal stone mineral composition has been well understood and incorporated as a routine part of stone removal, however, the protein composition, an essential fraction of the stone matrix has been inadequately understood and not adeptly established. Stone proteomics consists of a number of techniques including crystal analysis using X-ray diffractometry and IR spectroscopy, sample purification, identification and characterization of proteins using high throughput mass spectrometric methods. However, not many studies have utilized the data obtained from these experiments to assign functional significance to associated identified proteins. Protein network analysis using bioinformatic tools such as STRING to study protein-protein interactions will enable researchers to get better insight into stone formation mechanics. Hence, a comprehensive proteomic study of kidney stone matrix will help in deciphering protein-crystal pathways generating novel information useful for clinical application.

Heat stability of homogenized milk: role of interfacial protein

1994 ◽  
Vol 61 (4) ◽  
pp. 507-516 ◽  
Author(s):  
Catharina H. McCrae ◽  
David Hirst ◽  
Andrew J. R. Law ◽  
D. Donald Muir
Keyword(s):  
Serum Protein ◽  
Protein Interactions ◽  
Protein Composition ◽  
Surface Protein ◽  
Heat Stability ◽  
Protein Protein Interactions ◽  
Ph Profile ◽  
Protein Components ◽  
The Individual

SummaryThe role of interfacial protein in determining the heat stability of recombined milk was investigated by removing serum protein prior to homogenization and reincorporating it after homogenization. In addition, the surface protein composition of recombined fat globules was probed by analyses of protein load and by quantification of the individual surface protein components using FPLC. In the absence of serum protein, substantially more casein was bound to the fat surface during homogenization. Despite this, the detrimental effect of homogenization on heat stability did not occur when serum protein had been removed from the system. Reincorporation of serum protein after homogenization caused the heat coagulation time–pH profile to revert to a form very similar to that observed without removing serum protein from the system. Thus, adsorption of serum protein did not affect heat stability. It is more likely that heat-induced interactions of serum protein with surface-adsorbed casein promoted heat coagulation. Fat surface area rather than casein load affected these interfacial protein-protein interactions during heating.

scholarly journals Sequential Protein Association with Nascent 60S Ribosomal Particles

2003 ◽  
Vol 23 (13) ◽  
pp. 4449-4460 ◽  
Author(s):  
Cosmin Saveanu ◽  
Abdelkader Namane ◽  
Pierre-Emmanuel Gleizes ◽  
Alice Lebreton ◽  
Jean-Claude Rousselle ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Ribosome Biogenesis ◽  
Protein Composition ◽  
Protein Protein Interactions ◽  
Protein Association ◽  
Functional Interactions ◽  
Coordinated Action ◽  
Specific Proteins

ABSTRACT Ribosome biogenesis in eukaryotes depends on the coordinated action of ribosomal and nonribosomal proteins that guide the assembly of preribosomal particles. These intermediate particles follow a maturation pathway in which important changes in their protein composition occur. The mechanisms involved in the coordinated assembly of the ribosomal particles are poorly understood. We show here that the association of preribosomal factors with pre-60S complexes depends on the presence of earlier factors, a phenomenon essential for ribosome biogenesis. The analysis of the composition of purified preribosomal complexes blocked in maturation at specific steps allowed us to propose a model of sequential protein association with, and dissociation from, early pre-60S complexes for several preribosomal factors such as Mak11, Ssf1, Rlp24, Nog1, and Nog2. The presence of either Ssf1 or Nog2 in complexes that contain the 27SB pre-rRNA defines novel, distinct pre-60S particles that contain the same pre-rRNA intermediates and that differ only by the presence or absence of specific proteins. Physical and functional interactions between Rlp24 and Nog1 revealed that the assembly steps are, at least in part, mediated by direct protein-protein interactions.

scholarly journals Biotinylation-based proximity labeling proteomics: Basics, applications, and technical considerations

2021 ◽  
Author(s):  
Tomoya Niinae ◽  
Yasushi Ishihama ◽  
Koshi Imami
Keyword(s):  
Protein Interactions ◽  
Cultured Cells ◽  
Protein Complexes ◽  
Protein Composition ◽  
Protein Protein Interactions ◽  
Spatiotemporal Resolution ◽  
Recent Developments ◽  
Protein Nucleic Acid ◽  
Enrichment Techniques ◽  
Technical Considerations

Summary Recent advances in biotinylation-based proximity labeling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein-protein interactions, protein-nucleic acid interactions, (membraneless) organelle proteomes, and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics, and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.

Probing Protein-Protein Interactions and Druggable Site Identification: Mechanistic Binding Events between Ubiquitin and Zinc Finger with UFM1-Specific Peptidase Domain Protein (ZUFSP)

2021 ◽  
Vol 24 ◽  
Author(s):  
Mary B. Ajadi ◽  
Opeyemi S. Soremekun ◽  
Ahmed A Elrashedy ◽  
Fisayo A. Olotu ◽  
Hezekiel M. Kumalo ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Protein Interactions ◽  
Dynamics Simulation ◽  
Cell Cycle Gene ◽  
Protein Protein Interactions ◽  
Deubiquitinating Enzymes ◽  
Bioinformatic Tools ◽  
Ubiquitin Binding ◽  
Domain Protein ◽  
The Impact

Background: Deubiquitinating enzymes (DUBs) protein family have been implicated in some deregulated pathways involved in carcinogenesis such as cell cycle, gene expression, and DNA damage response (DDR). Zinc finger with UFM1-specific peptidase domain protein (ZUFSP) is one of the recently discovered members of the DUBs Objectives: To identify and cross validate the ZUFSP binding site using the bioinformatic tools including SiteMap & Metapocket respectively. To understand the molecular basis of complementary ZUFSP-Ub interaction and associated structural events using MD Simulation Methods: In this study, four binding pockets were predicted, characterized, and cross-validated based on physiochemical features such as site score, druggability score, site volume, and site size. Also, Molecular dynamics simulation technique was employed to determine the impact of ubiquitin-binding on ZUFSP Results: Site 1 with a site score 1.065, Size 102, D scores 1.00, and size volume 261 was predicted to be the most druggable site. Structural studies revealed that upon ubiquitin-binding, the motional movement of ZUFSP was reduced when compared to the unbound ZUFSP. Also, the ZUFSP helical arm (ZHA) domain orient in such a way that it moves closer to the Ub, this orientation enables the formation of a UBD which is very peculiar to ZUFSP. Conclusion: The impact of ubiquitin on ZUFSP movement and the characterization of its predicted druggable site can be targeted in the development of therapeutics

scholarly journals CD82 and Gangliosides Tune CD81 Membrane Behavior

2021 ◽  
Vol 22 (16) ◽  
pp. 8459
Author(s):  
Laurent Fernandez ◽  
Morgane Malrieu ◽  
Christine Bénistant ◽  
Patrice Dosset ◽  
Eric Rubinstein ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Single Molecule ◽  
Protein Interactions ◽  
Mammary Epithelial Cells ◽  
Protein Composition ◽  
Mammary Epithelial ◽  
Protein Protein Interactions ◽  
Membrane Behavior ◽  
New Information ◽  
Lateral Segregation

Tetraspanins are a family of transmembrane proteins that form a network of protein–protein interactions within the plasma membrane. Within this network, tetraspanin are thought to control the lateral segregation of their partners at the plasma membrane through mechanisms involving specific lipids. Here, we used a single molecule tracking approach to study the membrane behavior of tetraspanins in mammary epithelial cells and demonstrate that despite a common overall behavior, each tetraspanin (CD9, CD81 and CD82) has a specific signature in terms of dynamics. Furthermore, we demonstrated that tetraspanin dynamics on the cell surface are dependent on gangliosides. More specifically, we found that CD82 expression increases the dynamics of CD81 and alters its localization at the plasma membrane, this has no effect on the behavior of CD9. Our results provide new information on the ability of CD82 and gangliosides to differentially modulate the dynamics and organization of tetraspanins at the plasma membrane and highlight that its lipid and protein composition is involved in the dynamical architecture of the tetraspanin web. We predict that CD82 may act as a regulator of the lateral segregation of specific tetraspanins at the plasma membrane while gangliosides could play a crucial role in establishing tetraspanin-enriched areas.

scholarly journals Application of Skyline for Analysis of Protein–Protein Interactions In Vivo

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7170
Author(s):  
Arman Kulyyassov
Keyword(s):  
Protein Interactions ◽  
Mammalian Cells ◽  
Protein Composition ◽  
Shotgun Proteomics ◽  
Cell Protein ◽  
Protein Protein Interactions ◽  
Proteomics Data ◽  
Liquid Chromatography Tandem Mass ◽  
High Level

Quantitative and qualitative analyses of cell protein composition using liquid chromatography/tandem mass spectrometry are now standard techniques in biological and clinical research. However, the quantitative analysis of protein–protein interactions (PPIs) in cells is also important since these interactions are the bases of many processes, such as the cell cycle and signaling pathways. This paper describes the application of Skyline software for the identification and quantification of the biotinylated form of the biotin acceptor peptide (BAP) tag, which is a marker of in vivo PPIs. The tag was used in the Proximity Utilizing Biotinylation (PUB) method, which is based on the co-expression of BAP-X and BirA-Y in mammalian cells, where X or Y are interacting proteins of interest. A high level of biotinylation was detected in the model experiments where X and Y were pluripotency transcription factors Sox2 and Oct4, or heterochromatin protein HP1γ. MRM data processed by Skyline were normalized and recalculated. Ratios of biotinylation levels in experiment versus controls were 86 ± 6 (3 h biotinylation time) and 71 ± 5 (9 h biotinylation time) for BAP-Sox2 + BirA-Oct4 and 32 ± 3 (4 h biotinylation time) for BAP-HP1γ + BirA-HP1γ experiments. Skyline can also be applied for the analysis and identification of PPIs from shotgun proteomics data downloaded from publicly available datasets and repositories.

Protein-protein interactions of the p53 family with the Bcl-2 family in hepatocellular carcinoma

2011 ◽  
Vol 49 (08) ◽  
Author(s):  
LC König ◽  
M Meinhard ◽  
C Sandig ◽  
MH Bender ◽  
A Lovas ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Protein Interactions ◽  
Protein Protein Interactions ◽  
P53 Family

Partial Purification of a Specific Plasminogen Activator from Porcine Parotid Glands

1974 ◽  
Vol 31 (03) ◽  
pp. 403-414 ◽  
Author(s):  
Terence Cartwright
Keyword(s):  
Nucleic Acid ◽  
Salivary Glands ◽  
Plasminogen Activator ◽  
Protein Interactions ◽  
Partial Purification ◽  
Protein Protein Interactions ◽  
Parotid Glands ◽  
Two Stage ◽  
Preliminary Characterization ◽  
Specific Inhibitors

SummaryA method is described for the extraction with buffers of near physiological pH of a plasminogen activator from porcine salivary glands. Substantial purification of the activator was achieved although this was to some extent complicated by concomitant extraction of nucleic acid from the glands. Preliminary characterization experiments using specific inhibitors suggested that the activator functioned by a similar mechanism to that proposed for urokinase, but with some important kinetic differences in two-stage assay systems. The lack of reactivity of the pig gland enzyme in these systems might be related to the tendency to protein-protein interactions observed with this material.

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