A newcomer to the -omics era, proteomics, is a broad instrument-intensive research area that has advanced rapidly since its inception less than 20 years ago. Although the 'wet-bench' aspects of proteomics have undergone a renaissance with the improvement in protein and peptide separation techniques, including various improvements in two-dimensional gel electrophoresis ...

Poor fertility rates are often observed when fresh ram semen stored in conventional extenders is used for cervical artificial insemination (AI). Heat-shock 70-kDa protein 8 (HSPA8), found within the oviduct, prolongs boar, ram and bull sperm survival at body temperatures in vitro. Here, we aimed to determine whether supplementing extenders ...

We describe improved methods for large format, two-dimensional gel electrophoresis (2DE) that improve protein solubility and recovery, minimize proteolysis, and reduce the loss of resolution due to contaminants and manipulations of the gels, and thus enhance quantitative analysis of protein spots. Key modifications are: (i) the use of 7 M ...

Since its initial discovery as an atypical protein kinase C (PKC)-interacting protein, p62 has emerged as a crucial molecule in a myriad of cellular functions. This multifunctional role of p62 is explained by its ability to interact with several key components of various signaling mechanisms. Not surprisingly, p62 is required ...

A study was carried out to assess the effect of sequestration of PDC-109 protein, a majority constituent of heparin binding proteins (HBP) of seminal plasma, on freezability and in vitro fertilizing ability of crossbred bull spermatozoa after cryopreservation. The study consisted of isolation and characterization of PDC-109 protein to raise ...

SMAD transcription factors are key mediators of the transforming growth factor-beta (TGFß) family of cytokines. Reversible phosphorylation of SMAD proteins plays a key role in regulating their function. Several phosphatases have been proposed to act on SMAD proteins to influence TGFß/BMP signalling. Here we provide an overview of the SMAD ...

Linking bioactive compounds to their cellular targets is a central challenge in chemical biology. Herein we report the mode of action of perthamide C, a natural cyclopeptide isolated from the marine sponge Theonella swinhoei. Through an emerging mass spectrometry-based chemical proteomics approach, Heat Shock Protein 90 and Glucose Regulated Protein ...

Improved protein assays promise to offer new insights into biological processes as well as the identification of new, clinically important biomarkers. In recent years, a number of approaches have been developed where protein-binding reagents, typically antibodies, are equipped with DNA strands to enable protein analyses via powerful nucleic acid detection ...

In biochemical networks, identifying key proteins and protein-protein reactions that regulate fluctuation-driven transitions leading to pathological cellular function is an important challenge. Using large deviation theory, we develop a semianalytical method to determine how changes in protein expression and rate parameters of protein-protein reactions influence the rate of such transitions. ...

Filtering of protein secondary structure prediction aims to provide physicochemically realistic results, while it usually improves the predictive performance. We performed a comparative study on this challenging problem, utilising both machine learning techniques and empirical rules and we found that combinations of the two lead to the highest improvement.

The ability to engineer novel protein folds, conformations, and enzymatic activities offers enormous potential for the development of new protein therapeutics and biocatalysts. However, many de novo and redesigned proteins exhibit poor hydrophobic packing in their predicted structures, leading to instability or insolubility. The general utility of rational, structure-based design ...

Chemical modification or mutation of proteins may bring about significant changes in the net charge or surface hydrophobicity of a protein structure. Such events may be of major physiological significance and may provide important insights into the genetics of amyloid diseases. In the present study, fibrillation potential of native and ...

Cyan variants of green fluorescent protein are widely used as donors in Förster resonance energy transfer experiments. The popular, but modestly bright, Enhanced Cyan Fluorescent Protein (ECFP) was sequentially improved into the brighter variants Super Cyan Fluorescent Protein 3A (SCFP3A) and mTurquoise, the latter exhibiting a high-fluorescence quantum yield and ...

Generating diverse protein libraries that contain improved variants at a sufficiently high frequency is critical for improving the properties of proteins using directed evolution. Many studies have illustrated how random mutagenesis, cassette mutagenesis, DNA shuffling and similar approaches are effective diversity generating methods for directed evolution. Very few studies have ...

Very large proteins (subunit sizes >200 kDa) are difficult to electrophoretically separate on polyacrylamide gels. A SDS vertical agarose gel system has been developed that has vastly improved resolving power for very large proteins. Proteins with molecular masses between 200 and 4,000 kDa can be clearly separated. Inclusion of a ...

Over the recent years, a number of genomes have been successfully sequenced and this was followed by genome annotation projects to help understand the biological capabilities of newly sequenced genomes. To improve the annotation of Plasmodium falciparum proteins, we earlier developed parasite specific matrices (PfSSM) and demonstrated their (Smat80 and ...

Genomic analyses have identified segments with high fiber-forming propensity in many proteins not known to form amyloid. Proteins are often protected from entering the amyloid state by molecular chaperones that permit them to fold in isolation from identical molecules; but how do proteins self-chaperone their folding in the absence of ...

HET-s is a prion protein of the filamentous fungus Podospora anserina. An orthologue of this protein, called FgHET-s has been identified in Fusarium graminearum. The region of the FgHET-s protein corresponding to the prion forming domain of HET-s, forms amyloid fibrils in vitro. These fibrils seed HET-s(218-289) fibril formation in ...

In well-characterised species of the Rhodobacter (Rba.) genus of purple photosynthetic bacteria it is known that the photochemical reaction centre (RC) is intimately-associated with an encircling LH1 antenna pigment protein, and this LH1 antenna is prevented from completely surrounding the RC by a single copy of the PufX protein. In ...

Dimers formed by seven isoforms of the human 14-3-3 protein participate in multiple cellular processes. The dimeric form has been extensively characterized, however, little is known about the structure and properties of the monomeric form of 14-3-3. The monomeric form is involved in the assembly of homo- and heterodimers, which ...

Oligomer forms of proteins are formed by self and cross association or complex formation with ligands. Modelling studies using an ion-exchange adsorbent have demonstrated that the formation of an oligomer form of a target protein can improve a chromatographic separation because the oligomer form displaces the impurities. The results of ...

Nutrients are primary requirements for development of conceptuses (embryo and extra-embryonic membranes), including protein synthesis. We have shown that arginine (Arg), leucine (Leu), and glucose stimulate protein synthesis through phosphorylation of MTOR signaling molecules, thereby increasing proliferation of ovine trophectoderm cells. This study determined whether Arg, Leu, glutamine (Gln) and ...

Oral contraceptive (OC) treatment has an inhibiting effect on protein synthesis in tendon and muscle connective tissue. We aimed to investigate whether OC influence myofibrillar protein turnover in young women. OC-users (24±2 years; Lindynette® n=7, Cilest® n=4) and non-OC-users (controls, 24±4 years n=12) performed one-legged kicking exercise. The next day, ...

We here report in Pisum sativum system a novel protein-protein interaction of β-subunit of heterotrimeric G-proteins (PsGβ) with a Mitogen activated protein kinase (PsMPK3) during cDNA library screening by yeast-two-hybrid assay. The transcript of these two genes also showed co-regulation under abscisic acid (ABA) and methyl jasmonate (MeJA) treatments. The ...

Sepsis-induced muscle atrophy is produced in part by decreased protein synthesis mediated by inhibition of mTOR (mammalian target of rapamycin). The present study tests the hypothesis that alteration of specific protein-protein interactions within the mTORC1 (mTOR complex 1) contributes to the decreased mTOR activity observed after cecal ligation and puncture ...

The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming ...

Glucagon-like peptide-2 (GLP-2) is a nutrient-responsive neuropeptide that exerts diverse actions in the gastrointestinal tract, including enhancing mucosal cell survival and proliferation. GLP-2 stimulates mucosal growth in vivo with an increased rate of protein synthesis. However, it was unclear whether GLP-2 can directly stimulate protein synthesis. The objective was to ...

Current evidence suggests that exercise and glial cell line-derived neurotrophic factor (GDNF) independently cause significant morphological changes in the neuromuscular system. The aim of the current study was to determine if increased physical activity regulates GDNF protein content in rat skeletal muscle. Extensor Digitorum Longus (EDL) and Soleus (SOL) hind ...

Growing evidence supports the conclusion that consumption of protein in close temporal proximity to the performance of resistance exercise promotes greater muscular hypertrophy. We can also state with good certainty that merely consuming energy, as carbohydrate for example, is also not sufficient to maximise muscle protein synthesis leading to anabolism ...

Tenderness is a key palatability trait influencing perception of consumers of meat quality and is influenced by a multitude of factors, including postmortem proteolysis. A fundamental understanding of this biological mechanism regulating tenderness is necessary to decrease variability and increase consumer satisfaction. However, reports regarding the enzyme systems involved in ...

A relatively new technology in wound care, negative pressure wound therapy (NPWT), has become widely used for the management of open abdomens and soft tissue wounds and provides a means to collect wound exudate to quantify protein loss. A prospective observational study was conducted in surgical, trauma, or burn patients ...

We previously showed that human muscle protein synthesis (MPS) increased during infusion of amino acids (AAs) and peaked at ≈120 min before returning to baseline rates, despite elevated plasma AA concentrations. We tested whether a protein meal elicited a similar response and whether signaling responses that regulate messenger RNA translation ...

To investigate the effects of a neonatal low-protein diet on the morphology of myotubes in culture and the expression of key proteins that regulate myogenesis in young and adult rats. Male Wistar rats (n = 18) were suckled by mothers fed diets containing 17% protein (controls, C) or 8% protein (undernourished, UN). ...

Cre/loxP recombination enables cellular specificity and, in the case of inducible systems, temporal control of genomic deletions. Here we used a SM22α tamoxifen-inducible Cre line to inactivate β1 integrin in adult smooth muscle. Interestingly, analysis of two distinct β1 loxP transgenic mice revealed vastly different outcomes after β1 integrin deletion. ...

An ethanolic extract of Artemisia dracunculus L. (PMI 5011) has been observed to decrease glucose and insulin levels in animal models and enhance cellular signaling in cultured cells. To determine the mechanism of action of PMI-5011, we have measured changes in protein expression in human primary skeletal muscle culture (HSMC) ...

To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo. None of the available methods for determining protein breakdown can be used to determine the breakdown rate of specific proteins ...

Erectile dysfunction (ED) is a serious medical condition that affects 16-82% of prostate cancer patients treated by radical prostatectomy and current treatments are ineffective in 50-60% of prostatectomy patients. The reduced efficacy of treatments makes novel therapeutic approaches to treat ED essential. The secreted protein Sonic hedgehog (SHH) is a ...

Dietary protein intake is known to affect whole body and interorgan protein turnover. We examined if moderate-nitrogen and carbohydrate casein and soy meals have a different effect on skeletal muscle protein and amino acid kinetics in healthy young subjects. Muscle protein and amino acid kinetics were measured in the postabsorptive ...

The organophosphate pesticide chlorpyrifos significantly decreased the specific activities of catalase (CAT) and lactate dehydrogenase (LDH) in brain, liver, gill and skeletal muscle of the freshwater catfish, Heteropneustes fossilis. It may be due to binding of the pesticide or its metabolite(s) with the enzyme molecules or affecting the synthesis and/or ...

Leucine-rich repeat containing proteins are involved in immune response in many capacities. In insects, these include Toll-like receptors and the Anopheles gambiae proteins APL1 and LRIM1. Here we describe the identification and characterization of leureptin, a novel extracellular protein with 13 leucine-rich repeats from hemolymph of the insect Manduca sexta. ...

Accumulation of protein aggregates is a hallmark of several neurodegenerative disorders as well as for a number of protein conformation-based diseases, including those affecting muscle, liver and heart. Desminopathy or desmin-related myopathy (DRM) is a skeletal myopathy characterized by bilateral muscle weakness, but is often accompanied by cardiomyopathy as well. ...

Depletion of skeletal muscle protein mainly results from enhanced protein breakdown, caused by activation of proteolytic systems such as the Ca2+-dependent and the ATP-ubiquitin-dependent ones. In the last few years, enhanced expression and bioactivity of myostatin have been reported in several pathologies characterized by marked skeletal muscle depletion. More recently, ...

Skeletal muscle is a plastic tissue with known gender dimorphism, especially at the metabolic level. A proteomic comparison of male and female murine biceps brachii was undertaken, resolving an average of 600 protein spots of MW 15-150 kDa and pI 5-8. Twenty-six unique full-length proteins spanning 11 KOG groups demonstrated ...

The objective was to determine the effect of muscle location on protein solubility and protein degradation in deep (DSM) and superficial (SSM) portion of beef semimembranosus. At 24 h postmortem, the semimembranosus was removed from beef carcasses (n=10), packaged in high-oxygen modified atmosphere (80% O2+20% CO2), and displayed for 7 ...

The global turnover rates of cellular proteins and the secretion rate of a recombinant immunoglobulin G (IgG) in a myeloma cell line, NS0, were determined using SILAC proteomic analysis. After complete labeling of cellular proteins with (13)C(6), (15)N(4)-arginine, cells were transferred to unlabeled medium and the decay of the labeled ...

Defects in insulin/IGF-1 signaling stimulate muscle protein loss by suppressing protein synthesis and increasing protein degradation. Since an herbal compound, berberine, lowers blood levels of glucose and lipids, we proposed that it would improve insulin/IGF-1 signaling, blocking muscle protein losses. We evaluated whether berberine ameliorates muscle atrophy in db/db mice, ...

We investigated the physiological and behavioral consequences for prey breeding at different distances from a nesting predator. In a natural setting, Pied Flycatchers (Ficedula hypoleuca) made territory location decisions relative to established Sparrowhawk (Accipiter nisus) nests. From female flycatchers attending nests at different distances from Sparrowhawk nests, we measured body ...

Prior to the emergence of life, it is believed that only L-amino acids were selected for formation of proteins, and that D-amino acids were eliminated on the primitive Earth. Whilst homochirality is essential for life, recently the occurrence of proteins containing D-beta-aspartyl (Asp) residues from various tissues of elderly subjects ...

During continuous tracer infusion and steady state conditions, it is unclear whether different study designs (single vs. multiple biopsies) will yield identical rates of intestinal protein synthesis. We reviewed the available literature and used hypothetical pool models to derive protein synthetic rates for different study techniques. There is strong evidence ...

It is certain that meat tenderness is a highly valued consumer trait and thus definition of the multiple processes that influence meat tenderness will provide clues toward improving meat quality and value. The natural process by which meat becomes tender is complex. Tenderness development is dependent on the architecture and ...