Repair of larynx, trachea, and other fibrocartilaginous tissues
... mercial softWare package produced by DNAstar, Inc. The teachings by both sources are incorporated by reference herein. An initial alignment can be re?ned by comparison to a multi-sequence alignment of a family of related proteins. Once the alignment betWeen the candidate sequence and the seven-cyste ...
... mercial softWare package produced by DNAstar, Inc. The teachings by both sources are incorporated by reference herein. An initial alignment can be re?ned by comparison to a multi-sequence alignment of a family of related proteins. Once the alignment betWeen the candidate sequence and the seven-cyste ...
Identification and Cloning of a Cryptococcal Deacetylase That
... aqueous phase with chloroform-isoamyl-alcohol (24:1), RNA was precipitated with 1 volume of 5 M LiCl. Por Northern blot analysis, thè RNA preparation was size fractioned on a 1.3% agarose formaldehyde gel and transferred to a nylon membrane (Hybond N; Amersham Pharmacia). Hybridization was performed ...
... aqueous phase with chloroform-isoamyl-alcohol (24:1), RNA was precipitated with 1 volume of 5 M LiCl. Por Northern blot analysis, thè RNA preparation was size fractioned on a 1.3% agarose formaldehyde gel and transferred to a nylon membrane (Hybond N; Amersham Pharmacia). Hybridization was performed ...
{PDOC00000} {BEGIN
... - Rhizobium nodulation protein nodF, which probably acts as an ACP in the synthesis of the nodulation Nod factor fatty acyl chain. The sequence around the phosphopantetheine attachment site is conserved in all these proteins and can be used as a signature pattern. -Consensus pattern: [LIVY]-G-[LIVMF ...
... - Rhizobium nodulation protein nodF, which probably acts as an ACP in the synthesis of the nodulation Nod factor fatty acyl chain. The sequence around the phosphopantetheine attachment site is conserved in all these proteins and can be used as a signature pattern. -Consensus pattern: [LIVY]-G-[LIVMF ...
History of the Glycosaminoglycan Symposia in the Scientific Context
... (1771-1851) moved to Milan at the end of the 18th century from Frankfurt. They fostered cultural exchange between Italy and Germany. They acquired Villa Vigoni estate for their son and his wife. Unfortunately the son died and Heinrich transformed the villa into a place of remembrance with a wide col ...
... (1771-1851) moved to Milan at the end of the 18th century from Frankfurt. They fostered cultural exchange between Italy and Germany. They acquired Villa Vigoni estate for their son and his wife. Unfortunately the son died and Heinrich transformed the villa into a place of remembrance with a wide col ...
Forced Expression of Dystrophin Deletion Constructs Reveals
... muscle has not yet been fully elucidated, although it is thought to provide a crucial link between the intracellular actin cytoskeleton and the extracellular matrix (15). The mdx mouse contains a nonsense mutation in the dystrophin gene that leads to a complete absence of dystrophin in muscle, which ...
... muscle has not yet been fully elucidated, although it is thought to provide a crucial link between the intracellular actin cytoskeleton and the extracellular matrix (15). The mdx mouse contains a nonsense mutation in the dystrophin gene that leads to a complete absence of dystrophin in muscle, which ...
Phylogenetic Classification of Protozoa Based on the
... the linker in P. falciparum is 89 amino acids. The linker in ChDHFR-TS plays an important role in the structure of the enzyme. Compared with the structure of DHFR-TS from PfDHFR-TS (8) in which major portions of the linker domain are not built into the model, the entire linker domain of ChDHFR-TS is ...
... the linker in P. falciparum is 89 amino acids. The linker in ChDHFR-TS plays an important role in the structure of the enzyme. Compared with the structure of DHFR-TS from PfDHFR-TS (8) in which major portions of the linker domain are not built into the model, the entire linker domain of ChDHFR-TS is ...
Phylogenetic Classification of Protozoa Based on the Structure of
... the linker in P. falciparum is 89 amino acids. The linker in ChDHFR-TS plays an important role in the structure of the enzyme. Compared with the structure of DHFR-TS from PfDHFR-TS (8) in which major portions of the linker domain are not built into the model, the entire linker domain of ChDHFR-TS is ...
... the linker in P. falciparum is 89 amino acids. The linker in ChDHFR-TS plays an important role in the structure of the enzyme. Compared with the structure of DHFR-TS from PfDHFR-TS (8) in which major portions of the linker domain are not built into the model, the entire linker domain of ChDHFR-TS is ...
Lipoprotein structure
... 1.1. Main lipoprotein classes Although the assembly, structure, metabolism, and receptor interactions of lipoproteins are determined by their apolipoprotein components, the most common classifications of lipoproteins are based on their hydrated density or mobility on agarose gel-electrophoresis. The ...
... 1.1. Main lipoprotein classes Although the assembly, structure, metabolism, and receptor interactions of lipoproteins are determined by their apolipoprotein components, the most common classifications of lipoproteins are based on their hydrated density or mobility on agarose gel-electrophoresis. The ...
Sequence and Structure Classification of Kinases
... in one family produces a significant hit to at least one sequence in the other family within three iterations of PSI-BLAST1 (E-value cutoff 0.001). In this family, several sequences in each of the Pfam/COGs give significant PSI-BLAST1 hits to multiple sequences in PF00069 (protein kinase domain), wh ...
... in one family produces a significant hit to at least one sequence in the other family within three iterations of PSI-BLAST1 (E-value cutoff 0.001). In this family, several sequences in each of the Pfam/COGs give significant PSI-BLAST1 hits to multiple sequences in PF00069 (protein kinase domain), wh ...
Protein Sequencing Problems
... sequence. Lys has an NH2 on its side chain. That is why FDNB attacked it. Chain = Gly ~ Carb A – Carb A attacks the AA on the other end of the protein (the carboxylic acid side). Since Ser was released, it must have been the last AA in the chain. Chain = Gly ~~~~~~~~~~~~~~~~~~~~~~~~~~Ser Cyanobromid ...
... sequence. Lys has an NH2 on its side chain. That is why FDNB attacked it. Chain = Gly ~ Carb A – Carb A attacks the AA on the other end of the protein (the carboxylic acid side). Since Ser was released, it must have been the last AA in the chain. Chain = Gly ~~~~~~~~~~~~~~~~~~~~~~~~~~Ser Cyanobromid ...
Analysis of the genetic potential of the spongederived fungus
... lab and for introducing me into the puzzling world of polyketides. I am grateful for all suggestions that I got from him during the practical work in the lab, as well as for the writing of my thesis. Moreover, I want to thank him for his trust and unique experience in building up a laboratory togeth ...
... lab and for introducing me into the puzzling world of polyketides. I am grateful for all suggestions that I got from him during the practical work in the lab, as well as for the writing of my thesis. Moreover, I want to thank him for his trust and unique experience in building up a laboratory togeth ...
The enzymes of biotin dependent CO2 metabolism: What structures
... /,W angles of -119 and 122 , and this helix-turn-helix motif is a hallmark of proteins belonging to the ATP grasp superfamily as discussed below. Shown in Figure 2(b) is a ribbon representation of the biotin carboxylase dimer. The B-domains for each subunit are located on opposite edges of the dim ...
... /,W angles of -119 and 122 , and this helix-turn-helix motif is a hallmark of proteins belonging to the ATP grasp superfamily as discussed below. Shown in Figure 2(b) is a ribbon representation of the biotin carboxylase dimer. The B-domains for each subunit are located on opposite edges of the dim ...
Bacterial Protein Synthesis Inhibitors (Antimicrobials)
... eukaryotic cells (Table 10.2). • This inhibition can take place at any stage in protein synthesis. • However, some inhibitors have a specific action in that they inhibit protein synthesis in prokaryotic cells but not in eukaryotic cells, or vice versa. prof. aza ...
... eukaryotic cells (Table 10.2). • This inhibition can take place at any stage in protein synthesis. • However, some inhibitors have a specific action in that they inhibit protein synthesis in prokaryotic cells but not in eukaryotic cells, or vice versa. prof. aza ...
Identification of the Factors Responsible for the Interaction of
... out all forms of docking such as rigid, flexible and semi flexible docking. It calculates the intermolecular “energies” by adding up all intermolecular interactions (e.g. Vander Waals, electrostatic) that occur between a ligand and protein targe. Hex Server has an easy-to-use form-based interface, t ...
... out all forms of docking such as rigid, flexible and semi flexible docking. It calculates the intermolecular “energies” by adding up all intermolecular interactions (e.g. Vander Waals, electrostatic) that occur between a ligand and protein targe. Hex Server has an easy-to-use form-based interface, t ...
Hydrolyzed Source Proteins as Used in Cosmetics
... exposure from food use would result in a much larger systemic dose than that resulting from use in cosmetic products. These ingredients would be safe if absorbed into the body. Consequently, single dose toxicity, repeated dose toxicity, or other systemic toxicity studies are not addressed in this re ...
... exposure from food use would result in a much larger systemic dose than that resulting from use in cosmetic products. These ingredients would be safe if absorbed into the body. Consequently, single dose toxicity, repeated dose toxicity, or other systemic toxicity studies are not addressed in this re ...
A motif and amino acid bias bioinformatics
... (reviewed in Piovesan et al., 2017), tools available to assess large-scale proteomics data for IDP ...
... (reviewed in Piovesan et al., 2017), tools available to assess large-scale proteomics data for IDP ...
and Rhizobiales-Like PPP-Family Protein Phosphatases from
... Rhizobiales-like (RLPH2) phosphatases, which were named after their relatedness to phosphatase orthologs from Shewanella and Rhizobiales bacteria. Heterologous protein phosphatase expression in, and purification from, Escherichia coli revealed unique biochemical characteristics including a complete ...
... Rhizobiales-like (RLPH2) phosphatases, which were named after their relatedness to phosphatase orthologs from Shewanella and Rhizobiales bacteria. Heterologous protein phosphatase expression in, and purification from, Escherichia coli revealed unique biochemical characteristics including a complete ...
Structural Analyses of Zinc Finger Domains for Specific Interactions
... they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two cysteine and two histidine residues (Cys2His2) coordinate to the zinc ion for the structural functions to generate a ββα fold, and this secondary structure supports specific interactions with their binding partn ...
... they provide critical roles in physiological systems from prokaryotes to eukaryotes. Two cysteine and two histidine residues (Cys2His2) coordinate to the zinc ion for the structural functions to generate a ββα fold, and this secondary structure supports specific interactions with their binding partn ...
The Major Component of the Paraflagellar Rod of Trypanosoma
... The antiserum was entirely specific as tested by immunoblotting of wholecell extracts and was used for immunoscreening without further purification. A monoclonal antibody against the PFR proteins was a gift from J.-M. Gallo (University of Poitiers, Poitiers, France) (Gallo and Schrevel, 1985). Perox ...
... The antiserum was entirely specific as tested by immunoblotting of wholecell extracts and was used for immunoscreening without further purification. A monoclonal antibody against the PFR proteins was a gift from J.-M. Gallo (University of Poitiers, Poitiers, France) (Gallo and Schrevel, 1985). Perox ...
Identification and Structural Characterization of the ATP/ADP
... Hsp70/DnaK. Although the apparent involvement of ATP in p23 binding remains unexplained, it has become widely accepted that unlike Hsp70/DnaK and Hsp60/ GroEL, Hsp90 does not bind ATP. Although the structure of the intact Hsp90 molecule has not yet been determined, crystal structures of an amino-ter ...
... Hsp70/DnaK. Although the apparent involvement of ATP in p23 binding remains unexplained, it has become widely accepted that unlike Hsp70/DnaK and Hsp60/ GroEL, Hsp90 does not bind ATP. Although the structure of the intact Hsp90 molecule has not yet been determined, crystal structures of an amino-ter ...
Attachment 1 - Food Standards Australia New Zealand
... epsps gene codes for an enzyme, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS), which confers tolerance to the herbicide glyphosate. The EPSPS enzyme is present in all plants, bacteria and fungi and is essential for aromatic amino acid biosynthesis. The normal mode of action of glyphosate is t ...
... epsps gene codes for an enzyme, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS), which confers tolerance to the herbicide glyphosate. The EPSPS enzyme is present in all plants, bacteria and fungi and is essential for aromatic amino acid biosynthesis. The normal mode of action of glyphosate is t ...
Candida rugosa - Universität Stuttgart
... Allen ehemaligen und jetzigen Mitgliedern der Bioinformatik-Gruppe und der Biokatalyse-Gruppe danke ich für das tolle und menschliche Klima, bei der Arbeit und nach Dienstschluß. Allen Mitarbeitern des ITB gilt mein Dank für die schöne und produktive Zeit der ...
... Allen ehemaligen und jetzigen Mitgliedern der Bioinformatik-Gruppe und der Biokatalyse-Gruppe danke ich für das tolle und menschliche Klima, bei der Arbeit und nach Dienstschluß. Allen Mitarbeitern des ITB gilt mein Dank für die schöne und produktive Zeit der ...
Purification of Arrestin from Bovine Retinas
... freshly bleached phosphorylated rhodopsin occurs rapidly (<200 msec) and quenches the activation of G protein (transducin) (1-4). We have shown that arrestin also acts in the phototransduction process by blocking rapid dephosphorylation of phosphorylated and photolyzed rhodopsin until activated rhod ...
... freshly bleached phosphorylated rhodopsin occurs rapidly (<200 msec) and quenches the activation of G protein (transducin) (1-4). We have shown that arrestin also acts in the phototransduction process by blocking rapid dephosphorylation of phosphorylated and photolyzed rhodopsin until activated rhod ...
The DELLA protein family and gibberellin signal transduction
... stability and phosphate groups to mark them for F-box recognition. However, the precise nature, and role of these modifications is yet to be shown. DELLA-repressive action is mediated by interaction with other proteins and not through direct DNA binding. Few DELLA-interacting proteins are known. ...
... stability and phosphate groups to mark them for F-box recognition. However, the precise nature, and role of these modifications is yet to be shown. DELLA-repressive action is mediated by interaction with other proteins and not through direct DNA binding. Few DELLA-interacting proteins are known. ...
Homology modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the ""target"" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the ""template""). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been shown that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure.It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone.The sequence alignment and template structure are then used to produce a structural model of the target. Because protein structures are more conserved than DNA sequences, detectable levels of sequence similarity usually imply significant structural similarity.The quality of the homology model is dependent on the quality of the sequence alignment and template structure. The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. Model quality declines with decreasing sequence identity; a typical model has ~1–2 Å root mean square deviation between the matched Cα atoms at 70% sequence identity but only 2–4 Å agreement at 25% sequence identity. However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different.Regions of the model that were constructed without a template, usually by loop modeling, are generally much less accurate than the rest of the model. Errors in side chain packing and position also increase with decreasing identity, and variations in these packing configurations have been suggested as a major reason for poor model quality at low identity. Taken together, these various atomic-position errors are significant and impede the use of homology models for purposes that require atomic-resolution data, such as drug design and protein–protein interaction predictions; even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP.