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Protein Research

02:20 EDT 19th August 2018 | BioPortfolio

The Effect of Surfactants on Surface-Induced Denaturation of Proteins: Evidence of an Orientation-Dependent Mechanism.

When proteins bind to interfaces, the resulting changes in protein structure can lead to loss of protein function. We investigate the mechanism by which surfactant molecules can counteract surface-induced protein denaturation through a detailed study of the stability of the GB1 peptide at the air-water, ice-water and silica-water interfaces using molecular dynamics simulations coupled with metadyn...

Detecting Proline and Non-Proline Cis-Isomers In Protein Structures from Sequences Using Deep Residual Ensemble Learning.

It has been long established that cis conformations of amino acid residues play many biologically important roles despite their rare occurrence in protein structure. Due to this rarity, few methods have been developed for predicting cis-isomers from protein sequences, most of which are based on outdated datasets and lack the means for independent testing. In this work, using a database of >10000 h...

Correction: Environment-sensitive turn-on fluorescent probes for p53-MDM2 protein-protein interaction.

[This corrects the article DOI: 10.1039/C7MD00287D.].

Auto-regulated Protein Assembly on a Supramolecular Scaffold.

Controlled protein assembly provides a means to regulate function. Supramolecular building blocks, including rigid macrocycles, have proven to be versatile triggers of protein assembly. Here, we show that sulfonato-calix[8]arene (sclx8) mediates the formation of cytochrome c tetramers in solution. This tetramer spontaneously disassembles at ≥ 2 equivalents of sclx8 providing a remarkable example...

Mutations of G38R and D40G cause amyotrophic lateral sclerosis by reducing Annexin A11 protein stability.

To explore the role of the mutations G38R and D40G of Annexin A11 (ANXA11) in the onset of amyotrophic lateral sclerosis (ALS).
 Methods: The plasmids expressing ANXA11 wild type protein, ANXA11 G38R protein and ANXA11 D40G protein were constructed, respectively. The recombinant plasmids were then transfected into HEK293 cells respectively followed by cycloheximide (CHX) treatment for 0, 2, 4 an...

Research progress in PRAS40.

Prolin-rich Akt substrate of 40 kD (PRAS40) is firstly identified as a partner of 14-3-3 protein and a substrate of Akt kinase by Roth et al in 2003. Accumulated evidence shows that PRAS40 is mainly activated by phosphorylate modification at different sites. PRAS40 may be involved in various of signaling pathways, such as mammalian target of rapamycin complex 1 (mTORC1), protein kinase B (Akt), NF...

Effects of baicalin on inflammatory reaction, oxidative stress and PKDl and NF-kB protein expressions in rats with severe acute pancreatitis1.

To investigate the effects of baicalin on inflammatory reaction, oxidative stress and protein kinase D1 (PKD1) and nuclear factor-kappa B (NF-κB) protein expressions in severe acute pancreatitis (SAP) rats.

The 3-D structure of VNG0258H/RosR - a haloarchaeal DNA-binding protein in its ionic shell.

Protein-DNA interactions are highly dependent on salt concentration. To gain insight into how such interactions are maintained in the highly saline cytoplasm of halophilic archaea, we determined the 3-D structure of VNG0258H/RosR, the first haloarchaeal DNA-binding protein from the extreme halophilic archaeon Halobactrium salinarum. It is a dimeric winged-helix-turn-helix (wHTH) protein with uniqu...

Alpha-synuclein modulates the physical properties of DNA.

Fundamental research on Parkinson's disease (PD) most often focuses on the ability of alpha-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here we have investigated the interaction between monomeric aS and DNA in vitro with single molecule techniques. Using a...

A new biomarker candidate for spinal muscular atrophy: Identification of a peripheral blood cell population capable of monitoring the level of survival motor neuron protein.

Spinal muscular atrophy (SMA) is a severe genetic neuromuscular disorder caused by insufficiency of functional survival motor neuron (SMN) protein. Several clinical trials have been conducted with the aim of upregulating the expression of the SMN protein in SMA patients. In order to evaluate the efficiency of these SMN-targeted approaches, it has become necessary to verify SMN protein levels in th...

The use of a surface active agent in the protection of a fusion protein during bioprocessing.

The bioprocessing of a fusion protein is characterised by low yields and at a series of recovery and purification stages which leads to an overall 90% loss. Much of this apparent loss is due to the denaturation of a protein, missing a vital affinity ligand. However there is evidence of the protection of degradation products which occurs in the presence of shear plus air/liquid interfaces. This wor...

Bioavailability of Pyrene Associated with Different Types of Protein Compounds: Direct Evidence for Its Uptake by Daphnia magna.

The protein-like dissolved organic matter (DOM) is ubiquitous in aquatic environments. However, the bioavailability of protein-like DOM-associated hydrophobic organic compounds (HOCs) is not well understood, and in particular, the direct evidence of their uptake by organisms is scarce. In the present work, the tryptone (2 000 Da), bovine serum albumin (BSA, 66 000 Da), and phycocyanin (120 000 Da)...

A fully automated three-step protein purification procedure for up to five samples using the NGC chromatography system.

The drug discovery process in the biopharmaceutical industry usually starts with the generation of plasmids coding for certain proteins. Due to advances in cloning techniques the generation of thousands of different plasmids is not a limiting factor anymore. The next step is the expression and evaluation of the proteins. In recent years significant progress has been made in the miniaturization of ...

Computer-Guided Surface Engineering for Enzyme Improvement.

Protein engineering strategies are often guided by our understanding of how the structure of a protein determines its function. However, our understanding is generally restricted to small regions of a protein, namely the active site and its immediate vicinity, while the remainder of the protein is something of an enigma. Studying highly homologous transaminases with strictly conserved active sites...

Accelerated pharmaceutical protein development with integrated cell free expression, purification, and bioconjugation.

The use of living cells for the synthesis of pharmaceutical proteins, though state-of-the-art, is hindered by its lengthy process comprising of many steps that may affect the protein's stability and activity. We aimed to integrate protein expression, purification, and bioconjugation in small volumes coupled with cell free protein synthesis for the target protein, ciliary neurotrophic factor. Split...

The Roles of Acetic Acid and Methanol During Fixing and Staining Proteins in an SDS-Polyacrylamide Electrophoresis Gel.

After SDS-polyacrylamide gel electrophoresis proteins are "fixed" in the gel to prevent dispersion of the proteins and visualized by staining with a chromogenic dye. Dyes like Coomassie Blue R-250, Amido Black, and Direct Red 81 are usually dissolved in an acetic acid-methanol-water mixture. During staining the dye solvent mixture infuses the gel and interacts with the protein. Acetic acid and met...

Multicolored Prestained Standard Protein Marker Generation Using a Variety of Remazol Dyes for Easy Visualization of Protein Bands During SDS-PAGE.

Isolation and detection of a specific protein from a complex mixture of proteins using molecular sieves provided by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is a widely used technique in molecular biology and biochemistry. The detection is achieved usually by running prestained standard markers along with the sample protein mixture. Multicolored standard markers are pre...

In-Gel Protein Phosphatase Assay Using Fluorogenic Substrates.

Protein phosphorylation plays important roles in regulating a variety of biological processes in animals, plants, and microorganisms. Therefore, it is important to use appropriate techniques to detect and analyze protein kinases and protein phosphatases. In this chapter, we describe the method to detect protein phosphatase activities using fluorogenic substrates such as 4-methylumbelliferyl phosph...

The P Granules of C. elegans: A Genetic Model for the Study of RNA-Protein Condensates.

P granules are RNA/protein condensates in the germline of C. elegans. Genetic analyses have begun to identify the proteins that regulate P granule assembly in the cytoplasm of zygotes. Among them, the RGG-domain protein PGL-3, the intrinsically-disordered protein MEG-3, and the RNA helicase LAF-1 all bind and phase separate with RNA in vitro. We discuss how RNA-induced phase separation, competitio...

Ischemic tau protein gene induction as an additional key factor driving development of Alzheimer's phenotype changes in CA1 area of hippocampus in an ischemic model of Alzheimer's disease.

Tauopathies are a class of neurodegenerative illnesses associated with the aberrant accumulation of the tau protein in the brain. The best known out of these diseases is Alzheimer's disease, a disorder where the microtubule associated tau protein becomes hyperphosphorylated (which lowers its binding affinity to microtubules) and accumulates inside neurons in the form of tangles. In this study, we ...

Water-Mediated Protein-Protein Interactions at High Pressures are Controlled by a Deep-Sea Osmolyte.

The influence of natural cosolvent mixtures on the pressure-dependent structure and protein-protein interaction potential of dense protein solutions is studied and analyzed using small-angle X-ray scattering in combination with a liquid-state theoretical approach. The deep-sea osmolyte trimethylamine-N-oxide is shown to play a crucial and singular role in its ability to not only guarantee sustaina...

Upregulation of miR-370 and miR-543 is associated with reduced expression of heat shock protein 40 in spinocerebellar ataxia type 3.

Molecular chaperones are important regulators of protein folding and proteasomal removal of misfolded proteins. In spinocerebellar ataxia type 3 (SCA3), the co-chaperone DnaJ homology subfamily B member 1 (DNAJB1 or heat shock protein 40) is recruited to protein aggregates formed by the disease-causing mutant polyglutamine (polyQ) protein ataxin-3 (ATXN3). Over-expression of DNAJB1 reduces polyQ p...

Quantitative characterization of UDP-glucuronosyltransferase 2B17 in human liver and intestine and its role in testosterone first-pass metabolism.

Protein abundance and activity of UGT2B17, a highly variable drug- and androgen-metabolizing enzyme, was quantified in microsomes, S9, and primary cells isolated from human liver and intestine by a validated LC-MS/MS methods. UGT2B17 protein abundance showed >160-fold variation (mean ± SD, 1.7 ± 2.7 pmol/mg microsomal protein) in adult human liver microsomes (n=26) and significant correlation (r...

Functionalised dairy streams: Tailoring protein functionality using sonication and heating.

Ultrasound can be used to modify the functional interactions between casein and whey proteins in dairy systems. This study reports on ongoing developments in understanding the effect of ultrasound and heating on milk proteins in systems with modified casein-whey protein ratios (97:3, 80:20 and 50:50), prepared from milk protein concentrates that were fractionated by microfiltration, based on prote...

Application of non-canonical crosslinking amino acids to study protein-protein interactions in live cells.

The genetic incorporation of non-canonical amino acids (ncAAs) equipped with photo-crosslinking and chemical crosslinking moieties has found broad application in the study of protein-protein interactions from a unique perspective in live cells. We highlight here applications of photo-activatable ncAAs to map protein interaction surfaces and to capture protein-protein interactions, and we describe ...

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