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  • peptides
  • Polypeptide toxins and many antibacterial peptides , such as colicins or hemolysins , and certain proteins involved in apoptosis , are sometimes considered a separate category. (wikipedia.org)
  • To identify integral proteins of the NE, we took advantage of recent advances in high-throughput shotgun proteomics using multidimensional protein identification technology (MudPIT) ( 4 , 5 ), by which the coupling of tandem mass spectrometry with multiple liquid chromatography steps allows analysis of the enormous number of peptides generated by direct digestion of a complex biochemical fraction. (sciencemag.org)
  • Proteins in all three pellets were proteolytically cleaved, and the complex peptide mixtures were separated by sequential salt steps followed by acetonitrile gradients to slowly release peptides into the mass spectrometer. (sciencemag.org)
  • Several families of intramembrane proteases have been characterized, including metallo-intramembrane proteases, which regulate important cellular pathways such as sterol metabolism ( 5 ) and the unfolded protein response ( 6 ), and aspartyl intramembrane proteases such as presenilin, the catalytic subunit of γ-secretase, which generates the β-amyloid peptides involved in Alzheimer disease ( 3 ). (pnas.org)
  • MHC class I molecules are expressed on the plasma membranes of all nucleated cells and present peptides derived from intracellular proteins to cytotoxic T lymphocytes (CTLs). (asm.org)
  • CTLs monitor these MHC class I molecules for peptides derived from viral proteins and kill the infected cells. (asm.org)
  • The vast majority of peptides presented by MHC class I molecules are generated by the degradation of proteins in the cytosol by the proteasome complex ( 38 ). (asm.org)
  • Alzheimer's disease (AD) is characterized pathologically by a massive deposition of amyloid β peptides (Aβ), which are proteolytically produced from β-amyloid precursor proteins (βAPP) through two sequential cleavages by as yet unidentified proteases termed the β- and γ-secretases ( Selkoe, 1991 , 1994 ). (jneurosci.org)
  • 1996
  • Molecular chaperones bind nonnative protein conformations, sequestering misfolded protein or aggregation-prone folding intermediates from the cytosol, thereby reducing the likelihood of aggregate formation ( Hartl, 1996 ). (rupress.org)
  • The minimal set of proteins constituting a functional translocase complex comprises SecA, SecY, SecE and SecG, which mediate the ATP‐ and proton motive force‐dependent translocation across the membrane ( Schatz and Dobberstein, 1996 ). (embopress.org)
  • eukaryotic
  • Given the potentially pathogenic consequences of intracellular protein aggregation, it is not surprising that eukaryotic cells have evolved mechanisms to prevent their formation or accumulation. (rupress.org)
  • Eukaryotic cells must transport transmembrane proteins between different subcellular compartments, often in response to specific signals or conditions. (frontiersin.org)
  • segment
  • The E. coli SecY channel is closed at the periplasmic face of the membrane by a small re-entrance loop that connects transmembrane segment 1 with 2b. (tcdb.org)
  • Preceding the first putative transmembrane segment is a highly charged 204-residue-long amino terminal region that contains two consensus sites for phosphorylation by protein kinase A. Since the lamin B receptor has been shown to be phosphorylated by protein kinase A in vitro and in vivo and this phosphorylation affects lamin B binding (Applebaum, J., G. Blobel, and S. D. Georgatos. (rupress.org)
  • It has a signal sequence-like N-terminal segment that, according to studies with green and red fluorescent protein chimeras, anchors unassembled PulG in the inner membrane. (asm.org)
  • sequence
  • Methods of computer modeling based on the data on the primary protein structure or the symbolic amino acid sequence have become an actual alternative to the experimental method of X-ray crystallography for investigating the structure of membrane proteins. (hindawi.com)
  • It is supposed that all information about the ultimate structure of a protein is contained in its amino acid sequence. (hindawi.com)
  • If the mentioned repetition is periodic, it can be detected using the known method of Fourier transform, applied to a digital image of a symbolic sequence of amino acids in a protein, as was done in our previous works [ 4 , 5 ]. (hindawi.com)
  • If the repetition of transmembrane regions is aperiodic, it can be revealed by another method, that is, the method of the reiterated (four to five times) averaging of the protein hydrophobicity function in a window within the limits of 9-11 amino acids that moves along the sequence. (hindawi.com)
  • The fragmentation pattern often yields amino acid sequence information, allowing protein identification from a single unique peptide, thus increasing sensitivity. (sciencemag.org)
  • The starting residue numbers of the indicated sequence fragments within their full-length proteins are given. (pnas.org)
  • The former refers to proteins in which some part of the peptide sequence spans all or part of the membrane (in theory, it could also be used for RNAs embedded in a membrane, if any such exist). (geneontology.org)
  • We deduced the amino acid sequence of the chicken lamin B receptor from overlapping clones obtained by screening cDNA libraries with a probe generated by the polymerase chain reaction with primers based on the partial protein sequence of the isolated protein. (rupress.org)
  • The carrier protein sequence is a tripartite repeat, in which each repeat consists of a pair of membrane-spanning domains connected by a matrix-sided loop. (rupress.org)
  • precursor
  • Consequently, it is necessary to maintain precursor proteins in an export‐competent conformation prior to the interaction with the translocase. (embopress.org)
  • It was first reported that precursor maltose‐binding protein is competent for transport into the periplasm only before it has achieved its final, stably folded, conformation. (embopress.org)
  • eukaryotes
  • Many proteins are translocated through the SecY channel in bacteria and archaea and through the related Sec61 channel in eukaryotes. (tcdb.org)
  • secretion
  • Here we discuss recent developments in our understanding of the archaeal protein secretion mechanisms, the assembly of macromolecular cell surface structures, and the release of S-layer-coated vesicles from the archaeal membrane. (hindawi.com)
  • Until recently most of our knowledge of protein secretion and on the assembly of the cell surface components in archaea was obtained by comparative genomic studies. (hindawi.com)
  • Central to these machineries is their ability to assemble and disassemble filaments that either remain periplasmic and function in protein secretion (pseudopili) or extend well beyond the cell surface and play a role in adhesion, surface motility, or microcolony or biofilm formation (type IV pili) ( 12 ). (asm.org)
  • structural biology
  • The Protein Structure Initiative (PSI), funded by the U.S. National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH), has among its aim to determine three-dimensional protein structures and to develop techniques for use in structural biology , including for membrane proteins. (wikipedia.org)
  • genes
  • Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. (embl-heidelberg.de)
  • Presenilin 1 (PSN1) and presenilin 2 (PSN2) are membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. (embl-heidelberg.de)
  • The β-galactosidase activity in strains producing a PulG-LacZ hybrid protein increased substantially when the dsbA , dsbB , or all sec genes tested except secB were compromised by mutations. (asm.org)
  • The connexin protein family is encoded by at least 13 genes in rodents, with many homologues cloned from other species. (embl-heidelberg.de)
  • Thus
  • Thus, NE-specific proteins were determined by subtracting the proteins present in MM fractions from those of the NE fractions after proteomic analysis. (sciencemag.org)
  • Photobleaching experiments (FRAP) indicate that relocation of membrane proteins from the ER to LDs is independent of temperature and energy, and thus not mediated by classical vesicular transport routes. (biologists.org)
  • cargo proteins
  • Targeting information is usually present in the cargo proteins themselves. (rupress.org)
  • These targeting signals are thought to be recognized in the TGN or endosomes, which leads to the sorting of cargo proteins into transport vesicles destined for the apical or basolateral plasma membrane. (rupress.org)
  • lamin
  • Separately, NEs were extracted with salt and detergent to identify integral proteins more closely associated with the lamin polymer. (sciencemag.org)
  • The lamin B receptor is a previously identified integral membrane protein in the nuclear envelope of turkey erythrocytes that associates with the nuclear intermediate filament protein lamin B (Worman, H. J., J. Yuan, G. Blobel, and S. D. Georgatos. (rupress.org)
  • The amino terminal region also contains three DNA-binding motifs that are found in gene regulatory proteins and histones, suggesting that the lamin B receptor may additionally play a role in gene regulation and/or chromatin organization. (rupress.org)
  • conformation
  • Compared to other classes of proteins, the determination of membrane protein structure s has remained a challenge in large part due to the difficulty in establishing experimental conditions where the correct conformation of the protein in isolation from its native environment is preserved. (wikipedia.org)
  • intramembrane
  • Here we provide evidence that after cleavage by signal peptidase, the signal peptide is further processed by the intramembrane-cleaving protease SPP that promotes the release of core protein from the ER membrane. (embl-heidelberg.de)
  • topologies
  • Subsequent to the elucidation of the primary structure of PLP, several topologies for this protein have been proposed based on mathematical modeling, chemical labeling, limited protease digestion, and immunolabeling. (jneurosci.org)