Two conformations of a crystalline human tRNA synthetasetRNA
... synthetases of the bifunctional glutamyl-prolyl-tRNA synthetase (Glu-ProRS) (Lee et al, 2004; Sampath et al, 2004; Yang et al, 2004). The WHEP-TRS domain adopted a helix–turn– helix structure in a crystal structure of human TrpRS (in complex with Trp-AMP) (Yang et al, 2003) and in the NMR structure ...
... synthetases of the bifunctional glutamyl-prolyl-tRNA synthetase (Glu-ProRS) (Lee et al, 2004; Sampath et al, 2004; Yang et al, 2004). The WHEP-TRS domain adopted a helix–turn– helix structure in a crystal structure of human TrpRS (in complex with Trp-AMP) (Yang et al, 2003) and in the NMR structure ...
Susan Viggiano and Michael S. Cosgrove
... complexes are linked to H3K4 monomethylation at active enhancers (39). In contrast, it has been suggested that SETd1A/B complexes catalyze the bulk of H3K4 trimethylation in cells (40, 41), but it is dependent on other factors that are unique to SETd1A/B complexes, such as WDR82 (Swd2 in yeast) (40, ...
... complexes are linked to H3K4 monomethylation at active enhancers (39). In contrast, it has been suggested that SETd1A/B complexes catalyze the bulk of H3K4 trimethylation in cells (40, 41), but it is dependent on other factors that are unique to SETd1A/B complexes, such as WDR82 (Swd2 in yeast) (40, ...
Science
... design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1a and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal do ...
... design. Yet controversy exists around the mechanism of sirtuin-activating compounds (STACs). We found that specific hydrophobic motifs found in SIRT1 substrates such as PGC-1a and FOXO3a facilitate SIRT1 activation by STACs. A single amino acid in SIRT1, Glu230, located in a structured N-terminal do ...
A 1-Megadalton Translocation Complex Containing
... intact Toc159, 86- and 52-kD fragments of Toc159, and Tic22. An asterisk denotes a nonspecific cross-reacting band. (C) A gel strip corresponding to lane 1 (without protease) of (A) was subjected to 2D-BN/SDS-PAGE. (D) A gel strip corresponding to lane 3 (with thermolysin) of (A) was analyzed as in ...
... intact Toc159, 86- and 52-kD fragments of Toc159, and Tic22. An asterisk denotes a nonspecific cross-reacting band. (C) A gel strip corresponding to lane 1 (without protease) of (A) was subjected to 2D-BN/SDS-PAGE. (D) A gel strip corresponding to lane 3 (with thermolysin) of (A) was analyzed as in ...
Structure and function of haemoglobin: II. Some
... Residues are defined here as invariant when they occur at structurally identical sites in all the normal myoglobins and haemoglobins so far investigated. Abnormal haemoglobins have been excluded, because some of their abnormalities interfere with the oxygen-combining function, so that the protein ca ...
... Residues are defined here as invariant when they occur at structurally identical sites in all the normal myoglobins and haemoglobins so far investigated. Abnormal haemoglobins have been excluded, because some of their abnormalities interfere with the oxygen-combining function, so that the protein ca ...
Substrate Specificity and Mechanism from the Structure of
... atoms. Biochemical studies have shown that Pf GalK will also utilise GTP as a phosphoryl donor with only a 40% decrease in activity compared to ATP.24 This is consistent with the analysis of the purine-binding pocket, which suggests that a GTP molecule could be accommodated with only minor modificat ...
... atoms. Biochemical studies have shown that Pf GalK will also utilise GTP as a phosphoryl donor with only a 40% decrease in activity compared to ATP.24 This is consistent with the analysis of the purine-binding pocket, which suggests that a GTP molecule could be accommodated with only minor modificat ...
Effects of Marine Toxins on the Reproduction and Early
... 1. Main Marine Toxins Produced by Bacteria and Phytoplankton Many species of marine microorganisms produce toxins that have significant impact in other species such as invertebrates, vertebrates and in many cases, human populations. Among other groups, Bacteria, Cyanobacteria, Diatoms, Crysophytes a ...
... 1. Main Marine Toxins Produced by Bacteria and Phytoplankton Many species of marine microorganisms produce toxins that have significant impact in other species such as invertebrates, vertebrates and in many cases, human populations. Among other groups, Bacteria, Cyanobacteria, Diatoms, Crysophytes a ...
12. Molecular Recognition: The Thermodynamics of
... measuring the concentration of the free and associated species at equilibrium we can calculate the strength of the molecular interaction. We focus on noncovalent interactions between proteins and their ligands, a term that is typically used to describe a smaller molecule that binds to a larger one. ...
... measuring the concentration of the free and associated species at equilibrium we can calculate the strength of the molecular interaction. We focus on noncovalent interactions between proteins and their ligands, a term that is typically used to describe a smaller molecule that binds to a larger one. ...
Role of Cell Membrane Fluidity in Living and Non
... of such regulation is to keep the viscosity of the membrane approximately the same despite changes in temperature.When the bacterial cells are transferred from warmer to cooler environment, a drop in temperature results in an increase in the proportion of 16-carbon rather than 18-carbon fatty acids ...
... of such regulation is to keep the viscosity of the membrane approximately the same despite changes in temperature.When the bacterial cells are transferred from warmer to cooler environment, a drop in temperature results in an increase in the proportion of 16-carbon rather than 18-carbon fatty acids ...
Protein proteinase inhibitors from avian egg whites
... serpin family is a frequently encountered phenomenon rather than a rarity [33 – 35]. The hypervariability is not limited to the third domain but may occur in the first and second domains. Ardelt and Laskowski [36] have shown that eight different proteinases, including chymotrypsin, subtilisin, elast ...
... serpin family is a frequently encountered phenomenon rather than a rarity [33 – 35]. The hypervariability is not limited to the third domain but may occur in the first and second domains. Ardelt and Laskowski [36] have shown that eight different proteinases, including chymotrypsin, subtilisin, elast ...
The PRT protein family Sangita C Sinha* and Janet L Smith
... The available structures provide a wealth of information on states of PRTases relevant to catalysis, effectively providing snapshots along the reaction pathway [31,40]. The closed-loop structures, in particular, provide a remarkably consistent picture of Mg•PRPP binding. Mg•PRPP binds in a virtually ...
... The available structures provide a wealth of information on states of PRTases relevant to catalysis, effectively providing snapshots along the reaction pathway [31,40]. The closed-loop structures, in particular, provide a remarkably consistent picture of Mg•PRPP binding. Mg•PRPP binds in a virtually ...
1-3 flagellum - Instituto de Higiene
... surface membrane [20]. Localization of these two isoforms by confocal immunofluorescence and immunoelectron microscopy revealed that ISO1 is restricted to the flagellar membrane (Fig. 4), whereas ISO2 is located in the pellicular plasma membrane but not the flagellar membrane [21]. Furthermore, a ch ...
... surface membrane [20]. Localization of these two isoforms by confocal immunofluorescence and immunoelectron microscopy revealed that ISO1 is restricted to the flagellar membrane (Fig. 4), whereas ISO2 is located in the pellicular plasma membrane but not the flagellar membrane [21]. Furthermore, a ch ...
Statistical Analysis of Amino Acid Patterns in Transmembrane
... database of transmembrane domains. Our analysis was performed with a novel formalism, which we call TMSTAT, for exactly calculating the expectancies of all pairs and triplets of residues in individual sequences, taking into account differential sequence composition and the substantial effect of ®nit ...
... database of transmembrane domains. Our analysis was performed with a novel formalism, which we call TMSTAT, for exactly calculating the expectancies of all pairs and triplets of residues in individual sequences, taking into account differential sequence composition and the substantial effect of ®nit ...
The Early Interaction of the Outer Membrane Protein PhoE with
... of folding in the periplasm. Furthermore, the order of interactions with accessory proteins and the timing of the various reactions are largely unknown. In the studies described in this report, we used an unbiased approach to study these processes. We present evidence that the initial interaction of ...
... of folding in the periplasm. Furthermore, the order of interactions with accessory proteins and the timing of the various reactions are largely unknown. In the studies described in this report, we used an unbiased approach to study these processes. We present evidence that the initial interaction of ...
How to move an amphipathic molecule across a lipid
... subunit in an arrangement termed ‘domain swapping’ [47]. Interestingly, ABCD proteins have a significant number of conserved hydrophilic residues in predicted transmembrane helices, several of which are predicted to face into a putative permeant binding cavity identified in Sav1866 (Figure 2) [46]. ...
... subunit in an arrangement termed ‘domain swapping’ [47]. Interestingly, ABCD proteins have a significant number of conserved hydrophilic residues in predicted transmembrane helices, several of which are predicted to face into a putative permeant binding cavity identified in Sav1866 (Figure 2) [46]. ...
tubulin - Journal of Cell Science
... that longitudinal interactions between FtsZ subunits involve identical structural elements to those in tubulin (Nogales et al., 1998a), a view that was later confirmed by electron microscopy and image reconstruction (Löwe and Amos, 1999). A striking characteristic of the γ-tubulin sequence is the Gl ...
... that longitudinal interactions between FtsZ subunits involve identical structural elements to those in tubulin (Nogales et al., 1998a), a view that was later confirmed by electron microscopy and image reconstruction (Löwe and Amos, 1999). A striking characteristic of the γ-tubulin sequence is the Gl ...
Quantum binding energy features of the T3-785
... to expand the electronic Kohn–Sham orbitals taking into account all electrons with unrestricted spin explicitly, being 10 to 100 times faster and in good agreement with those obtained using the large scale Gaussian basis sets, such as 6311+G(3df,2pd).34,35 The orbital cutoff radius was set to 3.7 Å ...
... to expand the electronic Kohn–Sham orbitals taking into account all electrons with unrestricted spin explicitly, being 10 to 100 times faster and in good agreement with those obtained using the large scale Gaussian basis sets, such as 6311+G(3df,2pd).34,35 The orbital cutoff radius was set to 3.7 Å ...
Functional and structural roles of parasite-specific inserts in the bifunctional S-adenosylmethionine decarboxylase/ornithine
... AdoMetDClODC were expressed as Strep-Tag fusion proteins as described in Chapter 3, section 3.2.2 (Krause, et al., 2000; Miiller, et al., 2000; Wrenger, et al., 2001). Mutant forms of PfAdoMetDC/ODC with individual deletion of the parasite-specific inserts, as well as single and combined insert dele ...
... AdoMetDClODC were expressed as Strep-Tag fusion proteins as described in Chapter 3, section 3.2.2 (Krause, et al., 2000; Miiller, et al., 2000; Wrenger, et al., 2001). Mutant forms of PfAdoMetDC/ODC with individual deletion of the parasite-specific inserts, as well as single and combined insert dele ...
Review Non-ribosomal peptide synthetases: Identifying the cryptic
... mechanism for such peptides. In total, five subtypes of condensation domains have been recognized (Rausch et al. 2007). Besides the two mentioned above, there is a starter Cdomain which acylates the first activated amino acid with β-hydroxy fatty acid, a dual E/C domain responsible for epimerization ...
... mechanism for such peptides. In total, five subtypes of condensation domains have been recognized (Rausch et al. 2007). Besides the two mentioned above, there is a starter Cdomain which acylates the first activated amino acid with β-hydroxy fatty acid, a dual E/C domain responsible for epimerization ...
NMR studies of the methionine methyl groups in calmodulin
... obtained in this work are identical [4]. The latter and our results are however at variance with earlier published assignments for the Met residues in calcium CaM [31]. Our assignments for the CaM-MLCK complex are consistent with those in [29]; the assignments for apo-CaM have not been reported yet. ...
... obtained in this work are identical [4]. The latter and our results are however at variance with earlier published assignments for the Met residues in calcium CaM [31]. Our assignments for the CaM-MLCK complex are consistent with those in [29]; the assignments for apo-CaM have not been reported yet. ...
Stockholm University
... purchased from Missouri University of Science and Technology cDNA Resource Center (MO, U.S.A.). All mutations, including addition of the FLAG-tag, was performed using the QuikChange1 II Site Directed mutagenesis kit (Stratagene, La Jolla, CA, U.S.A.) according to the manufacturer’s instructions with ...
... purchased from Missouri University of Science and Technology cDNA Resource Center (MO, U.S.A.). All mutations, including addition of the FLAG-tag, was performed using the QuikChange1 II Site Directed mutagenesis kit (Stratagene, La Jolla, CA, U.S.A.) according to the manufacturer’s instructions with ...
STRUCTURAL INSIGHTS INTO NOVEL MICROBIAL METALLOENZYMES
... sources. Structural homology of YcfD, the second metalloenzyme, to the 2OG oxygenase family, particularily human proteins involved in ribosome assembly, combined with evidence that YcfD interacts with the essential ribosomal protein L-16 provides the first evidence of translational regulation by a 2 ...
... sources. Structural homology of YcfD, the second metalloenzyme, to the 2OG oxygenase family, particularily human proteins involved in ribosome assembly, combined with evidence that YcfD interacts with the essential ribosomal protein L-16 provides the first evidence of translational regulation by a 2 ...
A Survey of Left-handed Helices in Protein Structures
... very rare. Stretches of amino acids with unusual backbone conformations (e.g. left-handed helices) often appear at ligand-binding sites, protein–protein interfaces or other functional sites. It has been suggested that proteins may sacrifice a part of their stability to form an effective functional s ...
... very rare. Stretches of amino acids with unusual backbone conformations (e.g. left-handed helices) often appear at ligand-binding sites, protein–protein interfaces or other functional sites. It has been suggested that proteins may sacrifice a part of their stability to form an effective functional s ...
Serine/Threonine Phosphatases
... mately 70% or greater protein sequence identity in any pairwise alignment. These sequences support a conserved fold and a similarly positioned active site for all members of the PPP family. At least 100 putative PP1-binding R subunits have been identified, with many more expected to be found (Cohen, ...
... mately 70% or greater protein sequence identity in any pairwise alignment. These sequences support a conserved fold and a similarly positioned active site for all members of the PPP family. At least 100 putative PP1-binding R subunits have been identified, with many more expected to be found (Cohen, ...
Strain in Protein Structures as Viewed Through Nonrotameric Side
... techniques. They observed that most side chains adopt one of the rotameric states. Schrauber et al.1 used a much larger protein structure set and observed that a significant fraction (up to 30%) of particular side-chain types could not be assigned to a rotameric state based on the criterion that rot ...
... techniques. They observed that most side chains adopt one of the rotameric states. Schrauber et al.1 used a much larger protein structure set and observed that a significant fraction (up to 30%) of particular side-chain types could not be assigned to a rotameric state based on the criterion that rot ...
Anthrax toxin
Anthrax toxin is a three-protein exotoxin secreted by virulent strains of the bacterium, Bacillus anthracis—the causative agent of anthrax. The toxin was first discovered by Harry Smith in 1954. Anthrax toxin is composed of a cell-binding protein, known as protective antigen (PA), and two enzyme components, called edema factor (EF) and lethal factor (LF). These three protein components act together to impart their physiological effects. Assembled complexes containing the toxin components are endocytosed. In the endosome, the enzymatic components of the toxin translocate into the cytoplasm of a target cell. Once in the cytosol, the enzymatic components of the toxin disrupts various immune cell functions, namely cellular signaling and cell migration. The toxin may even induce cell lysis, as is observed for macrophage cells. Anthrax toxin allows the bacteria to evade the immune system, proliferate, and ultimately kill the host animal. Research on anthrax toxin also provides insight into the generation of macromolecular assemblies, and on protein translocation, pore formation, endocytosis, and other biochemical processes.