Quality Control, Preparation, and Protein Stability Issues for Blood Serum and Plasma Used In Biomarker Discovery and Proteomic Profiling Assays

2004 ◽  
Vol 3 (4) ◽  
pp. 45-50 ◽  
Author(s):  
Richard Drake ◽  
Lisa Cazares ◽  
Alberto Corsica ◽  
Gunjan Malik ◽  
Ellen Schwegler ◽  
...  
Keyword(s):  
Quality Control ◽  
Blood Serum ◽  
Protein Stability ◽  
Biomarker Discovery ◽  
Proteomic Profiling ◽  
Stability Issues

scholarly journals A glycine-specific N-degron pathway mediates the quality control of protein N-myristoylation

Science ◽  
2019 ◽  
Vol 365 (6448) ◽  
pp. eaaw4912 ◽  
Author(s):  
Richard T. Timms ◽  
Zhiqian Zhang ◽  
David Y. Rhee ◽  
J. Wade Harper ◽  
Itay Koren ◽  
...  
Keyword(s):  
Quality Control ◽  
Protein Stability ◽  
Protein Degradation ◽  
E3 Ligase ◽  
Cleavage Sites ◽  
Caspase Cleavage ◽  
E3 Ligases ◽  
Ring E3 Ligase ◽  
The Stability ◽  
Ring E3

The N-terminal residue influences protein stability through N-degron pathways. We used stability profiling of the human N-terminome to uncover multiple additional features of N-degron pathways. In addition to uncovering extended specificities of UBR E3 ligases, we characterized two related Cullin-RING E3 ligase complexes, Cul2ZYG11B and Cul2ZER1, that act redundantly to target N-terminal glycine. N-terminal glycine degrons are depleted at native N-termini but strongly enriched at caspase cleavage sites, suggesting roles for the substrate adaptors ZYG11B and ZER1 in protein degradation during apoptosis. Furthermore, ZYG11B and ZER1 were found to participate in the quality control of N-myristoylated proteins, in which N-terminal glycine degrons are conditionally exposed after a failure of N-myristoylation. Thus, an additional N-degron pathway specific for glycine regulates the stability of metazoan proteomes.

scholarly journals Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform

2012 ◽  
Vol 2012 ◽  
pp. 1-8
Author(s):  
Amita R. Oka ◽  
Matthew P. Kuruc ◽  
Ketan M. Gujarathi ◽  
Swapan Roy
Keyword(s):  
Biomarker Discovery ◽  
Brain Homogenate ◽  
Disease Diagnosis ◽  
Bovine Brain ◽  
Tissue Cell ◽  
Kinetic Properties ◽  
Proteomic Profiling ◽  
Tissue Samples ◽  
Camp Hydrolysis ◽  
Few Data

Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. It begins with surface-based proteome separations of tissue/cell-line extracts, using SeraFILE, a proprietary protein separations platform. Enzyme kinetic properties of resulting subproteomes are then characterized, and the data integrated into proteomic profiles. As a model, SeraFILE-derived subproteomes of cyclic nucleotide-hydrolyzing phosphodiesterases (PDEs) from bovine brain homogenate (BBH) and rat brain homogenate (RBH) were characterized for cAMP hydrolysis activity in the presence (challenge condition) and absence of cGMP. Functional profiles of RBH and BBH were compiled from the enzyme activity response to the challenge condition in each of the respective subproteomes. Intersample analysis showed that comparable profiles differed in only a few data points, and that distinctive subproteomes can be generated from comparable tissue samples from different animals. These results demonstrate that the proposed methods provide a means to simplify intersample differences, and to localize proteins attributable to sample-specific responses. It can be potentially applied for disease and nondisease sample comparison in biomarker discovery and drug discovery profiling.

Proteomic Profiling for Colorectal Cancer Biomarker Discovery

2018 ◽  
pp. 241-269 ◽  
Author(s):  
Paula Álvarez-Chaver ◽  
Loretta De Chiara ◽  
Vicenta Soledad Martínez-Zorzano
Keyword(s):  
Colorectal Cancer ◽  
Biomarker Discovery ◽  
Cancer Biomarker ◽  
Proteomic Profiling

scholarly journals Genetics Meets Proteomics: Correlating the Portuguese Water Dog Blood Serum Proteome with Genetic Markers

2011 ◽  
Vol 4 ◽  
pp. PRI.S6470
Author(s):  
Sandra Sénéchal ◽  
Martin Kussmann
Keyword(s):  
Blood Serum ◽  
Biomarker Discovery ◽  
Protein Quantification ◽  
Label Free ◽  
Blood Profile ◽  
Serum Proteome ◽  
Genetic Level ◽  
Portuguese Water ◽  
Dog Blood ◽  
Genetically Determined

Blood serum is a body fluid widely used for biomarker discovery and therefore numerous studies aim at defining its proteome. The serum proteome is subject to fluctuations resulting from biological variability (eg, diurnal variations) reflecting both healthy and/or disease-related conditions. Inter-individual differences originate partly at the genetic level and may influence clinical blood profile including the serum proteome. Therefore we investigated whether serum protein abundance is genetically determined: we report the study of a cohort of 146 Portuguese Water Dogs, a dog breed whose genetic background has been well characterized. We generated protein profiles of dog sera on 1D-gels and correlated them with microsatellite markers. We detected correlations between 7 gel bands and 11 genetic regions and developed a label-free protein quantification method to identify and quantify the proteins most accountable for serum proteome variation. An association between the abundance of RBP4 in dog serum and the adiponectin gene was detected.

scholarly journals Protein stability: a crystallographer's perspective

2016 ◽  
Vol 72 (2) ◽  
pp. 72-95 ◽  
Author(s):  
Marc C. Deller ◽  
Leopold Kong ◽  
Bernhard Rupp
Keyword(s):  
Protein Stability ◽  
Conformational Stability ◽  
Factors Affecting ◽  
Food Industries ◽  
Compositional Stability ◽  
Major Interest ◽  
Protein Conformational Stability ◽  
Academic Researchers ◽  
Stability Issues ◽  
Practical Level

Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.

Proteomic Profiling of the Blood Serum for Prediction of Premature Delivery

2016 ◽  
Vol 161 (6) ◽  
pp. 829-832 ◽  
Author(s):  
V. O. Gunko ◽  
T. N. Pogorelova ◽  
V. A. Linde
Keyword(s):  
Blood Serum ◽  
Premature Delivery ◽  
Proteomic Profiling

scholarly journals Proteomic profiling in MPTP monkey model for early Parkinson disease biomarker discovery

2015 ◽  
Vol 1854 (7) ◽  
pp. 779-787 ◽  
Author(s):  
Xiangmin Lin ◽  
Min Shi ◽  
Jeyaraj Gunasingh Masilamoni ◽  
Romel Dator ◽  
James Movius ◽  
...  
Keyword(s):  
Parkinson Disease ◽  
Biomarker Discovery ◽  
Proteomic Profiling ◽  
Disease Biomarker ◽  
Monkey Model

Direct proteomic profiling of human urine and blood serum in an experiment with five-day dry immersion

2015 ◽  
Vol 41 (7) ◽  
pp. 732-737
Author(s):  
L. Kh. Pastushkova ◽  
N. A. Pakharukova ◽  
N. M. Novoselova ◽  
I. V. Dobrokhotov ◽  
O. A. Valeeva ◽  
...  
Keyword(s):  
Blood Serum ◽  
Human Urine ◽  
Proteomic Profiling ◽  
Dry Immersion
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