DLocalMotif: a discriminative approach for discovering local motifs in
... between two extremes: On the one extreme, sequences are highly enriched with a particular motif, but motifs are not spatially confined. Such problems can be addressed by available motif discovery methods. The other extreme has sequences with only weakly enriched motifs, but when they occur, they are ...
... between two extremes: On the one extreme, sequences are highly enriched with a particular motif, but motifs are not spatially confined. Such problems can be addressed by available motif discovery methods. The other extreme has sequences with only weakly enriched motifs, but when they occur, they are ...
2006 Program
... “Gelatinase contributes to the release of extracellular DNA in the development of Enterococcus faecalis biofilms” Lance R. Thurlow and Lynn E. Hancock “The genetic basis for capsular polysaccharide production in Enterococcus faecalis serogroups C and D” ...
... “Gelatinase contributes to the release of extracellular DNA in the development of Enterococcus faecalis biofilms” Lance R. Thurlow and Lynn E. Hancock “The genetic basis for capsular polysaccharide production in Enterococcus faecalis serogroups C and D” ...
Chemistry 1010
... Catalysis - biological catalysts are enzymes Movement - muscle: actin and myosin Transport - hemoglobin, transport thru membranes Hormones - insulin, oxytocin, HGH, etc. Protection - antigen-antibody reactions, fibrinogen in clotting Storage - casein in milk, ovalbumin in eggs, ferritin in liver-sto ...
... Catalysis - biological catalysts are enzymes Movement - muscle: actin and myosin Transport - hemoglobin, transport thru membranes Hormones - insulin, oxytocin, HGH, etc. Protection - antigen-antibody reactions, fibrinogen in clotting Storage - casein in milk, ovalbumin in eggs, ferritin in liver-sto ...
Engineering carbonic anhydrase for highly selective ester hydrolysis Gunnar Höst
... substrates with long acyl chains. The mutant V121A/V143A hydrolyzes pNPV, which has four carbon atoms in the acyl chain, with an efficiency that is increased by a factor of 3000 compared to HCAII. Further, transition state analogues (TSAs) were docked to HCAII and mutant variants, and the results we ...
... substrates with long acyl chains. The mutant V121A/V143A hydrolyzes pNPV, which has four carbon atoms in the acyl chain, with an efficiency that is increased by a factor of 3000 compared to HCAII. Further, transition state analogues (TSAs) were docked to HCAII and mutant variants, and the results we ...
What is similarity and homology? What is a good match? How does
... homologous • If two sequence are not similar, we don’t know if they are homologous • If two sequences are not homologous, their sequences are usually not similar (but may be by chance) • If two sequences are homologous, their sequences may or may not be ...
... homologous • If two sequence are not similar, we don’t know if they are homologous • If two sequences are not homologous, their sequences are usually not similar (but may be by chance) • If two sequences are homologous, their sequences may or may not be ...
A tribute to sulfur - Wiley Online Library
... was found that the active site Cys residue is located in the middle of a highly flexible loop of 12 amino acids, which may be able to adapt to varied geometries in acceptor proteins. The 3D structure of C-DES from Synechocystis has now also become available [52]. Contrary to the NifS type Cys desulf ...
... was found that the active site Cys residue is located in the middle of a highly flexible loop of 12 amino acids, which may be able to adapt to varied geometries in acceptor proteins. The 3D structure of C-DES from Synechocystis has now also become available [52]. Contrary to the NifS type Cys desulf ...
2. Yi-Kuo Yu, John C. Wootton, and Stephen F. Altschul The compositional adjustment of amino acid substitution matrices PNAS 2003 100: 15688-15693.
... increases in bit score and statistical significance (Table 1) and as improved alignment length and quality (Fig. 1 and Table 5). Adjusting background frequencies for organism proteome frequencies (the rows denoted ‘‘Organism’’ in Table 1, column 5) yielded improvements in most cases, and adjusting t ...
... increases in bit score and statistical significance (Table 1) and as improved alignment length and quality (Fig. 1 and Table 5). Adjusting background frequencies for organism proteome frequencies (the rows denoted ‘‘Organism’’ in Table 1, column 5) yielded improvements in most cases, and adjusting t ...
Chapter 22
... ingredients, usually served cold with a dressing • Veggies, Fruits and Protein foods in salads contribute important nutrients to your diet • Salads can be served as any part of a meal ...
... ingredients, usually served cold with a dressing • Veggies, Fruits and Protein foods in salads contribute important nutrients to your diet • Salads can be served as any part of a meal ...
The Organellar Genome and Metabolic Potential
... mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron ...
... mitochondrion, in combination with that of more than 9,000 genomic DNA and cDNA sequences, allows a preliminary reconstruction of the organellar metabolism. The sequence data indicate that N. ovalis possesses hydrogen-producing mitochondria that have a truncated, two step (Complex I and II) electron ...
pH-induced conformational changes in human ABO(H) blood group
... H-antigen acceptor (Alfaro et al. 2008). Accordingly, with the exception of GTA, which has recently been shown to form the closed state most readily even in the absence of the acceptor fucose moiety (Johal et al. 2012; Alfaro et al. 2008), the C-terminal loop is not ordered in any of the structures ...
... H-antigen acceptor (Alfaro et al. 2008). Accordingly, with the exception of GTA, which has recently been shown to form the closed state most readily even in the absence of the acceptor fucose moiety (Johal et al. 2012; Alfaro et al. 2008), the C-terminal loop is not ordered in any of the structures ...
Lactococcus lactis as expression host for the biosynthetic
... strains to stimulate the incorporation of Trp analogues [18]. This approach was explored for L. lactis PA1001 in CDM. A concentration of 0.2 mg/ml of IAA completely inhibited the growth of L. lactis PA1001 (Figure 3A). However, addition of Trp did not elevate the IAA-inhibitory effect, suggesting th ...
... strains to stimulate the incorporation of Trp analogues [18]. This approach was explored for L. lactis PA1001 in CDM. A concentration of 0.2 mg/ml of IAA completely inhibited the growth of L. lactis PA1001 (Figure 3A). However, addition of Trp did not elevate the IAA-inhibitory effect, suggesting th ...
Energy Calculations for 4-Hydroxy-3
... Diphosphate, changed when a MM2 energy minimization was performed on the hetero compound. Not only do the values in Table 1 reflect the differences in energy of the two structures of the hetero compound but also it is evident in Figure 3 that 4-Hydroxy-3-MethylButyl Diphosphate was rotated, bent, an ...
... Diphosphate, changed when a MM2 energy minimization was performed on the hetero compound. Not only do the values in Table 1 reflect the differences in energy of the two structures of the hetero compound but also it is evident in Figure 3 that 4-Hydroxy-3-MethylButyl Diphosphate was rotated, bent, an ...
Gregory Moy - University of Pennsylvania
... because it was already known that only 0.0425 g/mL would be soluble. The next step was the preparation of the titrants. The titrants used in this experiment were 1M NaOH and 1M HCl. The molarity of NaOH and HCl that was initially used was 5X10-4 M to compensate for the small amount of ovalbumin, 5g, ...
... because it was already known that only 0.0425 g/mL would be soluble. The next step was the preparation of the titrants. The titrants used in this experiment were 1M NaOH and 1M HCl. The molarity of NaOH and HCl that was initially used was 5X10-4 M to compensate for the small amount of ovalbumin, 5g, ...
Regulators of Ubiquitin Dependent Protein Degradation in the
... split into two independent open reading frames encoding the N- and C-terminal part (candA-N, candA-C) of the mammalian homolog. Deletion of the single or both candA genes leads to mutants with identical phenotypes. They produce only few asexual spores, are blocked in early sexual development and app ...
... split into two independent open reading frames encoding the N- and C-terminal part (candA-N, candA-C) of the mammalian homolog. Deletion of the single or both candA genes leads to mutants with identical phenotypes. They produce only few asexual spores, are blocked in early sexual development and app ...
Free Full Text ( Final Version , 5mb ) - EUR RePub
... Intracellular catabolism of macromolecules ensures a counterbalance to the pro· cesses of biosynthesis and endocytosis and prevents the improper accumulation of products that would in turn impair the normal physiology of the cell. By means of degradation a cell can remove toxic or damaged components ...
... Intracellular catabolism of macromolecules ensures a counterbalance to the pro· cesses of biosynthesis and endocytosis and prevents the improper accumulation of products that would in turn impair the normal physiology of the cell. By means of degradation a cell can remove toxic or damaged components ...
Protein targeting, translocation and Escherichia coli Proteomic analysis of substrate-pathway relationships
... So far, β-barrel membrane proteins have only been found in the outer membrane of Gram-negative bacteria and mitochondria, and in the outer envelope of chloroplasts. β-barrel membrane proteins are composed of an even number of anti-parallel β-strands arranged in a barrel like structure. The amide and ...
... So far, β-barrel membrane proteins have only been found in the outer membrane of Gram-negative bacteria and mitochondria, and in the outer envelope of chloroplasts. β-barrel membrane proteins are composed of an even number of anti-parallel β-strands arranged in a barrel like structure. The amide and ...
Nitrate reductase activity in chicory roots
... is controlled by the nitrate flux and is tightly linked to modifications between sink and source strength during the developmental cycle. In roots, NRA is controlled by NR synthesis in response to nitrate (Oaks, 1985), cytokinins (Hanisch Ten Cate and Breteler, 1982), or by NR proteolysis (Poulle et ...
... is controlled by the nitrate flux and is tightly linked to modifications between sink and source strength during the developmental cycle. In roots, NRA is controlled by NR synthesis in response to nitrate (Oaks, 1985), cytokinins (Hanisch Ten Cate and Breteler, 1982), or by NR proteolysis (Poulle et ...
Assessment of the mathematical issues involved
... acid on protein synthesis is a difficult task. There is a large body of literature, which has recently been reviewed in [4], indicating that leucine flooding doses promote protein synthesis in vitro when other amino acids are plentiful. One should be cautious, however, when extrapolating from these ...
... acid on protein synthesis is a difficult task. There is a large body of literature, which has recently been reviewed in [4], indicating that leucine flooding doses promote protein synthesis in vitro when other amino acids are plentiful. One should be cautious, however, when extrapolating from these ...
Nucleus-Encoded Genes for Plastid
... cDNA sequences produced from an ongoing Helicosporidium sp. (strain AT2000, originally isolated from the black fly, Simulium jonesii) EST project. Genes were identified for further characterization based on the following three criteria: (i) their association with pathways known to occur in the plast ...
... cDNA sequences produced from an ongoing Helicosporidium sp. (strain AT2000, originally isolated from the black fly, Simulium jonesii) EST project. Genes were identified for further characterization based on the following three criteria: (i) their association with pathways known to occur in the plast ...
Comparison of the activities of protein disulphide
... surface proteins. The cellular and subcellular distribution of the its developmental properties and its catalytic activities in vitro are all consistent with this role (reviewed in Freedman, 1984; Freedman et al., 1989). The activity of PDI as a catalyst of protein folding in vitro is remarkable for ...
... surface proteins. The cellular and subcellular distribution of the its developmental properties and its catalytic activities in vitro are all consistent with this role (reviewed in Freedman, 1984; Freedman et al., 1989). The activity of PDI as a catalyst of protein folding in vitro is remarkable for ...
Dairy and Milk Allergies
... extensively hydrolyzed protein (such as Nutramigen, Alimentum, and Pregestimil), and free amino acid-based formulas (such as Neocate, EleCare, and Nutramigen AA). Soy based formula does have a risk of allergic sensitivity, as some infants who are allergic to milk may also be allergic to soy. Hydroly ...
... extensively hydrolyzed protein (such as Nutramigen, Alimentum, and Pregestimil), and free amino acid-based formulas (such as Neocate, EleCare, and Nutramigen AA). Soy based formula does have a risk of allergic sensitivity, as some infants who are allergic to milk may also be allergic to soy. Hydroly ...
Src protein–tyrosine kinase structure and regulation
... The human Src gene encodes a protein of 536 amino acids, and the chicken Src gene encodes a 533-residue protein. The three additional amino acids in humans are inserted near the amino terminus. For historical reasons, the chicken numbering system is used in most of the literature, even when studies ...
... The human Src gene encodes a protein of 536 amino acids, and the chicken Src gene encodes a 533-residue protein. The three additional amino acids in humans are inserted near the amino terminus. For historical reasons, the chicken numbering system is used in most of the literature, even when studies ...
Spectroscopic Techniques: I Spectrophotometric Techniques
... where h is the Planck constant (h = 6.63 1034 Js) and is the frequency of the radiation as introduced above. When considering a diatomic molecule (see Fig. 12.3), rotational and vibrational levels possess discrete energies that only merge into a continuum at very high energy. Each electronic st ...
... where h is the Planck constant (h = 6.63 1034 Js) and is the frequency of the radiation as introduced above. When considering a diatomic molecule (see Fig. 12.3), rotational and vibrational levels possess discrete energies that only merge into a continuum at very high energy. Each electronic st ...
Raw Glycerol as Substrate for the Production of Yeast Biomass
... as a raw material for the food, pharmaceutical and cosmetic industries, in addition to being an excellent source of nutrients, mainly proteins, vitamins of the B complex and essential minerals [12]. An important aspect in the production of yeast biomass is the development of a culture medium based o ...
... as a raw material for the food, pharmaceutical and cosmetic industries, in addition to being an excellent source of nutrients, mainly proteins, vitamins of the B complex and essential minerals [12]. An important aspect in the production of yeast biomass is the development of a culture medium based o ...
FASTA is a program for database searching by homology. FASTA
... This program uses the BLASTP or BLASTN algorithms for aligning two sequences. In terms of Statistics: BLAST calculates probabilities and this can fail if some assumptions are invalid for that search. There are versions of BLAST for searching nucleic acid and protein databases, which can be used to t ...
... This program uses the BLASTP or BLASTN algorithms for aligning two sequences. In terms of Statistics: BLAST calculates probabilities and this can fail if some assumptions are invalid for that search. There are versions of BLAST for searching nucleic acid and protein databases, which can be used to t ...
Protein–protein interaction
Protein–protein interactions (PPIs) refer to physical contacts established between two or more proteins as a result of biochemical events and/or electrostatic forces.In fact, proteins are vital macromolecules, at both cellular and systemic levels, but they rarely act alone. Diverse essential molecular processes within a cell are carried out by molecular machines that are built from a large number of protein components organized by their PPIs. Indeed, these interactions are at the core of the entire interactomics system of any living cell and so, unsurprisingly, aberrant PPIs are on the basis of multiple diseases, such as Creutzfeld-Jacob, Alzheimer's disease, and cancer.PPIs have been studied from different perspectives: biochemistry, quantum chemistry, molecular dynamics, signal transduction, among others. All this information enables the creation of large protein interaction networks – similar to metabolic or genetic/epigenetic networks – that empower the current knowledge on biochemical cascades and disease pathogenesis, as well as provide putative new therapeutic targets.