Computational Pharmacology - Carnegie Mellon School of
... have we understood how aspirin works, and how it might be improved http://www.rcsb.org/pdb/molecules/pdb17_1.html ...
... have we understood how aspirin works, and how it might be improved http://www.rcsb.org/pdb/molecules/pdb17_1.html ...
Outline Visualizing proteins with PyMol
... What are some of the unique features of disordered proteins? • Extensive binding interfaces can be created with rela/vely small proteins • Conforma/onal flexibility allows a protein segment to bind its target as well as to a modifying enzyme (i.e. posttransla/onal modifica/on). • Pliable (unst ...
... What are some of the unique features of disordered proteins? • Extensive binding interfaces can be created with rela/vely small proteins • Conforma/onal flexibility allows a protein segment to bind its target as well as to a modifying enzyme (i.e. posttransla/onal modifica/on). • Pliable (unst ...
CSCE590/822 Data Mining Principles and Applications
... Protein bioinformatics: what and why? Protein Secondary Structure Prediction: problem & algorithm Summary ...
... Protein bioinformatics: what and why? Protein Secondary Structure Prediction: problem & algorithm Summary ...
CHAPTER 4 Proteins: Structure, Function, Folding
... • This structure is able to fulfill a specific biological function • This structure is called the native fold • The native fold has a large number of favorable interactions within the protein • There is a cost in conformational entropy of folding the protein into one specific native fold ...
... • This structure is able to fulfill a specific biological function • This structure is called the native fold • The native fold has a large number of favorable interactions within the protein • There is a cost in conformational entropy of folding the protein into one specific native fold ...
AMPK and mTOR: Antagonist ATP Sensors
... The Mammalian Target of Rapamycin (mTOR) is one of the body's protein synthesis regulators. mTOR functions as an energy sensor; it is activated when ATP levels are high and blocked when ATP levels are decreased (AMPK is activated when ATP decreases, which works antagonistically to mTOR). The main en ...
... The Mammalian Target of Rapamycin (mTOR) is one of the body's protein synthesis regulators. mTOR functions as an energy sensor; it is activated when ATP levels are high and blocked when ATP levels are decreased (AMPK is activated when ATP decreases, which works antagonistically to mTOR). The main en ...
Cell signalling - The Open University
... paracrine signalling. In this scenario, the secreted signal acts back on the same cell or group of cells it was secreted from. In development, autocrine signalling reinforces a particular developmental commitment of a cell type. Autocrine signalling can promote inappropriate proliferation, as may be ...
... paracrine signalling. In this scenario, the secreted signal acts back on the same cell or group of cells it was secreted from. In development, autocrine signalling reinforces a particular developmental commitment of a cell type. Autocrine signalling can promote inappropriate proliferation, as may be ...
EXPLORING PROTEIN STRUCTURE
... Microtubules are composed of filaments of the protein, tubulin (top left) . These filaments are compressed like springs allowing microtubules to ‘stretch and contract’. 13 of these filaments attach side to side, a little like the slats in a barrel, to form a microtubule. This barrel shaped structure ...
... Microtubules are composed of filaments of the protein, tubulin (top left) . These filaments are compressed like springs allowing microtubules to ‘stretch and contract’. 13 of these filaments attach side to side, a little like the slats in a barrel, to form a microtubule. This barrel shaped structure ...
Unknown function, JCSG
... As part of its mission to increase structural coverage of protein families, JCSG is targeting proteins from the large CATH homologous superfamily 3.40.630.10 of zinc peptidases, which belong to the phosphorylase/hydrolase-like fold in SCOP and are comprised of proteins from several Pfam families (th ...
... As part of its mission to increase structural coverage of protein families, JCSG is targeting proteins from the large CATH homologous superfamily 3.40.630.10 of zinc peptidases, which belong to the phosphorylase/hydrolase-like fold in SCOP and are comprised of proteins from several Pfam families (th ...
TAK1-binding protein 1 is a pseudophosphatase
... necrosis factor) and IL-1 (interleukin-1). It plays a key role in switching on several pro-inflammatory signalling pathways, including those that activate the MAPKs (mitogen-activated protein kinases), termed p38α MAPK, JNK1/2 (c-Jun N-terminal kinase 1/2) and ERK1/2 (extracellular-signal-regulated ...
... necrosis factor) and IL-1 (interleukin-1). It plays a key role in switching on several pro-inflammatory signalling pathways, including those that activate the MAPKs (mitogen-activated protein kinases), termed p38α MAPK, JNK1/2 (c-Jun N-terminal kinase 1/2) and ERK1/2 (extracellular-signal-regulated ...
substances that target tumor metabolism
... The goal of this review is to summarize current knowledge on cancer metabolism, draw hypothesis explaining metabolic alterations and associated gene changes. Most importantly, we indicate a list of possible pharmacological targets. In short, tumor metabolism displays mixed glycolysis and neogluogene ...
... The goal of this review is to summarize current knowledge on cancer metabolism, draw hypothesis explaining metabolic alterations and associated gene changes. Most importantly, we indicate a list of possible pharmacological targets. In short, tumor metabolism displays mixed glycolysis and neogluogene ...
Caspary T, Garc a-Garc a MJ, Eggenschwiler JR, Wyler MR, Huangfu D, Rakeman AS, Lee JD, Alcorn HL, Anderson KV. Curr Biol. 2002 Sep 17;12(18):1628-32. Mouse Dispatched homologue1 is required for long-range, but not juxtacrine, Hh signaling.
... floor plate and other ventral neural cell types. As predicted from the morphological observations, no expression of the floor plate marker Hnf3! was detected in the bnb or icb mutant neural tubes (Figures 1 and 2). Similarly, Shh expression was initiated in the notochord but was never detected in th ...
... floor plate and other ventral neural cell types. As predicted from the morphological observations, no expression of the floor plate marker Hnf3! was detected in the bnb or icb mutant neural tubes (Figures 1 and 2). Similarly, Shh expression was initiated in the notochord but was never detected in th ...
Intro to and Thermodynamics In Metabolism:
... Insulin and Glucagon: Know the “Processing of Insulin” and the “Glucose Induced Biosynthesis and Release of Insulin” diagram. Don’t worry about the structure of the Insulin Receptor. Know the “Insulin Binding to it’s Receptor Followed by Activation of the Receptor” diagram. Skip the “Cascade of Even ...
... Insulin and Glucagon: Know the “Processing of Insulin” and the “Glucose Induced Biosynthesis and Release of Insulin” diagram. Don’t worry about the structure of the Insulin Receptor. Know the “Insulin Binding to it’s Receptor Followed by Activation of the Receptor” diagram. Skip the “Cascade of Even ...
GEFs: master regulators of G
... G proteins respond to extra- or intracellular signals, which can induce translocation of the GEFs to specific membrane compartments in the cell where they then activate G proteins. Certain GEFs also mediate crosstalk between different receptor-mediated signaling pathways, thereby acting as signal in ...
... G proteins respond to extra- or intracellular signals, which can induce translocation of the GEFs to specific membrane compartments in the cell where they then activate G proteins. Certain GEFs also mediate crosstalk between different receptor-mediated signaling pathways, thereby acting as signal in ...
Are nonessential amino acids not so redundant for Chinese hamster
... ishing phosphorylation of the mTOR signaling effectors, 4E-BP1 and S6, and increasing phosphorylation of the AAR sensor, eIF2α [13] . In addition to regulation of protein stability and translation rates, amino acid depletion enhances translation of a subset of mRNA molecules, including certain trans ...
... ishing phosphorylation of the mTOR signaling effectors, 4E-BP1 and S6, and increasing phosphorylation of the AAR sensor, eIF2α [13] . In addition to regulation of protein stability and translation rates, amino acid depletion enhances translation of a subset of mRNA molecules, including certain trans ...
Fatty Acid Metabolism
... IMM impermeable to FA-CoA transport of FA across IMM requires the carnitine shuttle ...
... IMM impermeable to FA-CoA transport of FA across IMM requires the carnitine shuttle ...
Dissecting protein structure and function using directed evolution
... technique that allows a limited analysis of many interface residues with smaller libraries14. Amino acids at a binding surface are ...
... technique that allows a limited analysis of many interface residues with smaller libraries14. Amino acids at a binding surface are ...
Asymmetric cell division in C. elegans - Development
... pathway. egl-20 is expressed by a small group of cells in the posterior body region. However, despite this localized expression in the animal, EGL-20 does not act as a positiondependent morphogen to specify these distinct migratory fates. Instead, QL and QR exhibit different responses because they h ...
... pathway. egl-20 is expressed by a small group of cells in the posterior body region. However, despite this localized expression in the animal, EGL-20 does not act as a positiondependent morphogen to specify these distinct migratory fates. Instead, QL and QR exhibit different responses because they h ...
Hormones of the Gut
... Cholecystokinin (CCK) • 1928: Fat in small intestine stimulates the gall bladder to contract--cholecystokinin. • 1940s: Extract of duodenal mucosa stimulates pancreas to secrete enzymes-pancreozymin. • 1964-8: Purification of a single substance that stimulated both contraction of the gall bladder a ...
... Cholecystokinin (CCK) • 1928: Fat in small intestine stimulates the gall bladder to contract--cholecystokinin. • 1940s: Extract of duodenal mucosa stimulates pancreas to secrete enzymes-pancreozymin. • 1964-8: Purification of a single substance that stimulated both contraction of the gall bladder a ...
Arfs and membrane lipids: sensing, generating and responding to
... nucleotide exchange under physiological conditions (i.e. 1 mM Mg2+ ) in the absence of a GEF [4,5]. Indeed these observations led some investigators to study N-terminally truncated Arf proteins (17 for Arf1 and 13 for Arf6) that could readily be loaded with GTP and interact with effector proteins ...
... nucleotide exchange under physiological conditions (i.e. 1 mM Mg2+ ) in the absence of a GEF [4,5]. Indeed these observations led some investigators to study N-terminally truncated Arf proteins (17 for Arf1 and 13 for Arf6) that could readily be loaded with GTP and interact with effector proteins ...
Jessica Sallander The mechanism of G protein coupled receptor
... different conformational states. GPCRs adopt inactive and active states. Activating ligands binding at the extracellular part of the receptor or constitutively active mutations stabilize active conformations that increase cytoplasmic G protein binding. Agonists or constitutively active mutations dis ...
... different conformational states. GPCRs adopt inactive and active states. Activating ligands binding at the extracellular part of the receptor or constitutively active mutations stabilize active conformations that increase cytoplasmic G protein binding. Agonists or constitutively active mutations dis ...
Identification of the Missing Links in Prokaryotic Pentose Oxidation
... as a sole carbon and energy source. At present, three main catabolic pathways have been described for pentoses. The first is present in Bacteria and uses isomerases, kinases, and epimerases to convert D- and L-arabinose (Ara) and D-xylose (Xyl) into D-xylulose 5-phosphate (Fig. 1A), which is further ...
... as a sole carbon and energy source. At present, three main catabolic pathways have been described for pentoses. The first is present in Bacteria and uses isomerases, kinases, and epimerases to convert D- and L-arabinose (Ara) and D-xylose (Xyl) into D-xylulose 5-phosphate (Fig. 1A), which is further ...
Gene Section TMPRSS2 (transmembrane protease, serine 2) Atlas of Genetics and Cytogenetics
... Subcellular location: Cell membrane; Single-pass type II membrane protein. Activated by cleavage and secreted. ...
... Subcellular location: Cell membrane; Single-pass type II membrane protein. Activated by cleavage and secreted. ...
Revving up glycolysis
... enzyme present nearly universally across tumor types. Based on that research, activating the enzyme might be most effective in tumors with low levels of serine or oxygen.1–3 Pyruvate kinase occurs as two isoforms: pyruvate kinase M1 isozyme (PKM1) is expressed by most nonproliferative healthy tissue ...
... enzyme present nearly universally across tumor types. Based on that research, activating the enzyme might be most effective in tumors with low levels of serine or oxygen.1–3 Pyruvate kinase occurs as two isoforms: pyruvate kinase M1 isozyme (PKM1) is expressed by most nonproliferative healthy tissue ...
inflammatory molecules
... • How are prostaglandins, leukotrienes, lipoxins, and thromboxanes synthesized (substrates, enzymes, cofactors)? • What is the nomenclature for prostaglandin, leukotriene, lipoxin, and thromboxane receptors? • How do NSAIDs work? • How do steroids work? • What are important characteristics of COX-1 ...
... • How are prostaglandins, leukotrienes, lipoxins, and thromboxanes synthesized (substrates, enzymes, cofactors)? • What is the nomenclature for prostaglandin, leukotriene, lipoxin, and thromboxane receptors? • How do NSAIDs work? • How do steroids work? • What are important characteristics of COX-1 ...
Paracrine signalling
Paracrine signaling is a form of cell-cell communication in which a cell produces a signal to induce changes in nearby cells, altering the behavior or differentiation of those cells. Signaling molecules known as paracrine factors diffuse over a relatively short distance (local action), as opposed to endocrine factors (hormones which travel considerably longer distances via the circulatory system), juxtacrine interactions, and autocrine signaling. Cells that produce paracrine factors secrete them into the immediate extracellular environment. Factors then travel to nearby cells in which the gradient of factor received determines the outcome. However, the exact distance that paracrine factors can travel is not certain.Although paracrine signaling elicits a diverse array of responses in the induced cells, most paracrine factors utilize a relatively streamlined set of receptors and pathways. In fact, different organs in the body -even between different species - are known to utilize a similar sets of paracrine factors in differential development. The highly conserved receptors and pathways can be organized into four major families based on similar structures: Fibroblast growth factor (FGF) family, Hedgehog family, Wnt family, and TGF-β superfamily. Binding of a paracrine factor to its respective receptor initiates signal transduction cascades, eliciting different responses.