Prediction of protease substrates using sequence
... Identifying these substrates has led to a wealth of knowledge about how the proteases contribute to apoptosis, how the cleavage events lead to cell death, and which substrates to target for therapeutic purposes. Substrates of the two protease types have been discovered with a variety of experimental ...
... Identifying these substrates has led to a wealth of knowledge about how the proteases contribute to apoptosis, how the cleavage events lead to cell death, and which substrates to target for therapeutic purposes. Substrates of the two protease types have been discovered with a variety of experimental ...
h-Barrel membrane protein folding and structure viewed through the
... dimensions of 100 Å 100 Å (Fig. 2). The seven-fold noncrystallographic axis of symmetry runs parallel to the channel opening, which spans the entire length of the protein assemblage. At its widest and narrowest points, the channel diameter is 46 and 14 Å, respectively. The overall architecture ...
... dimensions of 100 Å 100 Å (Fig. 2). The seven-fold noncrystallographic axis of symmetry runs parallel to the channel opening, which spans the entire length of the protein assemblage. At its widest and narrowest points, the channel diameter is 46 and 14 Å, respectively. The overall architecture ...
GYP5 - Genetics
... shown to be a GAP for Ypt1p (DE ANTONI et al. 2002), a Rab GTPase involved in ER to Golgi trafficking (BACON et al. 1989, SEGEV, 1991; for review see LAZAR et al. 1997). Gyl1p is a protein with sequence similarity to Gyp5 and has been shown to colocalize with Gyp5p (CHESNEAU et al. 2004). We show th ...
... shown to be a GAP for Ypt1p (DE ANTONI et al. 2002), a Rab GTPase involved in ER to Golgi trafficking (BACON et al. 1989, SEGEV, 1991; for review see LAZAR et al. 1997). Gyl1p is a protein with sequence similarity to Gyp5 and has been shown to colocalize with Gyp5p (CHESNEAU et al. 2004). We show th ...
Plant mitochondria contain the protein translocase subunits TatB
... believe that At5g43680 is a TatB like protein. This is also supported by basic sequence comparisons as At5g43680 shows a 14% identity and 29% similarity to EcTatB in comparison to 10% identity and 19% similarity to EcTatA. Furthermore, a sequence alignment between EcTatB and At5g43680 showed that it ...
... believe that At5g43680 is a TatB like protein. This is also supported by basic sequence comparisons as At5g43680 shows a 14% identity and 29% similarity to EcTatB in comparison to 10% identity and 19% similarity to EcTatA. Furthermore, a sequence alignment between EcTatB and At5g43680 showed that it ...
Poster
... its structure has a “C-terminal helix” in addition to its twelve armadillo repeats. •In contrast, HMP-2 functions in the formation of the adherens junctions and its structure does not contain the C-terminal helix. Future studies would seek to determine if the C-helix is the structural component tha ...
... its structure has a “C-terminal helix” in addition to its twelve armadillo repeats. •In contrast, HMP-2 functions in the formation of the adherens junctions and its structure does not contain the C-terminal helix. Future studies would seek to determine if the C-helix is the structural component tha ...
Supplemental Figure Legends
... preparations per group. Error bars indicate ±sem. The low concentration of Ca2+ (250 M) induced a permeability transition in Ppif+/+ mitochondria that was completely reversed by 1 M cyclosporine-A (CsA). However, high Ca2+ (2 mM) could completely overcome the inhibitory effects of CsA. Ppif-/- mit ...
... preparations per group. Error bars indicate ±sem. The low concentration of Ca2+ (250 M) induced a permeability transition in Ppif+/+ mitochondria that was completely reversed by 1 M cyclosporine-A (CsA). However, high Ca2+ (2 mM) could completely overcome the inhibitory effects of CsA. Ppif-/- mit ...
Tupai eBusiness Systems
... • Active - the values flowing within the structure changed the structure • Visible - the objects were found and connected to • Undirected - it didn’t matter what was found first • Dynamically extensible - new objects, new relations, new structure • Self-modifying - the structure extended itself • St ...
... • Active - the values flowing within the structure changed the structure • Visible - the objects were found and connected to • Undirected - it didn’t matter what was found first • Dynamically extensible - new objects, new relations, new structure • Self-modifying - the structure extended itself • St ...
Introduction:
... Prediction of Transmembrane helices: Prediction of transmembrane helices of the olfactory receptor O2D2 was done using TMHMM v. 2.0 (Sonnhammer, et. al., 1998). It was predicted to be a seven helix bundle similar to GPCR as shown in Fig. 1A. It is interesting to note that the putative metal binding ...
... Prediction of Transmembrane helices: Prediction of transmembrane helices of the olfactory receptor O2D2 was done using TMHMM v. 2.0 (Sonnhammer, et. al., 1998). It was predicted to be a seven helix bundle similar to GPCR as shown in Fig. 1A. It is interesting to note that the putative metal binding ...
Interaction with PI3-kinase contributes to the cytotoxic activity ofApoptin S Maddika
... towards transformed and cancer cells. In cells resistant to apoptin-mediated cell death, the protein has a cytoplasmic localization, whereas in sensitive cells, apoptin is found in the nucleus (Danen-Van Oorschot et al., 2003). Apoptin was described to be specifically phosphorylated in transformed ce ...
... towards transformed and cancer cells. In cells resistant to apoptin-mediated cell death, the protein has a cytoplasmic localization, whereas in sensitive cells, apoptin is found in the nucleus (Danen-Van Oorschot et al., 2003). Apoptin was described to be specifically phosphorylated in transformed ce ...
Protein translocation pathways across the inner and outer
... extends an N-terminal domain of ~85 amino acid residues into cytosol and has a single transmembrane segment and a smaller C-terminal domain (~45 residues) facing the intermembrane space. Tom40 protein appears to be deeply embedded in the outer membrane of mitochondria, although it does not have ...
... extends an N-terminal domain of ~85 amino acid residues into cytosol and has a single transmembrane segment and a smaller C-terminal domain (~45 residues) facing the intermembrane space. Tom40 protein appears to be deeply embedded in the outer membrane of mitochondria, although it does not have ...
Subviral-Particle Biogenesis Hepatitis B Virus Small Surface
... allowed reduced but well-detectable formation of SVP containing both M and S derivatives (Fig. 2B, upper right panel), although the protein pattern was abnormal. We have no explanation for this behavior. Insertion of two alanines in the central position of TM1 in the M background (mutant M2), howeve ...
... allowed reduced but well-detectable formation of SVP containing both M and S derivatives (Fig. 2B, upper right panel), although the protein pattern was abnormal. We have no explanation for this behavior. Insertion of two alanines in the central position of TM1 in the M background (mutant M2), howeve ...
Structure-activity Relationships in Flexible Protein Domains
... inhibit GDP dissociation as well, but have not been evaluated as inhibitors of GTP hydrolysis. The 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 ...
... inhibit GDP dissociation as well, but have not been evaluated as inhibitors of GTP hydrolysis. The 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 ...
Plant mitochondria contain the protein translocase subunits TatB
... believe that At5g43680 is a TatB like protein. This is also supported by basic sequence comparisons as At5g43680 shows a 14% identity and 29% similarity to EcTatB in comparison to 10% identity and 19% similarity to EcTatA. Furthermore, a sequence alignment between EcTatB and At5g43680 showed that it ...
... believe that At5g43680 is a TatB like protein. This is also supported by basic sequence comparisons as At5g43680 shows a 14% identity and 29% similarity to EcTatB in comparison to 10% identity and 19% similarity to EcTatA. Furthermore, a sequence alignment between EcTatB and At5g43680 showed that it ...
Chaperone-assisted protein folding: the path to discovery from a
... the mitochondrial double membrane2, and definitive evidence for this came in 1986 from the group of Gottfried Schatz3. In 1988, two papers, one from Günter Blobel and the other from Randy Schekman and Elizabeth Craig, showed that the cytosolic precursors of mitochondrial and secretory proteins inter ...
... the mitochondrial double membrane2, and definitive evidence for this came in 1986 from the group of Gottfried Schatz3. In 1988, two papers, one from Günter Blobel and the other from Randy Schekman and Elizabeth Craig, showed that the cytosolic precursors of mitochondrial and secretory proteins inter ...
Understanding P53-Mdm2 Interactions: Future Prospect of Anti
... advantage. MDM2 is not common in healthy individuals, and is only seen in tumors. MDM2 is an important negative regulator of the P53 tumor suppressor. MDM2 protein shows dual functions, both as an E3 ubiquitin ligase recognizing the N-terminal transactivation domain (TAD) of the P53 tumor suppressor ...
... advantage. MDM2 is not common in healthy individuals, and is only seen in tumors. MDM2 is an important negative regulator of the P53 tumor suppressor. MDM2 protein shows dual functions, both as an E3 ubiquitin ligase recognizing the N-terminal transactivation domain (TAD) of the P53 tumor suppressor ...
Cytochrome c Is Released in a Reactive Oxygen
... against cyt c. Both cytosolic and mitochondrial fractions, obtained from TBY-2 cells subjected to HS (cells in these conditions will be referred to as HS cells), were examined. Typical immunoblots are shown in Figure 1A. Two hours after HS (2-h HS cells), when, due to technical reasons (see ‘‘Materi ...
... against cyt c. Both cytosolic and mitochondrial fractions, obtained from TBY-2 cells subjected to HS (cells in these conditions will be referred to as HS cells), were examined. Typical immunoblots are shown in Figure 1A. Two hours after HS (2-h HS cells), when, due to technical reasons (see ‘‘Materi ...
The orphan histidine protein kinase SgmT is a cdiGMP receptor and
... (Jenal and Malone, 2006; Hengge, 2009). In general, c-di-GMP controls the switch from a planktonic, motile lifestyle to a surface-associated, sessile lifestyle by regulating EPS accumulation, surface adhesion, motility, subcellular localization of proteins and cell-surface protein localization (Jena ...
... (Jenal and Malone, 2006; Hengge, 2009). In general, c-di-GMP controls the switch from a planktonic, motile lifestyle to a surface-associated, sessile lifestyle by regulating EPS accumulation, surface adhesion, motility, subcellular localization of proteins and cell-surface protein localization (Jena ...
Plant mitochondria contain the protein translocase subunits TatB
... The twin-arginine translocation (Tat) pathway differs from most other protein translocating systems in that it transports fully folded proteins (Lee et al., 2006). It is named after its targeting signal, which contains a pair of adjacent arginine residues (the twin arginines). Identified in all doma ...
... The twin-arginine translocation (Tat) pathway differs from most other protein translocating systems in that it transports fully folded proteins (Lee et al., 2006). It is named after its targeting signal, which contains a pair of adjacent arginine residues (the twin arginines). Identified in all doma ...
Programmed Cell Death in Neurons
... the SCG are obtained from embryonic-day-21 rats and are maintained in culture in the presence of NGF for 5–7 days; the removal of NGF initiates PCD and causes the apoptotic death of all neurons 24 – 48 hr after NGF deprivation in culture (16). The advantage of this model is that its relatively homog ...
... the SCG are obtained from embryonic-day-21 rats and are maintained in culture in the presence of NGF for 5–7 days; the removal of NGF initiates PCD and causes the apoptotic death of all neurons 24 – 48 hr after NGF deprivation in culture (16). The advantage of this model is that its relatively homog ...
Expression of the papillomavirus E2 protein in HeLa cells leads to
... et al., 1991). However, endogenous transcriptionally active p53 can be activated when these cells are exposed to genotoxic agents (Butz et al., 1995). Since E2 could repress E6 expression, we next investigated whether this resulted in stabilization of p53. The activity of p53 was assayed via co-tran ...
... et al., 1991). However, endogenous transcriptionally active p53 can be activated when these cells are exposed to genotoxic agents (Butz et al., 1995). Since E2 could repress E6 expression, we next investigated whether this resulted in stabilization of p53. The activity of p53 was assayed via co-tran ...
Rab cascades and tethering factors in the endomembrane system
... membrane in mammalian cells was lately proposed by the Sacher lab [28]. Their model assumes that the Ypt1/Rab1 activation/inactivation cycles must happen at least twice during the whole tethering process. In the first step, p115 interacts in a Rab1/Ypt1-GTP-dependent manner with vesicles that bud fr ...
... membrane in mammalian cells was lately proposed by the Sacher lab [28]. Their model assumes that the Ypt1/Rab1 activation/inactivation cycles must happen at least twice during the whole tethering process. In the first step, p115 interacts in a Rab1/Ypt1-GTP-dependent manner with vesicles that bud fr ...
Electron Transport Chain (Respiratory Chain)
... In reactions of the RCH a) oxygen is reduced to H2O b) protons (H+) are transfered into an intermembrane space c) ATP is produced by the Complex I d) all reduced coenzymes (NADH+H+ and FADH2) are reoxidized by the same ...
... In reactions of the RCH a) oxygen is reduced to H2O b) protons (H+) are transfered into an intermembrane space c) ATP is produced by the Complex I d) all reduced coenzymes (NADH+H+ and FADH2) are reoxidized by the same ...
The caspase-cleaved DAP5 protein supports internal ribosome entry
... the translation of a reporter gene in dying cells, whereas the cap-dependent translation mode is abrogated severely. These IRESs are referred to in this work as ‘‘death IRESs,’’ because they maintain their translation rate in the dying cell. What molecular mechanisms underlie the switch from capdepe ...
... the translation of a reporter gene in dying cells, whereas the cap-dependent translation mode is abrogated severely. These IRESs are referred to in this work as ‘‘death IRESs,’’ because they maintain their translation rate in the dying cell. What molecular mechanisms underlie the switch from capdepe ...
How migration occurs
... • Extracellular signal activated receptor protein activated PI-3-kinase PI(3,4,5)P3 docked Rac GEF • How Rac GEF promotes GTP loading o PI(3,4,5)P3 binding relieves interaction between PH and DH domain to stimulate activity o Loss of activity due to deletion of PH domain is restored by addition of a ...
... • Extracellular signal activated receptor protein activated PI-3-kinase PI(3,4,5)P3 docked Rac GEF • How Rac GEF promotes GTP loading o PI(3,4,5)P3 binding relieves interaction between PH and DH domain to stimulate activity o Loss of activity due to deletion of PH domain is restored by addition of a ...
Apoptosome
The apoptosome is a large quaternary protein structure formed in the process of apoptosis. Its formation is triggered by the release of cytochrome c from the mitochondria in response to an internal (intrinsic) or external (extrinsic) cell death stimulus. Stimuli can vary from DNA damage and viral infection to developmental cues such as those leading to the degradation of a tadpole's tail.In mammalian cells, once cytochrome c is released, it binds to the cytosolic protein Apaf-1 to facilitate the formation of apoptosome. An early biochemical study suggests a two-to-one ratio of cytochrome c to apaf-1 for apoptosome formation. However, recent structural studies suggest the cytochrome c to apaf-1 ratio is one-to-one. It has also been shown that the nucleotide dATP as third component binds to apaf-1, however its exact role is still debated. The mammalian apoptosome had never been crystallized, but a human APAF-1/cytochrome-c apoptosome has been imaged at lower (2 nm) resolution by cryogenic transmission electron microscopy 10 years ago, revealing a wheel-like particle with 7-fold symmetry. Recently, a medium resolution (9.5 Ångström) structure of human apoptosome was also solved by cryo-electron microscopy, which allows unambiguous inference for positions of all the APAF-1 domains (CARD, NBARC and WD40) and cytochrome c. There is also now a crystal structure of the monomeric, inactive Apaf-1 subunit (PDB 3SFZ). Once formed, the apoptosome can then recruit and activate the inactive pro-caspase-9. Once activated, this initiator caspase can then activate effector caspases and trigger a cascade of events leading to apoptosis.