Top down - The Fenyo Lab
... RED: triplicate experiments, FAl treated grindate BLACK: duplicated experiments, FAl treated cells (then ground) SCORE: Log Ion Current / Log protein abundance ...
... RED: triplicate experiments, FAl treated grindate BLACK: duplicated experiments, FAl treated cells (then ground) SCORE: Log Ion Current / Log protein abundance ...
Functional Control by Codon Bias in Magnetic Bacteria
... presence of identical primary sequences of proteins in absence of any nucleotide level homology was a function specific feature in magnetic bacteria. Thus, we carried out similar blast searches for Iron Regulatory Proteins (IRPs: IRP1 and IRP2) from mammalian18–20 as well as bacterial sources (in bac ...
... presence of identical primary sequences of proteins in absence of any nucleotide level homology was a function specific feature in magnetic bacteria. Thus, we carried out similar blast searches for Iron Regulatory Proteins (IRPs: IRP1 and IRP2) from mammalian18–20 as well as bacterial sources (in bac ...
University of Groningen Archaeal type IV prepilin-like signal
... Crenarchaeota were long thought to be restricted to hot environments but have recently been shown to be ubiquitous in aquatic and terrestrial ecosystems. The Euryarchaeota is a diverse group and includes all the methanogenic and halophilic archaea and some hyperthermophiles. The ability of many arch ...
... Crenarchaeota were long thought to be restricted to hot environments but have recently been shown to be ubiquitous in aquatic and terrestrial ecosystems. The Euryarchaeota is a diverse group and includes all the methanogenic and halophilic archaea and some hyperthermophiles. The ability of many arch ...
A New Method to Detect Related Function Among Proteins
... A new method has been developed to detect functional relationships among proteins independent of a given sequence or fold homology. It is based on the idea that protein function is intimately related to the recognition and subsequent response to the binding of a substrate or an endogenous ligand in ...
... A new method has been developed to detect functional relationships among proteins independent of a given sequence or fold homology. It is based on the idea that protein function is intimately related to the recognition and subsequent response to the binding of a substrate or an endogenous ligand in ...
Supporting Information Heim et al. 10.1073/pnas.1413018111
... DNA encoding full-length recombinant P1 lacking the signal sequence (rP1, amino acids 39–1566) was cloned into the pQE-30 vector and used to transform Escherichia coli M15-pREP4 cells as described previously (2, 3). In a previous study, the P1 mutant PC967, in which Cla1 restriction sites had been i ...
... DNA encoding full-length recombinant P1 lacking the signal sequence (rP1, amino acids 39–1566) was cloned into the pQE-30 vector and used to transform Escherichia coli M15-pREP4 cells as described previously (2, 3). In a previous study, the P1 mutant PC967, in which Cla1 restriction sites had been i ...
occasional article intracellular protein degradation: from a vague
... when needed. The lysosomal membrane provided this fencing mechanism. Obviously, nobody could have predicted that a new mode of post-translational modification -ubiquitination- could function as a proteolysis signal, and that untagged proteins will remain protected. Thus, while the structure of the l ...
... when needed. The lysosomal membrane provided this fencing mechanism. Obviously, nobody could have predicted that a new mode of post-translational modification -ubiquitination- could function as a proteolysis signal, and that untagged proteins will remain protected. Thus, while the structure of the l ...
Structure-activity Relationships in Flexible Protein Domains
... physiological role of the interaction of RhoGDI with the GTP-bound form of a GTPase remains to be established. Overall, when exogenously introduced into cells the GDIs behave as negative regulators by maintaining rho GTPases as inactive cytosolic forms which are unable to effectively interact with G ...
... physiological role of the interaction of RhoGDI with the GTP-bound form of a GTPase remains to be established. Overall, when exogenously introduced into cells the GDIs behave as negative regulators by maintaining rho GTPases as inactive cytosolic forms which are unable to effectively interact with G ...
intact-protein based sample preparation strategies for
... number of highly acidic and basic proteins in the fractionated sample compared to whole plasma. Pedersen applied the same technology to fractionate alkaline proteins from Saccharomyes cerevisiae solubilized-membrane protein mixtures within the MCE compartment between pH 7.5 and 10.5. The concentrate ...
... number of highly acidic and basic proteins in the fractionated sample compared to whole plasma. Pedersen applied the same technology to fractionate alkaline proteins from Saccharomyes cerevisiae solubilized-membrane protein mixtures within the MCE compartment between pH 7.5 and 10.5. The concentrate ...
MINI REVIEW Lectin-like proteins in model organisms: implications
... 1998). Lectins are often complex, multidomain proteins, but sugar-binding activity can usually be ascribed to a single protein module within the lectin polypeptide. Such a module is designated a carbohydrate-recognition domain (CRD). CRDs in vertebrate lectins fall into a number of structurally dist ...
... 1998). Lectins are often complex, multidomain proteins, but sugar-binding activity can usually be ascribed to a single protein module within the lectin polypeptide. Such a module is designated a carbohydrate-recognition domain (CRD). CRDs in vertebrate lectins fall into a number of structurally dist ...
Final Report SID5
... The bacterium Streptococcus uberis is a common cause of intramammary infection in dairy cattle and is a leading cause of bovine mastitis worldwide. In the UK it has recently been shown that S. uberis is the most common cause of clinical mastitis. The ability of the organism to grow in milk has been ...
... The bacterium Streptococcus uberis is a common cause of intramammary infection in dairy cattle and is a leading cause of bovine mastitis worldwide. In the UK it has recently been shown that S. uberis is the most common cause of clinical mastitis. The ability of the organism to grow in milk has been ...
Gene Section SFRP2 (secreted frizzled-related protein 2) Atlas of Genetics and Cytogenetics
... MMPs, CCND1, PTGS2, MYC, JUN and VEGFR) (Reya et al., 2005). B) Wnt signaling is regulated by several classes of negative regulators. The Secreted Frizzled-Related Protein (SFRP) class comprises SFRP1-SFRP5, Wnt inhibitory factor 1 (WIF1) and Cerberus. SFRPs are a family of soluble glycoproteins tha ...
... MMPs, CCND1, PTGS2, MYC, JUN and VEGFR) (Reya et al., 2005). B) Wnt signaling is regulated by several classes of negative regulators. The Secreted Frizzled-Related Protein (SFRP) class comprises SFRP1-SFRP5, Wnt inhibitory factor 1 (WIF1) and Cerberus. SFRPs are a family of soluble glycoproteins tha ...
Novel Biomolecular Structural and Functional Information from
... Structure plays a key role on understanding biomolecular properties and biochemical activities, as well as related biomimetic studies. Currently the most widely used technique to determine biomolecular structure is X-ray crystallography. But it suffers from some accuracy prob ...
... Structure plays a key role on understanding biomolecular properties and biochemical activities, as well as related biomimetic studies. Currently the most widely used technique to determine biomolecular structure is X-ray crystallography. But it suffers from some accuracy prob ...
3 | biological macromolecules
... source. In these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ...
... source. In these animals, certain species of bacteria and protists reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix of grazing animals also contains bacteria that digest cellulose, giving it an important role in the digestive systems of ...
The Right Whey Protein
... Whey peptides are comprised of two or more amino acids linked together in sequence, like the pearls of a necklace. Each pearl represents a single amino acid, such as tryptophan or leucine. When two amino acids are connected to each other they become a peptide. A dipeptide is defined as two amino aci ...
... Whey peptides are comprised of two or more amino acids linked together in sequence, like the pearls of a necklace. Each pearl represents a single amino acid, such as tryptophan or leucine. When two amino acids are connected to each other they become a peptide. A dipeptide is defined as two amino aci ...
PROTEIN SEQUENCING First Sequence
... • Traditional Methods – SDS-PAGE, SEC, or RP-HPLC are used to separate the subunits after cleavage of disulfide bonds – Mw standards and a calibration curve are used to determine the molecular weights – The approximate number of amino acids can be estimated from the Mw of the subunit using 110 Da as ...
... • Traditional Methods – SDS-PAGE, SEC, or RP-HPLC are used to separate the subunits after cleavage of disulfide bonds – Mw standards and a calibration curve are used to determine the molecular weights – The approximate number of amino acids can be estimated from the Mw of the subunit using 110 Da as ...
Protein Sentezi
... An NAD+-dependent ADP ribosylase One target of this enzyme is EF-2 EF-2 has a diphthamide (see Figure 33.27) Toxin-mediated ADP-ribosylation of EF-2 allows it to bind GTP but makes it inactive in protein synthesis One toxin molecule ADP-ribosylates many EF-2s, so just a little is lethal! ...
... An NAD+-dependent ADP ribosylase One target of this enzyme is EF-2 EF-2 has a diphthamide (see Figure 33.27) Toxin-mediated ADP-ribosylation of EF-2 allows it to bind GTP but makes it inactive in protein synthesis One toxin molecule ADP-ribosylates many EF-2s, so just a little is lethal! ...
Proteomic Strategies to Analyze Cell
... imperative since post-transcriptional modification can produce dramatic changes in protein levels and activity that are invisible to DNA arrays. The introduction of new and improved proteomics solutions with increased sensitivity, specificity and ease of use has been integral in facilitating this pr ...
... imperative since post-transcriptional modification can produce dramatic changes in protein levels and activity that are invisible to DNA arrays. The introduction of new and improved proteomics solutions with increased sensitivity, specificity and ease of use has been integral in facilitating this pr ...
Improved detection and identification of low
... preliminary trials revealed that optimal spot resolution and number of detected spots could be achieved using the paper bridge application method. Based on these findings, 3 mg BALF or 5 mg plasma were separated using Immobiline DryStrip pH 4.5–5.5, 18 cm gels. Samples were loaded onto paper bridges ...
... preliminary trials revealed that optimal spot resolution and number of detected spots could be achieved using the paper bridge application method. Based on these findings, 3 mg BALF or 5 mg plasma were separated using Immobiline DryStrip pH 4.5–5.5, 18 cm gels. Samples were loaded onto paper bridges ...
Chapter 8 Part A Power Point
... that was calculated • Residuals are the part of the data that has not been modeled in our linear model ...
... that was calculated • Residuals are the part of the data that has not been modeled in our linear model ...
Atomic contacts in protein structures. A detailed analysis of atomic
... for a large number of proteins, and compared the results with a synthetic reference. The reference was constructed from a set of 1000 freely rotatable amino acids in solution, distributed according to the frequency as observed in natural proteins (see Supplementary Materials for details). This syste ...
... for a large number of proteins, and compared the results with a synthetic reference. The reference was constructed from a set of 1000 freely rotatable amino acids in solution, distributed according to the frequency as observed in natural proteins (see Supplementary Materials for details). This syste ...
Accurate Peptide Fragment Mass Analysis: Multiplexed
... To date, the most popular method for peptide and protein identification using mass spectrometry is bottom-up or shotgun proteomics coupled with data dependent acquisition (DDA) mass spectrometry. Multiplexed fragmentation, or simultaneous isolation and fragmentation of multiple peptides, has been de ...
... To date, the most popular method for peptide and protein identification using mass spectrometry is bottom-up or shotgun proteomics coupled with data dependent acquisition (DDA) mass spectrometry. Multiplexed fragmentation, or simultaneous isolation and fragmentation of multiple peptides, has been de ...
analysis of membrane protein dimerization
... Sedimentation equilibrium analysis can overcome many of these problems. Sedimentation equilibrium has long been recognized as the technique of choice for analysis of solution interactions of macromolecules.(2) While the determination of a membrane protein molecular weight formally requires knowledg ...
... Sedimentation equilibrium analysis can overcome many of these problems. Sedimentation equilibrium has long been recognized as the technique of choice for analysis of solution interactions of macromolecules.(2) While the determination of a membrane protein molecular weight formally requires knowledg ...
Topological characterization of the essential Escherichia coli cell
... Fig. 1. Predicted transmembrane segments of FtsW by di¡erent methods and the predicted and proposed models. A: Open bars represent transmembrane or uncharged segments. The prediction methods DAS, SOSUI, TMpred, TMAP, and pHDtopology are described in the text. The HYDROPHOBIC prediction was obtained ...
... Fig. 1. Predicted transmembrane segments of FtsW by di¡erent methods and the predicted and proposed models. A: Open bars represent transmembrane or uncharged segments. The prediction methods DAS, SOSUI, TMpred, TMAP, and pHDtopology are described in the text. The HYDROPHOBIC prediction was obtained ...
Cyclol
The cyclol hypothesis is the first structural model of a folded, globular protein. It was developed by Dorothy Wrinch in the late 1930s, and was based on three assumptions. Firstly, the hypothesis assumes that two peptide groups can be crosslinked by a cyclol reaction (Figure 1); these crosslinks are covalent analogs of non-covalent hydrogen bonds between peptide groups. These reactions have been observed in the ergopeptides and other compounds. Secondly, it assumes that, under some conditions, amino acids will naturally make the maximum possible number of cyclol crosslinks, resulting in cyclol molecules (Figure 2) and cyclol fabrics (Figure 3). These cyclol molecules and fabrics have never been observed. Finally, the hypothesis assumes that globular proteins have a tertiary structure corresponding to Platonic solids and semiregular polyhedra formed of cyclol fabrics with no free edges. Such ""closed cyclol"" molecules have not been observed either.Although later data demonstrated that this original model for the structure of globular proteins needed to be amended, several elements of the cyclol model were verified, such as the cyclol reaction itself and the hypothesis that hydrophobic interactions are chiefly responsible for protein folding. The cyclol hypothesis stimulated many scientists to research questions in protein structure and chemistry, and was a precursor of the more accurate models hypothesized for the DNA double helix and protein secondary structure. The proposal and testing of the cyclol model also provides an excellent illustration of empirical falsifiability acting as part of the scientific method.