scholarly journals Profiling of lysine-acetylated proteins in human urine

2017 ◽  
Author(s):  
Weiwei Qin ◽  
Zhenhuan Du ◽  
He Huang ◽  
Youhe Gao
Keyword(s):  
Human Urine ◽  
High Resolution Mass Spectrometry ◽  
The Body ◽  
Lysine Acetylation ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Normal Human ◽  
Measurable Change

AbstractBiomarker is the measurable change associated with a physiological or pathophysiological process, its nature is change. Contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of the lysine acetylated proteins as biomarker in urine.

Separation and Characterization of Dermatan Sulfate in Normal Human Urine.

1993 ◽  
Vol 16 (4) ◽  
pp. 340-342 ◽  
Author(s):  
Guoning QIU ◽  
Masahiko TANIKAWA ◽  
Hiroshi AKIYAMA ◽  
Toshihiko TOIDA ◽  
Ichiro KOSHIISHI ◽  
...  
Keyword(s):  
Human Urine ◽  
Dermatan Sulfate ◽  
Normal Human

scholarly journals Lysine methylation is an endogenous post-translational modification of tau protein in human brain and a modulator of aggregation propensity

2014 ◽  
Vol 462 (1) ◽  
pp. 77-88 ◽  
Author(s):  
Kristen E. Funk ◽  
Stefani N. Thomas ◽  
Kelsey N. Schafer ◽  
Grace L. Cooper ◽  
Zhongping Liao ◽  
...  
Keyword(s):  
Human Brain ◽  
Tau Protein ◽  
Protein Function ◽  
Lysine Methylation ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
Aggregation Propensity ◽  
Normal Human ◽  
Tau Aggregation

Diverse post-translational modifications regulate tau protein function and misfolding. In the present study we identified lysine methylation as a tau post-translational modification in normal human brain, and found it depressed tau aggregation propensity when modelled in vitro.

scholarly journals VDACs Post-Translational Modifications Discovery by Mass Spectrometry: Impact on Their Hub Function

2021 ◽  
Vol 22 (23) ◽  
pp. 12833
Author(s):  
Maria Gaetana Giovanna Pittalà ◽  
Stefano Conti Nibali ◽  
Simona Reina ◽  
Vincenzo Cunsolo ◽  
Antonella Di Francesco ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Structural Characterization ◽  
High Performance ◽  
High Resolution Mass Spectrometry ◽  
Complex Mixture ◽  
Reversed Phase ◽  
Vital Role ◽  
Membrane Pore ◽  
Post Translational Modifications

VDAC (voltage-dependent anion selective channel) proteins, also known as mitochondrial porins, are the most abundant proteins of the outer mitochondrial membrane (OMM), where they play a vital role in various cellular processes, in the regulation of metabolism, and in survival pathways. There is increasing consensus about their function as a cellular hub, connecting bioenergetics functions to the rest of the cell. The structural characterization of VDACs presents challenging issues due to their very high hydrophobicity, low solubility, the difficulty to separate them from other mitochondrial proteins of similar hydrophobicity and the practical impossibility to isolate each single isoform. Consequently, it is necessary to analyze them as components of a relatively complex mixture. Due to the experimental difficulties in their structural characterization, post-translational modifications (PTMs) of VDAC proteins represent a little explored field. Only in recent years, the increasing number of tools aimed at identifying and quantifying PTMs has allowed to increase our knowledge in this field and in the mechanisms that regulate functions and interactions of mitochondrial porins. In particular, the development of nano-reversed phase ultra-high performance liquid chromatography (nanoRP-UHPLC) and ultra-sensitive high-resolution mass spectrometry (HRMS) methods has played a key role in this field. The findings obtained on VDAC PTMs using such methodologies, which permitted an in-depth characterization of these very hydrophobic trans-membrane pore proteins, are summarized in this review.

scholarly journals SwissPalm: Protein Palmitoylation database

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 261 ◽  
Author(s):  
Mathieu Blanc ◽  
Fabrice David ◽  
Laurence Abrami ◽  
Daniel Migliozzi ◽  
Florence Armand ◽  
...  
Keyword(s):  
Protein S ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Chemical Methods ◽  
Post Translational Modifications ◽  
P Protein ◽  
Multiple Alignments ◽  
Protein Palmitoylation ◽  
Recent Developments ◽  
Pathway Analyses

Protein S-palmitoylation is a reversible post-translational modification that regulates many key biological processes, although the full extent and functions of protein S-palmitoylation remain largely unexplored. Recent developments of new chemical methods have allowed the establishment of palmitoyl-proteomes of a variety of cell lines and tissues from different species.  As the amount of information generated by these high-throughput studies is increasing, the field requires centralization and comparison of this information. Here we present SwissPalm (http://swisspalm.epfl.ch), our open, comprehensive, manually curated resource to study protein S-palmitoylation. It currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than 500 specific sites of S-palmitoylation. SwissPalm also provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments. Systems analysis of the palmitoyl-proteome screens indicate that 10% or more of the human proteome is susceptible to S-palmitoylation. Moreover, ontology and pathway analyses of the human palmitoyl-proteome reveal that key biological functions involve this reversible lipid modification. Comparative analysis finally shows a strong crosstalk between S-palmitoylation and other post-translational modifications. Through the compilation of data and continuous updates, SwissPalm will provide a powerful tool to unravel the global importance of protein S-palmitoylation.

scholarly journals Structural Diversity of Ubiquitin E3 Ligase

Molecules ◽  
2021 ◽  
Vol 26 (21) ◽  
pp. 6682
Author(s):  
Sachiko Toma-Fukai ◽  
Toshiyuki Shimizu
Keyword(s):  
E3 Ligase ◽  
Structural Diversity ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
E3 Ligases ◽  
Cellular Processes ◽  
Ubiquitin E3 Ligase ◽  
Ubiquitin Ligase E3 ◽  
Ubiquitin Conjugating Enzyme

The post-translational modification of proteins regulates many biological processes. Their dysfunction relates to diseases. Ubiquitination is one of the post-translational modifications that target lysine residue and regulate many cellular processes. Three enzymes are required for achieving the ubiquitination reaction: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2), and ubiquitin ligase (E3). E3s play a pivotal role in selecting substrates. Many structural studies have been conducted to reveal the molecular mechanism of the ubiquitination reaction. Recently, the structure of PCAF_N, a newly categorized E3 ligase, was reported. We present a review of the recent progress toward the structural understanding of E3 ligases.

DIABETES-POST-TRANSLATIONAL PROTEIN MODIFICATION FOR DEVELOPMENT OF NEW DRUGS

INDIAN DRUGS ◽  
2014 ◽  
Vol 51 (09) ◽  
pp. 5-11
Author(s):  
P Menon ◽  
◽  
M S Kumar
Keyword(s):  
Glucose Level ◽  
Protein Modification ◽  
Epigenetic Modification ◽  
The Body ◽  
New Drugs ◽  
Metabolic Memory ◽  
Peroxisome Proliferator ◽  
Post Translational Modification ◽  
High Molecular Weight Adiponectin ◽  
Post Translational Modifications

Diabetes is a disorder associated with improper use of glucose by the body leading to increased level of glucose in the blood stream. Beta cells in the pancreas produce the hormone insulin, which is responsible for the movement of glucose into cells where it is utilized to produce energy. Due to the shortage of insulin in diabetic condition, the level of glucose in the bloodstream increases. The level of glucose within cells fall and thus the cells are not able to produce energy using glucose. It also gives rise to various other complications such as blindness, kidney failure, numbness in toes, delayed wound healing, cardiovascular complications, weight gain, loss of consciousness, disorientation etc. which in itself may be dangerous. The root cause of diabetes may either be lack of insulin being produced by the pancreas or development of resistance towards insulin leading to no effect of insulin on the glucose level. Post-translational modifications of protein control various biological processes. It is also considered as an important process in the pathogenesis of diabetes mellitus.In the current review, we will discuss the recent developments in post translational modification of genes associated with diabetes as well as epigenetic modification and metabolic memory that maybe responsible for the onset of diabetes and its associated complications. Currently research is being conducted on high molecular weight adiponectin, peroxisome proliferator-activated receptors (PPARγ), epigenetic histone modifications and Calpain 10 (CAPN10 gene encoded) protein based upon the post translational modifications they undergo and how these modifications affect glucose level regulation. This review article aims at shedding light upon recent advances in biotechnology that are focussed on studying the nature of protein modifications that result in diabetes and finding ways to prevent these modifications or stimulate a new modification that may result in better control of the disease state if not a cure.

scholarly journals In-Depth Mapping of the Urinary N-Glycoproteome: Distinct Signatures of ccRCC-related Progression

Cancers ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 239 ◽  
Author(s):  
Lucia Santorelli ◽  
Giulia Capitoli ◽  
Clizia Chinello ◽  
Isabella Piga ◽  
Francesca Clerici ◽  
...  
Keyword(s):  
Clear Cell ◽  
Glycosylation Site ◽  
Biological Processes ◽  
Label Free ◽  
Post Translational Modification ◽  
Cell Renal Cell Carcinoma ◽  
Altered Expression ◽  
Post Translational Modifications ◽  
Novel Biomarkers

Protein N-glycosylation is one of the most important post-translational modifications and is involved in many biological processes, with aberrant changes in protein N-glycosylation patterns being closely associated with several diseases, including the progression and spreading of tumours. In light of this, identifying these aberrant protein glycoforms in tumours could be useful for understanding the molecular mechanism of this multifactorial disease, developing specific biomarkers and finding novel therapeutic targets. We investigated the urinary N-glycoproteome of clear cell renal cell carcinoma (ccRCC) patients at different stages (n = 15 at pT1 and n = 15 at pT3), and of non-ccRCC subjects (n = 15), using an N-glyco-FASP-based method. Using label-free nLC-ESI MS/MS, we identified and quantified several N-glycoproteins with altered expression and abnormal changes affecting the occupancy of the glycosylation site in the urine of RCC patients compared to control. In particular, nine of them had a specific trend that was directly related to the stage progression: CD97, COCH and P3IP1 were up-expressed whilst APOB, FINC, CERU, CFAH, HPT and PLTP were down-expressed in ccRCC patients. Overall, these results expand our knowledge related to the role of this post-translational modification in ccRCC and translation of this information into pre-clinical studies could have a significant impact on the discovery of novel biomarkers and therapeutic target in kidney cancer.

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