P026 The role of histidine in tryptophan 2,3
... Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris is a heme-containing enzyme from a small family of homologous enzymes, which includes indoleamine 2,3-dioxygenase (IDO). TDO is a homotetrameric enzyme and displays high specificity for L-tryptophan (L-Trp) and related derivatives such as ...
... Tryptophan 2,3-dioxygenase (TDO) from Xanthomonas campestris is a heme-containing enzyme from a small family of homologous enzymes, which includes indoleamine 2,3-dioxygenase (IDO). TDO is a homotetrameric enzyme and displays high specificity for L-tryptophan (L-Trp) and related derivatives such as ...
What is the difference between basal and activated transcription?
... A. General transcription factor (TF) vs. promoterspecific 1. general TFs are required by all mRNA genes a. an absolute requirement b. transcription can occur alone with these factors is by definition the basal level of transcription 2. promoter-specific TFs are different for each gene 3. the promote ...
... A. General transcription factor (TF) vs. promoterspecific 1. general TFs are required by all mRNA genes a. an absolute requirement b. transcription can occur alone with these factors is by definition the basal level of transcription 2. promoter-specific TFs are different for each gene 3. the promote ...
An Exploration of the Dynamic-Function
... role of GPCRs’ active site dynamics in recognizing and binding the appropriate ligand and how these intrinsic dynamics differ between different classes of GPCRs have been the main focus of the current study. The preliminary results of this study will be presented. ...
... role of GPCRs’ active site dynamics in recognizing and binding the appropriate ligand and how these intrinsic dynamics differ between different classes of GPCRs have been the main focus of the current study. The preliminary results of this study will be presented. ...
Abstract The development of a RNA-aptamer
... (aptasensor) for C-reactive protein (CRP) is reported. CRP is an important clinical biomarker; it was the first acutephase protein to be discovered (1930) and is a sensitive sistemi marker of inflammation and tissue damage. It has also a prognostic value for patients with acute coronary syndrome. Th ...
... (aptasensor) for C-reactive protein (CRP) is reported. CRP is an important clinical biomarker; it was the first acutephase protein to be discovered (1930) and is a sensitive sistemi marker of inflammation and tissue damage. It has also a prognostic value for patients with acute coronary syndrome. Th ...
Cyanovirin-N
... Binding of Viral Envelope to CD4 Binding of Viral Envelope to other chemokines Fusion of Viral and Host Cell membranes Incorporation of viral DNA to host genome ...
... Binding of Viral Envelope to CD4 Binding of Viral Envelope to other chemokines Fusion of Viral and Host Cell membranes Incorporation of viral DNA to host genome ...
Summary Summary Glutaredoxins (Grx) and Glyoxalases 1 and 2
... are also the first Grx-isoforms targeted to the secretory pathway, namely the cis-Golgi. Both enzymes are highly suited to study structure-function relationships because they differ from all monothiol Grx-isoforms investigated so far and rather share features with canonical dithiol Grx. For example, ...
... are also the first Grx-isoforms targeted to the secretory pathway, namely the cis-Golgi. Both enzymes are highly suited to study structure-function relationships because they differ from all monothiol Grx-isoforms investigated so far and rather share features with canonical dithiol Grx. For example, ...
Characterization of Proteins and Nucleic Acids on
... approximate fraction of each secondary structure type that is present in any protein can thus be determined by analyzing its far-uv CD spectrum as a sum of fractional multiples of such reference spectra for each structural type. Like all spectroscopic techniques, the CD signal reflects an average of ...
... approximate fraction of each secondary structure type that is present in any protein can thus be determined by analyzing its far-uv CD spectrum as a sum of fractional multiples of such reference spectra for each structural type. Like all spectroscopic techniques, the CD signal reflects an average of ...
Quantification of transcription factor binding in cell extracts using an
... The kinetic response of our electrochemical sensor was assessed by performing repeated scans at 10 second intervals after addition of a saturating amount of TBP (500 nM) was introduced to the buffer (sensor was pre-equilibrated in buffer). After response current had stabilized, the solution was chan ...
... The kinetic response of our electrochemical sensor was assessed by performing repeated scans at 10 second intervals after addition of a saturating amount of TBP (500 nM) was introduced to the buffer (sensor was pre-equilibrated in buffer). After response current had stabilized, the solution was chan ...
Transcriptional Networks
... Correlation:Find the highest correlations between expression level of TF of interest (red) and number of cis-element occurrence (normalized). AA means high numbers of A. ...
... Correlation:Find the highest correlations between expression level of TF of interest (red) and number of cis-element occurrence (normalized). AA means high numbers of A. ...
No Slide Title
... Protein Dynamics and Relation to Function. Large-Scale Conformational Change. Ligand Binding and Macromolecular Association. Drug Design ...
... Protein Dynamics and Relation to Function. Large-Scale Conformational Change. Ligand Binding and Macromolecular Association. Drug Design ...
1.Jeremy_Introduction_of_Protein_Simulation_and_Drug_Design
... Protein Dynamics and Relation to Function. Large-Scale Conformational Change. Ligand Binding and Macromolecular Association. Drug Design ...
... Protein Dynamics and Relation to Function. Large-Scale Conformational Change. Ligand Binding and Macromolecular Association. Drug Design ...
L. RECEPTOR-LIGAND DISSOCIATION Simple Equilibrium Binding
... ligand. KH is the Hill coefficient (see below); 200 µM in this case. From a graphical perspective, cooperative binding is in evidence when a plot of fraction of bound receptor (Y) vs. ligand concentration gives a sigmoidal plot. Note that the x-axis is linear in Figure L.4; the weak binding observed ...
... ligand. KH is the Hill coefficient (see below); 200 µM in this case. From a graphical perspective, cooperative binding is in evidence when a plot of fraction of bound receptor (Y) vs. ligand concentration gives a sigmoidal plot. Note that the x-axis is linear in Figure L.4; the weak binding observed ...
Dioxygen Binding in the Active Site of Histone Demethylase
... Now we have studied the first step of demethylation by JmjC proteins, highlighting the importance of non-local energy contributions from residues and substrate. Our next steps will involve understanding the structural basis for substrate selectivity within the active site, and the full reaction coor ...
... Now we have studied the first step of demethylation by JmjC proteins, highlighting the importance of non-local energy contributions from residues and substrate. Our next steps will involve understanding the structural basis for substrate selectivity within the active site, and the full reaction coor ...
Overriding Imatinib Resistance with a Novel ABL Kinase
... • The primary consequence of all ABL kinase domain mutations associated with Gleevec resistance is the impairment of kinase domain flexibility such that the kinase domain is unable to assume the optimal inactive conformation needed for Gleevac binding. • Inhibitors with less stringent conformational ...
... • The primary consequence of all ABL kinase domain mutations associated with Gleevec resistance is the impairment of kinase domain flexibility such that the kinase domain is unable to assume the optimal inactive conformation needed for Gleevac binding. • Inhibitors with less stringent conformational ...
Chem452_Quiz_2
... e. What determines the ultimate speed limit of an enzyme-catalyzed reaction? That is, what is it that imposes a physical limit on catalytic perfection? f. ...
... e. What determines the ultimate speed limit of an enzyme-catalyzed reaction? That is, what is it that imposes a physical limit on catalytic perfection? f. ...
ChIP-seq - STAT 115
... • Could also be used to examine known motif enrichment • Is motif enrichment correlated with ChIP-seq enrichment? • Is motif more enriched in peak summits than peak flanks? • Motif analysis could identify transcription factor partners of ChIP-seq factors ...
... • Could also be used to examine known motif enrichment • Is motif enrichment correlated with ChIP-seq enrichment? • Is motif more enriched in peak summits than peak flanks? • Motif analysis could identify transcription factor partners of ChIP-seq factors ...
Role of Interactions and Volume Variation in Discriminating Active
... analysis on similarities and differences observed in hydrophobic interactions and hydrogen bond interactions of 170 X-ray crystal structures of active and inactive cyclin-dependent kinase-2 (CDK-2) ligand complexes obtained from the Protein Data Bank. We have also systematically analyzed variation o ...
... analysis on similarities and differences observed in hydrophobic interactions and hydrogen bond interactions of 170 X-ray crystal structures of active and inactive cyclin-dependent kinase-2 (CDK-2) ligand complexes obtained from the Protein Data Bank. We have also systematically analyzed variation o ...
Supplementary Methods (doc 30K)
... MiRNA quantitative stem-loop RT-PCR. We used single tube TaqMan miRNA assays as previously described (Chen et al., 2005) (Applied Biosystems, Foster City, CA). Normalization was performed with 18S. All RT reactions, including no-template controls and RT minus controls, were run in a GeneAmp PCR 9700 ...
... MiRNA quantitative stem-loop RT-PCR. We used single tube TaqMan miRNA assays as previously described (Chen et al., 2005) (Applied Biosystems, Foster City, CA). Normalization was performed with 18S. All RT reactions, including no-template controls and RT minus controls, were run in a GeneAmp PCR 9700 ...
biochemistry-4th-edition-voet-solution-manual
... Histidine-Proline-rich Glycoprotein as a Plasma pH sensor 1. a. According to the data shown, HPRG binds heparin at high affinity at pH = 5.2, but when the pH increases to 6.8, affinity of HPRG for heparin decreases by half. At pH = 7.2, there is virtually no binding of HPRG to heparin. Since heparin ...
... Histidine-Proline-rich Glycoprotein as a Plasma pH sensor 1. a. According to the data shown, HPRG binds heparin at high affinity at pH = 5.2, but when the pH increases to 6.8, affinity of HPRG for heparin decreases by half. At pH = 7.2, there is virtually no binding of HPRG to heparin. Since heparin ...
Effect of arachidonic acid on specific binding of [3H]naloxone to
... was significantly reduced by AA and the antagonist configuration of the opioid receptors were observed to be more susceptible to AA inhibition. The inhibitory effect of AA that was observed in our studies can not be explained simply by a negative feedback mechanism between the second messenger and t ...
... was significantly reduced by AA and the antagonist configuration of the opioid receptors were observed to be more susceptible to AA inhibition. The inhibitory effect of AA that was observed in our studies can not be explained simply by a negative feedback mechanism between the second messenger and t ...
Transcription Regulation
... • It shows that 29 pheromone-induced genes are regulated directly by Ste12. • 11 were already known to participate in various steps of the mating ...
... • It shows that 29 pheromone-induced genes are regulated directly by Ste12. • 11 were already known to participate in various steps of the mating ...
Mass spectrometric characterization of a conformational epitope of
... capture/isolation, chemical structure determination and affinity quantification of biopolymer ligands, dissociated from a biopolymer- ligand complex on a gold chip. Key tool of the biosensor-MS combination is a new integrated, and automated interface that provides sample concentration and in-situ de ...
... capture/isolation, chemical structure determination and affinity quantification of biopolymer ligands, dissociated from a biopolymer- ligand complex on a gold chip. Key tool of the biosensor-MS combination is a new integrated, and automated interface that provides sample concentration and in-situ de ...
Cytochrome c regulates SET-mediated acetylation of the C
... experiments were performed to determine the nature of such interaction. ITC studies confirmed un-acetylated (KD ca. 3 M) but not acetylated p53-CTD binds SET. Next, 1D 1H NMR - tracking Cc Met80-εCH3 – was used to assess the competition between p53-CTD and Cc for SET. Increasing concentrations of p5 ...
... experiments were performed to determine the nature of such interaction. ITC studies confirmed un-acetylated (KD ca. 3 M) but not acetylated p53-CTD binds SET. Next, 1D 1H NMR - tracking Cc Met80-εCH3 – was used to assess the competition between p53-CTD and Cc for SET. Increasing concentrations of p5 ...
Cooperative binding
Molecular binding is an interaction between molecules that results in a stable physical association between those molecules. Cooperative binding occurs in binding systems that are constituted by more than one type (species) of molecule (say molecules A and B) and in which one of the partners is not mono-valent; i.e., it binds more than one molecule of the other molecular species. For example, one molecule of type A can bind 6 molecules of type B (in such cases, B is usually referred to as the ""ligand""). Binding in this type of system can be considered ""cooperative"" if the binding of B to one site on A is affected by the binding of B to other site(s) on A. In other words, the binding of B molecules to the different sites on A do not constitute mutually independent events. This can be due, for instance, to an affinity for the ligand that depends on the amount of ligand bound. Cooperativity can be positive or negative. Cooperative binding is observed in many biopolymers, including proteins and nucleic acids. Cooperative binding has been shown to be the mechanism underlying a large range of biochemical and physiological processes.