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Protein Research

02:27 EDT 24th May 2018 | BioPortfolio

Proteomic analysis and prediction of amino acid variations that influence protein posttranslational modifications.

Accumulative studies have indicated that amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence protein posttranslational modifications (PTMs) and bring about a detrimental effect on protein function. Computational mutation analysis can greatly narrow down the efforts on experimental work. To increase the util...

Formation and characterization of chitosan-protein particles with fractal whey protein aggregates.

Hybrid protein-polysaccharide particles were formed by complexation of fractal whey protein aggregates and the cationic polysaccharide chitosan. The fractal aggregates were preformed by heating native whey protein isolate at pH 7 and subsequently mixed with chitosan at pH 3 where these proteins and polysaccharides don't interact with each other. Stable dispersions of protein-polysaccharide particl...

Influence of protein content and storage temperature on the particle morphology and flowability characteristics of milk protein concentrate powders.

Milk protein concentrate (MPC) powders are widely used as ingredients for food product formulations due to their nutritional profile and sensory attributes. Processing parameters, storage conditions, and composition influences the flow properties of MPC powders. This study investigated the bulk and shear flow properties of 70.3, 81.5, and 88.1% (wt/wt, protein content) MPC after storage for 12 wk ...

Glycation of whey protein with dextrans of different molar mass: Effect on immunoglobulin E-binding capacity with blood sera obtained from patients with cow milk protein allergy.

A growing concern around the world is the number of people who are suffering from food protein allergies. One potential approach to decrease protein allergenicity is to block IgE-binding epitopes of the protein allergen by attachment of polysaccharides via the Maillard reaction (i.e., glycation). Protein glycation has been extensively studied to modify various functional properties. We wanted to e...

Expression of a functional intrabody against hepatitis C virus core protein in Escherichia coli and silkworm pupae.

It has been shown that the single-domain intrabody 2H9-L against the hepatitis C virus (HCV) capsid (core) protein inhibits the viral propagation and NF-κB promoter activity induced by the HCV core. In this study, 2H9-L fused with the FLAG tag sequence was expressed in both Escherichia coli and silkworm pupae and then purified. In addition, the full-length and its C terminal deletions of the HCV ...

Interrogating the Dimerization Interface of the Prion Protein Via Site-Specific Mutations to p-Benzoyl-L-Phenylalanine.

Transmissible spongiform encephalopathies are centered on the conformational transition of the prion protein from a mainly helical, monomeric structure to a β-sheet rich ordered aggregate. Experiments indicate that the main infectious and toxic species in this process are however shorter oligomers, formation of which from the monomers is yet enigmatic. Here, we created 25 variants of the mouse pr...

The fine art of integral membrane protein crystallisation.

Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, h...

FTLD/ALS-linked TDP-43 mutations do not alter TDP-43's ability to self-regulate its expression in Drosophila.

TDP-43 is a major disease-causing protein in amyotrophic lateral sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD). Today, more than 50 missense mutations in the TARDBP/TDP-43 gene have been described in patients with FTLD/ALS. However, the functional consequences of FTLD/ALS-linked TDP-43 mutations are not fully elucidated. In the physiological state, TDP-43 expression is tightly regul...

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens.

Protein complexes are assemblies of subunits that have co-evolved to execute one or many coordinated functions in the cellular environment. Functional annotation of mammalian protein complexes is critical to understanding biological processes, as well as disease mechanisms. Here, we used genetic co-essentiality derived from genome-scale RNAi- and CRISPR-Cas9-based fitness screens performed across ...

Origin and pathophysiology of protein carbonylation, nitration and chlorination in age-related brain diseases and aging.

Non-enzymatic protein modifications occur inevitably in all living systems. Products of such modifications accumulate during aging of cells and organisms and may contribute to their age-related functional deterioration. This review presents the formation of irreversible protein modifications such as carbonylation, nitration and chlorination, modifications by 4-hydroxynonenal, removal of modified p...

Alternative Splicing of the Xmas mRNA Encoding the mRNA Export Protein in Drosophila melanogaster.

It is shown that Drosophila melanogaster has Xmas mRNA whose alternative splicing leads to the formation of three transcripts: Xmas, Xmas-2, and Xmas-1. As a result, three proteins are synthesized: Xmas, Xmas-2, and, presumably, Xmas-1. The size of the Xmas protein is close to the size of its homologue in humans. Adult flies contain large amounts of this protein, whereas in embryos it is absent.

Effects of protein kinase C and motigen-activated protein kinase kinase/extracellular regulated protein kinases signaling pathway on mRNA level of inducible nitric oxide synthase in Tca8113 cells.

To explore the regulatory mechanism of inducible nitric oxide synthase (NOS-2) expression related to proliferation of Tca8113 cells.

Dietary protein intake in school-age children and detailed measures of body composition: the Generation R Study.

A high-protein diet in infancy increases the risk of obesity, but the effects of dietary protein intake in mid-childhood on body composition are unclear. Therefore, we studied associations of protein intake (total, animal and plant-sourced) at 8 years of age with anthropometric measures and body composition up to age 10 years.

A brief practical review of size exclusion chromatography: Rules of thumb, limitations, and troubleshooting.

Through years of research, teaching, troubleshooting, and editing, I have developed a solid working understanding of many aspects of protein purification and protein biochemistry. I have also found that many researchers do not understand the basics, let alone the pitfalls, of the techniques they use. In the case of size exclusion chromatography (SEC), I summarize below some of the rules of thumb, ...

Shining a Light on Alport Syndrome.

In this issue of Cell Chemical Biology, Omachi et al. (2018) present a split Nanoluciferase system to identify successful protein trimerization in Alport syndrome. This elegant proof of concept suggests opportunities for drug screening for Alport syndrome and may be transferable to the study of other diseases affecting protein-protein interactions.

The direction of protein evolution is destined by the stability.

Protein evolution is potentially governed by protein stability. Here, we investigated the relationship between protein evolution and stability through the random mutational drift of a thermophilic bacterial protein, an esterase of Alicyclobacillus acidocaldarius (Aac-Est), at high and low temperatures. In the first random mutation of Aac-Est, few proteins exhibit increased activity at 65°C, indic...

Effects of environmental factors on C-type lectin recognition to zooxanthellae in the stony coral Pocillopora damicornis.

C-type lectin is a superfamily of Ca-dependent carbohydrate-recognition proteins that play significant roles in nonself-recognition and pathogen clearance. In the present study, a C-type lectin (PdC-Lectin) was chosen from stony coral Pocillopora damicornis to understand its recognition characteristics to zooxanthellae. PdC-Lectin protein contained a signal peptide and a carbohydrate-recognition d...

EB 2017 Article: Soy protein isolate feeding does not result in reproductive toxicity in the pre-pubertal rat testis.

The isoflavone phytoestrogens found in the soy protein isolate used in soy infant formulas have been shown to have estrogenic actions in the developing male reproductive tract resulting in reproductive toxicity. However, few studies have examined potential estrogenicity of soy protein isolate as opposed to that of pure isoflavones. In this study, we fed weanling male Sprague-Dawley rats a semi-pur...

Coomassie does it (better): A Robin Hood approach to total protein quantification.

Quantitative comparative proteomics require accurate and reproducible assessments of total protein concentration. We report a straightforward, cost-effective adaptation of an established commercial method for total protein quantification, utilising non-proprietary materials and colloidal Coomassie Brilliant Blue (cCBB) staining to achieve greater reproducibility, equal sensitivity, and optimal lin...

Abundant plasma protein depletion using ammonium sulfate precipitation and Protein A affinity chromatography.

Plasma is a highly valuable resource for biomarker research since it is easy obtainable and contains a high amount of information on patient health status. Although advancements in the field of proteomics enabled analysis of the plasma proteome, identification of low abundant proteins remains challenging due to high complexity and large dynamic range. In order to reduce the dynamic range of protei...

Protein aggregation in cell biology: An aggregomics perspective of health and disease.

Maintaining protein homeostasis (proteostasis) is essential for cellular health and is governed by a network of quality control machinery comprising over 800 genes. When proteostasis becomes imbalanced, proteins can abnormally aggregate or become mislocalized. Inappropriate protein aggregation and proteostasis imbalance are two of the central pathological features of common neurodegenerative disea...

Atomic displacement parameters in structural biology.

Atomic displacement parameters (ADPs, also known as B-factors), which depend on structural heterogeneity, provide a wide spectrum of information on protein structure and dynamics and find several applications, from protein conformational disorder prediction to protein thermostabilization, and from protein folding kinetics prediction to protein binding sites prediction. A crucial aspect is the stan...

Laser interferometry of the hydrolytic changes in protein solutions: the refractive index and hydration shells.

Using an original laser interferometer of enhanced sensitivity, an increase in the refractive index of a protein solution was observed during the reaction of proteolysis catalyzed by pepsin. The increase in the refractive index of the protein solution at a concentration of 4 mg/ml was [Formula: see text] for bovine serum albumin and [Formula: see text] for lysozyme. The observed effect disproves t...

Applications of proteomics in pharmaceutical research and development.

The significance of proteomics in the pharmaceutical industry has increased since overcoming initial difficulties. This review discusses recent proteomics publications from pharmaceutical companies to identify new trends in proteomics applications to research and development. Applications of proteomics such as chemical proteomics, protein expression profiling, targeted protein quantitation, analys...

A method for profiling the phosphorylation state of tyrosine protein kinases.

Protein kinases are known to be implicated in various biological phenomena and diseases through their involvement in protein phosphorylation. Therefore, analysis of the activity of protein kinases by examination of their phosphorylation state is important to elucidate their mechanisms. However, a method for analyzing the phosphorylation state of entire protein kinases in cells is not established. ...

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