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  • natural
  • Lager beer is the most produced fermented beverage: in 2015 the worldwide production reached a global volume of 170 × 10 +9 L. The fermentation workhorse of lager brewing is Saccharomyces pastorianus , a natural interspecific hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus [ 1 , 2 ] whose domestication is thought to have occurred in central Europe (Bohemia, nowadays Czech republic) in the late Middle Ages. (biomedcentral.com)

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  • interactions
  • From diverse functional genomics data, we show that phosphoproteins have a higher number of interactions than an average protein and interact with each other more than with a random protein. (pnas.org)
  • The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital. (wikipedia.org)
  • The BioGRID's original focus was on curation of binary protein-protein and genetic interactions, but has expanded over several updates to incorporate curated post-translational modification data, chemical interaction data, and complex multi-gene/protein interactions. (wikipedia.org)
  • The Biological General Repository for Interaction Datasets (BioGRID) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. (wikipedia.org)
  • The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control. (wikipedia.org)
  • (wikipedia.org)
  • Ubiquitination affects proteins in many ways: it can mark them for degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions. (wikipedia.org)
  • cellular
  • Consequences of loss of Vph1 protein-containing vacuolar ATPases (V-ATPases) for overall cellular pH homeostasis. (nih.gov)
  • This ubiquitin-like protein (ULP), becomes covalently conjugated to a limited number of cellular proteins in a manner analogous to ubiquitination. (wikipedia.org)
  • As with ubiquitin and SUMO, NEDD8 is conjugated to cellular proteins after its C-terminal tail is processed. (wikipedia.org)
  • In fact, only a small percentage of cellular (non-viral) nuclear proteins contained a sequence similar to the SV40 NLS. (wikipedia.org)
  • This domain is named after cellular retinaldehyde-binding protein (CRALBP) and TRIO guanine exchange factor. (wikipedia.org)
  • Molecular
  • Analysis of the hydrodynamic properties of a protein in a crude mixture can give insights into possible tertiary organization such as participation in high-molecular-mass protein complexes. (springer.com)
  • Using a protein called Nucleoplasmin, the archetypal 'molecular chaperone', they identified a domain in the protein that acts as a signal for nuclear entry. (wikipedia.org)
  • The ubiquitin protein itself consists of 76 amino acids and has a molecular mass of about 8.5 kDa. (wikipedia.org)
  • target proteins
  • Cullin neddylation increases CRL ubiquitylation activity via conformational changes that optimize ubiquitin transfer to target proteins There are several different proteases which can remove NEDD8 from protein conjugates. (wikipedia.org)
  • The discovery that ubiquitin chains target proteins to the proteasome, which degrades and recycles proteins, was honored with the Nobel Prize in chemistry in 2004. (wikipedia.org)
  • It performs its myriad functions through conjugation to a large range of target proteins. (wikipedia.org)
  • Isolation
  • Isolation of protein complexes was first attempted by affinity purification of a tagged version of Sec18p. (bl.uk)
  • sequence
  • View conserved domains detected in this protein sequence using CD-search. (nih.gov)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
  • A nuclear localization signal or sequence (NLS) is an amino acid sequence that 'tags' a protein for import into the cell nucleus by nuclear transport. (wikipedia.org)
  • These prokaryotic proteins, despite having little sequence identity (ThiS has 14% identity to ubiquitin), share the same protein fold. (wikipedia.org)
  • ATPase
  • Despite possessing a second domain with some similarity to ATPase domains, dimeric HPt proteins have not been shown to bind or hydrolyze ATP and lack key residues present in other ATPases. (wikipedia.org)
  • elegans
  • In the worm Caenorhabditis elegans, the MSH5 protein is required during meiosis both for normal spontaneous and for gamma-irradiation induced crossover recombination and chiasma formation. (wikipedia.org)
  • The family of MyRF-like-proteins also contains the orthologues pqn-47 from C. elegans and MYRFA from Dictyostelium. (wikipedia.org)
  • purification
  • The methods described here should be applicable to the hydrodynamic analysis and subsequent purification of any soluble protein from organisms amenable to genetic manipulation, such as yeast, as long as the function of that protein is not perturbed by the addition of an epitope tag. (springer.com)
  • Green C.M., Lowndes N.F. (2004) Purification and Analysis of Checkpoint Protein Complexes From Saccharomyces cerevisiae . (springer.com)
  • nuclear
  • The protein phosphatase Siw14 controls caffeine-induced nuclear localization and phosphorylation of Gln3 via the type 2A protein phosphatases Pph21 and Pph22 in Saccharomyces cerevisiae. (semanticscholar.org)
  • The protein Blm3 was found associated with the Ump1-associated half proteasome in nuclear extracts of S. cerevisiae. (hu-berlin.de)
  • The transcriptional activity of NF-κB is primarily regulated by physical interaction with inhibitory IκB proteins (IκBα and IκBβ), which prevents its nuclear translocation. (wikipedia.org)
  • Phyre2 found the most similar protein to be the human protein NDC80 kinetochore complex component, a nuclear protein that binds to microtubules. (wikipedia.org)
  • Different nuclear localized proteins may share the same NLS. (wikipedia.org)
  • An NLS has the opposite function of a nuclear export signal (NES), which targets proteins out of the nucleus. (wikipedia.org)
  • compared the nuclear localization efficiencies of eGFP fused NLSs of SV40 Large T-Antigen, Nucleoplasmin (AVKRPAATKKAGQAKKKKLD), EGL-13 (MSRRRKANPTKLSENAKKLAKEVEN), c-Myc (PAAKRVKLD) and TUS-protein (KLKIKRPVK) through rapid intracellular protein delivery. (wikipedia.org)
  • The first direct experimental examination of the ability of nuclear proteins to accumulate in the nucleus were carried out by John Gurdon when he showed that purified nuclear proteins accumulate in the nucleus of frog (Xenopus) oocytes after being micro-injected into the cytoplasm. (wikipedia.org)
  • The presence of several million pore complexes in the oocyte nuclear membrane and the fact that they appeared to admit many different molecules (insulin, bovine serum albumin, gold nanoparticles) led to the view that the pores are open channels and nuclear proteins freely enter the nucleus through the pore and must accumulate by binding to DNA or some other nuclear component. (wikipedia.org)
  • However, a functional NLS could not be identified in another nuclear protein simply on the basis of similarity to the SV40 NLS. (wikipedia.org)
  • peptides
  • To circumvent this problem, we have modified the LTQ mass spectrometer for ion/ion chemistry and now fragment both peptides ( 2 ) and intact proteins ( 3 ) by electron transfer dissociation (ETD). (pnas.org)
  • ubiquitin
  • Ubiquitin is a small (8.5 kDa) regulatory protein found in most tissues of eukaryotic organisms i.e. it occurs ubiquitously. (wikipedia.org)
  • The addition of ubiquitin to a substrate protein is called ubiquitination or less frequently ubiquitylation. (wikipedia.org)
  • The result of this sequential cascade is to bind ubiquitin to lysine residues on the protein substrate via an isopeptide bond, cysteine residues through a thioester bond, serine and threonine residues through an ester bond, or the amino group of the protein's N-terminus via a peptide bond. (wikipedia.org)
  • The protein modifications can be either a single ubiquitin protein (monoubiquitination) or a chain of ubiquitin (polyubiquitination). (wikipedia.org)
  • The first ubiquitin molecule is covalently bound through its C-terminal carboxylate group to a particular lysine, cysteine, serine, threonine or N-terminus of the target protein. (wikipedia.org)
  • Soon after APF-1-protein conjugation was characterised, APF-1 was identified as ubiquitin. (wikipedia.org)
  • Ubiquitin is believed to have descended from prokaryotic proteins similar to ThiS or MoaD. (wikipedia.org)
  • These proteins also share sulfur chemistry with ubiquitin. (wikipedia.org)
  • substrate
  • The regulatory complexes recognize substrate proteins and control the substrate access into the catalytically active 20S complex. (hu-berlin.de)
  • The C-terminal motif is required for association with LSm proteins and contributes to substrate (U6) binding and not the catalytic rate of splicing. (wikipedia.org)
  • A heat-stable polypeptide present in these extracts, ATP-dependent proteolysis factor 1 (APF-1), was found to become covalently attached to the model protein substrate lysozyme in an ATP- and Mg2+-dependent process. (wikipedia.org)
  • phosphorylation
  • With this approach, we identify 1,252 phosphorylation sites on 629 proteins in a single experiment with 30 μg (≈600 pmols) of protein from a yeast whole cell lysate. (pnas.org)
  • These sites are predicted to phosphorylate S169, T178, S236, T243, S276, and S285 by protein kinase C. GPS also predicts phosphorylation by protein kinase C at S285 and T178. (wikipedia.org)
  • amino
  • FAM98A is longest of the three paralogous protein products with 518 amino acids. (wikipedia.org)
  • This PY-NLS motif, so named because of the proline-tyrosine amino acid pairing in it, allows the protein to bind to Importin β2 (also known as transportin or karyopherin β2), which then translocates the cargo protein into the nucleus. (wikipedia.org)
  • complexes
  • It was hoped that the affinity of protein A for IgG Sepharose could be used to isolate protein complexes that formed in vivo with the Sec18p. (bl.uk)
  • histone
  • I reveal that Saccharomyces cerevisiae Rtt109p promotes genome stability and resistance to DNA-damaging agents, and that it does this by functionally cooperating with the histone chaperone Asf1p to maintain normal chromatin structure. (bl.uk)
  • Depending on cell type and cell cycle, mediating factors such as DNA-binding proteins like chromatin, composed of DNA tightly wound around histone proteins, and other environmental conditions and stresses affect the dynamic formation of quadraplexes. (wikipedia.org)
  • recombination
  • Moreover, I show that esc2Δ mutant cells exhibit increased recombination frequency and increased relocalisation of recombination repair protein Rad52p. (bl.uk)
  • proteasome
  • Accordingly, the protein Blm3 delays the maturation of the nascent proteasome into the mature 20S proteasome. (hu-berlin.de)
  • As a coordinating protein, Blm3 presumably exerts a regulating effect onto the maturation and, finally, onto the activation of the 20S proteasome. (hu-berlin.de)
  • interaction
  • In a search for further proteins interacting with Ccz1p, we identified the endosomal soluble N-ethylmaleimide-sensitive factor attachment protein receptor Pep12p as an interaction partner of Ccz1p. (uni-bielefeld.de)
  • clarification needed] It has been proposed that the LSm proteins and Prp24 interact both physically and functionally and the C-terminal motif of Prp24 is important for this interaction. (wikipedia.org)
  • precursor
  • Prp24 (precursor RNA processing, gene 24) is a protein part of the pre-messenger RNA splicing process and aids the binding of U6 snRNA to U4 snRNA during the formation of spliceosomes. (wikipedia.org)
  • nucleotide
  • The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
  • extracts
  • We here describe the determination of Stokes radius and sedimentation coefficients for the Rad24 protein, which enabled us to predict that this protein was a component of a protein complex in crude yeast extracts. (springer.com)
  • membranes
  • d ) Calculated membrane protein overexpression levels (as outlined in with the exception that Step 7 was omitted) in whole-cells versus membranes for fusions presented in panel c . (nih.gov)
  • Annotation
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein. (uniprot.org)
  • Users of The BioGRID can search for their protein or publication of interest and retrieve annotation, as well as curated data as reported, by the primary literature and compiled by in house large-scale curation efforts. (wikipedia.org)
  • natural
  • Lager beer is the most produced fermented beverage: in 2015 the worldwide production reached a global volume of 170 × 10 +9 L. The fermentation workhorse of lager brewing is Saccharomyces pastorianus , a natural interspecific hybrid of Saccharomyces cerevisiae and Saccharomyces eubayanus [ 1 , 2 ] whose domestication is thought to have occurred in central Europe (Bohemia, nowadays Czech republic) in the late Middle Ages. (biomedcentral.com)
  • Genes
  • In Saccharomyces cerevisiae, the initial steps of diphthamide biosynthesis are well characterized and require the DPH1-DPH5 genes. (nih.gov)
  • With the human genome sequenced, the next step is the verification and functional annotation of all predicted genes and their protein products. (wikipedia.org)
  • Nasmyth joined Ben Hall's lab in Seattle as a postdoctoral researcher where he developed ways of cloning genes by complementation in yeast and, in collaboration with Steve Reed, cloned the CDC28 gene from the budding yeast Saccharomyces cerevisiae. (wikipedia.org)
  • Together with Kelly Tatchell he cloned the S. cerevisiae mating-type locus and found, surprisingly, that 'silent' copies of the mating-type genes including their promoters are maintained in the yeast chromosome. (wikipedia.org)
  • While identifying these small RNAs, her lab discovered that some of these small RNAs encode small proteins that had previously been overlooked because they are not detected in many traditional biochemical assays and the corresponding genes are poorly annotated. (wikipedia.org)
  • genetic
  • The key of our method is the systematic purification of several tagged components of the protein complex in multiple genetic deletion strains, which serve to compromise the integrity of the complex. (embopress.org)
  • amino
  • Proteins are made of amino acids arranged in a linear chain joined together by peptide bonds. (wikipedia.org)
  • The human protein 26S proteasome non-ATPase regulatory subunit 14 is 37 kDa in size and composed of 324 amino acids. (wikipedia.org)
  • The amino acid sequences of both receptors contain high proportions of hydrophobic residues grouped into 7 domains, in a manner reminiscent of the rhodopsins and other receptors believed to interact with G-proteins. (wikipedia.org)
  • homolog
  • Abelson murine leukemia viral oncogene homolog 1 also known as ABL1 is a protein that, in humans, is encoded by the ABL1 gene (previous symbol ABL) located on chromosome 9. (wikipedia.org)
  • A possible homolog of Dot1 was found in archaea which shows the ability to methylate archaeal histone-like protein in recent studies. (wikipedia.org)
  • metabolism
  • The three main purposes of metabolism are the conversion of food/fuel to energy to run cellular processes, the conversion of food/fuel to building blocks for proteins, lipids, nucleic acids, and some carbohydrates, and the elimination of nitrogenous wastes. (wikipedia.org)
  • Metabolism is usually divided into two categories: catabolism, the breaking down of organic matter for example, the breaking down of glucose to pyruvate, by cellular respiration, and anabolism, the building up of components of cells such as proteins and nucleic acids. (wikipedia.org)
  • Many proteins are enzymes that catalyze the chemical reactions in metabolism. (wikipedia.org)
  • When Saccharomyces cerevisiae is grown below the sugar threshold and undergoes a respiration metabolism, the fermentation pathway is still fully expressed, while the respiration pathway is only expressed relative to the sugar availability. (wikipedia.org)
  • subunit
  • Furthermore, we identified a novel subunit of the ADA complex, termed Ahc2, and characterized Sgf29 as an ADA family protein present in all Gcn5 histone acetyltransferase complexes. (embopress.org)
  • Recent evidence of crystal structures of proteasomes isolated from Saccharomyces cerevisiae suggests that the catalytically active subunit Rpn8 and subunit Rpn11 form heterodimer. (wikipedia.org)
  • interact
  • Despite the availability of several large‐scale proteomics studies aiming to identify protein interactions on a global scale, little is known about how proteins interact and are organized within macromolecular complexes. (embopress.org)
  • NPs may interact with these proteins in a similar way, and the interaction may lead to beneficial outcomes in vaccine delivery. (scirp.org)
  • enzyme
  • The α-amylase and all include a huge proportion of tyrosine and tryptophan in the enzyme protein and denature at around 60°C. The α-amylase is an extracellular endo-glycoprotein having single polypeptide chain of 475 residues, two -SH groups and 4 disulfide bridges with a compactly bound Ca 2+ . (frontiersin.org)
  • Glycylpeptide N-tetradecanoyltransferase 1 also known as myristoyl-CoA:protein N-myristoyltransferase 1 (NMT-1) is an enzyme that in humans is encoded by the NMT1 gene. (wikipedia.org)
  • These proteolytic active sites located in the inner side of a chamber formed by 4 stacked rings of 20S subunits, preventing random protein-enzyme encounter and uncontrolled protein degradation. (wikipedia.org)
  • Lariat debranching enzyme is a protein that in humans is encoded by the DBR1 gene. (wikipedia.org)
  • interaction
  • We investigated the interaction of PEGylated and un-PEGylated PLGA NPs with Recombinant Human Mannose-Binding Protein (HMBP) in an effort to understand the effect of surface modification on their binding to the protein. (scirp.org)
  • The encoded protein is a component of the interleukin-17 receptor signaling complex, and the interaction between this protein and IL-17R does not require the interleukin. (genecards.org)
  • According to the protein interaction and topological characteristics of this multisubunit complex, the 19S regulatory particle is composed of a base and a lid subcomplex. (wikipedia.org)
  • sequence
  • View conserved domains detected in this protein sequence using CD-search. (nih.gov)
  • The "fingerprint" of each peptide's fragmentation mass spectrum is used to identify the protein from which they derive by searching against a sequence database with commercially available software (e.g. (wikipedia.org)
  • characterize
  • In this study, we developed and applied a novel method utilizing biochemistry, quantitative proteomics and computational approaches in order to characterize the organization of proteins in a complex. (embopress.org)
  • recognize
  • It can be activated by collectin proteins which recognize the structural pattern of polysaccharide on the surface of microorganisms. (scirp.org)
  • The 19S regulatory particles can recognize ubiquitin-labeled protein as degradation substrate, unfold the protein to linear, open the gate of 20S core particle, and guide the substate into the proteolytic chamber. (wikipedia.org)
  • To recognize protein as designated substrate, 19S complex has subunits that are capable to recognize proteins with a special degradative tag, the ubiquitinylation. (wikipedia.org)
  • conformational
  • On the other hand the fluorescence emission of the protein increased upon binding to the PLGA-PEG-NH2 indicating conformational changes in the protein structure. (scirp.org)
  • Light-induced isomerization of 11-cis to all-trans retinal triggers a conformational change leading to G-protein activation and release of all-trans retinal. (genecards.org)
  • structural
  • Other proteins have structural or mechanical functions, such as those that form the cytoskeleton, a system of scaffolding that maintains the cell shape. (wikipedia.org)
  • complex
  • However, those approaches are insufficient to provide information about the spatial arrangement and the interrelationship of the proteins of the respective complex. (embopress.org)
  • Purification of a RAS-responsive adenylyl cyclase complex from Saccharomyces cerevisiae by use of an epitope addition method. (abnova.com)
  • In 1975, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) was described by O'Farrell and Klose with the ability to resolve complex protein mixtures. (wikipedia.org)
  • The origin of aerobic fermentation, or the first step, in Saccharomyces crabtree-positive yeasts likely occurred in the interval between the ability to grow under anaerobic conditions, horizontal transfer of anaerobic DHODase (encoded by URA1 with bacteria), and the loss of respiratory chain Complex I. A more pronounced Crabtree effect, the second step, likely occurred near the time of the WGD event. (wikipedia.org)
  • type
  • Here, we describe a technique that consists of a combination of biochemistry approaches, quantitative proteomics and computational methods using wild‐type and deletion strains to investigate the organization of proteins within macromolecular protein complexes. (embopress.org)
  • The ability of S. cerevisiae to dominate in high sugar environments evolved more recently than aerobic fermentation and is dependent on the type of high-sugar environment. (wikipedia.org)
  • As indicated by their monikers, these differ in the presence of a SET domain, which is a type of protein domain. (wikipedia.org)
  • domain
  • Activity of ABL1 protein is negatively regulated by its SH3 domain, and deletion of the SH3 domain turns ABL1 into an oncogene. (wikipedia.org)
  • cells
  • The protein encoded by this gene is found in rod cells in the back of the eye and is essential for vision in low-light conditions. (genecards.org)
  • method
  • The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. (wikipedia.org)
  • spatial
  • To meet such complicated demands in biological process via spatial and temporal proteolysis, protein substrates have to be recognized, recruited, and eventually hydrolyzed in a well controlled fashion. (wikipedia.org)
  • affinity
  • The protein encoded by this gene is a high affinity calcium ion-binding protein that is structurally and functionally similar to calmodulin and troponin C. The encoded protein is thought to be involved in muscle relaxation. (genecards.org)
  • ability
  • Shotgun proteomics allows global protein identification as well as the ability to systematically profile dynamic proteomes. (wikipedia.org)
  • family
  • Solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2 is a protein that in humans is encoded by the SLC9B2 gene. (wikipedia.org)