Topology Prediction of Membrane Proteins
... internally within the helix. This lowers the cost of transferring polar entities into the hydrocarbon interior and makes the conformation energetically stable. Another stabilizing factor is the enrichment of aromatic residues (Tyr and Trp) near the ends of the transmembrane segments (Killian and von ...
... internally within the helix. This lowers the cost of transferring polar entities into the hydrocarbon interior and makes the conformation energetically stable. Another stabilizing factor is the enrichment of aromatic residues (Tyr and Trp) near the ends of the transmembrane segments (Killian and von ...
NAD - SBI
... • The fingerprint region (βαβ) is conserved in all proteins and have several conserved residues important for its function. • These residues are involved in NAD interactions with protein through VDW and HB (direct or through water). There is also a structurally water molecule conserved. • Interactio ...
... • The fingerprint region (βαβ) is conserved in all proteins and have several conserved residues important for its function. • These residues are involved in NAD interactions with protein through VDW and HB (direct or through water). There is also a structurally water molecule conserved. • Interactio ...
E. coli
... The property that distinguishes these two groups is the presence of the EPEC adherence factor plasmid (pEAF), which is only found in tEPEC aEPEC strains are emerging enteropathogens that have been detected worldwide The large variety of serotypes and genetic virulence properties of aEPEC strai ...
... The property that distinguishes these two groups is the presence of the EPEC adherence factor plasmid (pEAF), which is only found in tEPEC aEPEC strains are emerging enteropathogens that have been detected worldwide The large variety of serotypes and genetic virulence properties of aEPEC strai ...
Sculpting the b-peptide foldamer H12 helix via a designed side
... of aggregation origin would not be so specific. Although a sufficient number of characteristic NOEs were observed in CD3OH, some of the long-range ROESY cross-peaks could not be resolved because of the poorer resonance dispersion for the CbH2–4 protons. The CbH1–NH3 interaction could not be observed, b ...
... of aggregation origin would not be so specific. Although a sufficient number of characteristic NOEs were observed in CD3OH, some of the long-range ROESY cross-peaks could not be resolved because of the poorer resonance dispersion for the CbH2–4 protons. The CbH1–NH3 interaction could not be observed, b ...
A chitin-binding domain in a marine bacterial
... To examine the ecology and evolution of microbial chitinases, especially the chitin-binding domain, one of the chitinase genes (&A) from the marine bacterium Vibrio harveyi was analysed. The deduced amino acid sequence of ChiA is not very similar overall to other proteins, except for two regions, th ...
... To examine the ecology and evolution of microbial chitinases, especially the chitin-binding domain, one of the chitinase genes (&A) from the marine bacterium Vibrio harveyi was analysed. The deduced amino acid sequence of ChiA is not very similar overall to other proteins, except for two regions, th ...
Carbamoyl phosphate synthetase - Department of Biochemistry
... homology between the amino-terminal domain of the CPS small subunit and other proteins of known structure; however, it is absolutely clear that the carboxy-terminal domain of the small subunit is highly homologous to the amino-terminal domain of guanosine monophosphate synthetase and to other member ...
... homology between the amino-terminal domain of the CPS small subunit and other proteins of known structure; however, it is absolutely clear that the carboxy-terminal domain of the small subunit is highly homologous to the amino-terminal domain of guanosine monophosphate synthetase and to other member ...
pH-induced conformational changes in human ABO(H) blood group
... substrates at pH 10.0) were crystallized in the presence of galactose as an H-antigen acceptor analog. The formation of the closed state in which the C-terminal loop is ordered is strongly affected by contact from the C-terminal loop to the L-fucose residue of the H-antigen acceptor (Alfaro et al. 2 ...
... substrates at pH 10.0) were crystallized in the presence of galactose as an H-antigen acceptor analog. The formation of the closed state in which the C-terminal loop is ordered is strongly affected by contact from the C-terminal loop to the L-fucose residue of the H-antigen acceptor (Alfaro et al. 2 ...
Gastric lavage
... 4. The patient has underlying medical problems that could further complicate the situation ...
... 4. The patient has underlying medical problems that could further complicate the situation ...
Conformational Changes in HIV-1 Reverse Transcriptase Induced
... new contacts with residues in the drug binding pocket or make contacts with main-chain residues that are unlikely to be disrupted by single side chain mutations [11]. To illustrate these differences, the binding interactions between the HIV-1 NNRTI-BP and either HBY-097 [27] or capravirine (S1153 [5 ...
... new contacts with residues in the drug binding pocket or make contacts with main-chain residues that are unlikely to be disrupted by single side chain mutations [11]. To illustrate these differences, the binding interactions between the HIV-1 NNRTI-BP and either HBY-097 [27] or capravirine (S1153 [5 ...
Disallowed Ramachandran Conformations of Amino Acid Residues
... As a further check, for all the 66 cases an ‘‘Ala-dipeptide’’ model was constructed using the ideal bond angle and bond length and the observed disallowed f, c values in protein structure. Stereochemical non-hydrogen contacts were evaluated for all the ideal models and for the disallowed residues in ...
... As a further check, for all the 66 cases an ‘‘Ala-dipeptide’’ model was constructed using the ideal bond angle and bond length and the observed disallowed f, c values in protein structure. Stereochemical non-hydrogen contacts were evaluated for all the ideal models and for the disallowed residues in ...
Novel Riboswitch Ligand Analogs as Selective Inhibitors of Guanine
... Guanine riboswitches are involved in the regulation of transport and biosynthesis of purine metabolites, which are critical for the nucleotides cellular pool. Upon guanine binding, these riboswitches stabilize a 59-untranslated mRNA structure that causes transcription attenuation of the downstream o ...
... Guanine riboswitches are involved in the regulation of transport and biosynthesis of purine metabolites, which are critical for the nucleotides cellular pool. Upon guanine binding, these riboswitches stabilize a 59-untranslated mRNA structure that causes transcription attenuation of the downstream o ...
Regulation of Galactoside Transport by the PTS
... Among four proteins (LacY, MelB, MalK, and GlpK) that interact with IIAGlc, MelB is considered to be a little different one, since some of the conserved residues in REGION II are absent. In fact, our recent experiments demonstrated that deletion of Arg-215 to Leu-220, which corresponds to the latter ...
... Among four proteins (LacY, MelB, MalK, and GlpK) that interact with IIAGlc, MelB is considered to be a little different one, since some of the conserved residues in REGION II are absent. In fact, our recent experiments demonstrated that deletion of Arg-215 to Leu-220, which corresponds to the latter ...
Functional implications of the modeled structure of maspin
... of a genetically engineered inhibitory a|-antichymotrypsin has shown that the RSL in this molecule is not inserted, demonstrating that it is not an absolute prerequisite for inhibitory function in native serpins. Rather, the ability to insert is likely required for the formation of the serpin-protea ...
... of a genetically engineered inhibitory a|-antichymotrypsin has shown that the RSL in this molecule is not inserted, demonstrating that it is not an absolute prerequisite for inhibitory function in native serpins. Rather, the ability to insert is likely required for the formation of the serpin-protea ...
Biological significance of structural differences between two highly
... alignment, the residues important for binding Ub (Mms2-Ser32 and -Ile62) [18] and Ubc13 (Mms2-Phe13) [7] are identical between Uev1D30 and Mms2 (Fig. 1A). Interestingly, the 14 aminoacid stretch that contains 7 out of 12 total variable residues between Uev1D30 and Mms2 clusters on a surface of each ...
... alignment, the residues important for binding Ub (Mms2-Ser32 and -Ile62) [18] and Ubc13 (Mms2-Phe13) [7] are identical between Uev1D30 and Mms2 (Fig. 1A). Interestingly, the 14 aminoacid stretch that contains 7 out of 12 total variable residues between Uev1D30 and Mms2 clusters on a surface of each ...
Peroxisomes: family of versatile organelles
... Structural biology of the import pathways of peroxisomal matrix proteins The first minutes in the life of a peroxisomal matrix protein Peroxisomal protein import pores Role of AAA+-proteins in peroxisome biogenesis and function Regulation of peroxisomal matrix protein import by ubiquitination Peroxi ...
... Structural biology of the import pathways of peroxisomal matrix proteins The first minutes in the life of a peroxisomal matrix protein Peroxisomal protein import pores Role of AAA+-proteins in peroxisome biogenesis and function Regulation of peroxisomal matrix protein import by ubiquitination Peroxi ...
Anchoring of Surface Proteins to the Cell Wall of Staphylococcus
... in vivo and in vitro reactions of sortase can be inhibited with the thiolate reagent methylmethane thiosulfonate (for example MTSET)2 or parahydroxy-mercurybenzoic acid (12), but not with sulfhydryl reagents such as iodoacetate or iodoacetamide (7, 9). Surface proteins bearing LPXTG motifs as well a ...
... in vivo and in vitro reactions of sortase can be inhibited with the thiolate reagent methylmethane thiosulfonate (for example MTSET)2 or parahydroxy-mercurybenzoic acid (12), but not with sulfhydryl reagents such as iodoacetate or iodoacetamide (7, 9). Surface proteins bearing LPXTG motifs as well a ...
Figure 7. N-terminus sequence of the predicted
... N-terminal segment creates a constriction in the central region of the pore. The results of solid-state NMR study confirms this orientation of the helix [38] and the propensity of the N-terminus to adopt an helical fold was shown by experimental and computational approaches [39,40]. It should be wor ...
... N-terminal segment creates a constriction in the central region of the pore. The results of solid-state NMR study confirms this orientation of the helix [38] and the propensity of the N-terminus to adopt an helical fold was shown by experimental and computational approaches [39,40]. It should be wor ...
A first attempt to elucidate the amino acid sequence of some lichen
... Lichens are symbiotic associations between a fungus and a cyanobacterium (cyano-lichens) or a green alga (chlorolichens), joined to form a new biological entity different from its individual components. Recognition mechanisms used by lichens are based on the production and secretion of fungal lectin ...
... Lichens are symbiotic associations between a fungus and a cyanobacterium (cyano-lichens) or a green alga (chlorolichens), joined to form a new biological entity different from its individual components. Recognition mechanisms used by lichens are based on the production and secretion of fungal lectin ...
Substrate recognition by nonribosomal peptide
... L-Phe-, L-Glu- and L-Asp-activating domains have been mutated, using this method, to domains activating preferentially L-Leu, L-Gln and L-Asn, respectively, as evaluated by the ATP-pyrophosphate exchange assay. Because no kinetic parameters could be determined for the activation of the noncognate am ...
... L-Phe-, L-Glu- and L-Asp-activating domains have been mutated, using this method, to domains activating preferentially L-Leu, L-Gln and L-Asn, respectively, as evaluated by the ATP-pyrophosphate exchange assay. Because no kinetic parameters could be determined for the activation of the noncognate am ...
Protein Sorting and Transport - The Endoplasmic Reticulum, Golgi
... sequences are short stretches of hydrophobic amino acids that are cleaved from the polypeptide chain during its transfer into the ER lumen. The general role of signal sequences in targeting proteins to their appropriate locations within the cell was first elucidated by studies of the import of secre ...
... sequences are short stretches of hydrophobic amino acids that are cleaved from the polypeptide chain during its transfer into the ER lumen. The general role of signal sequences in targeting proteins to their appropriate locations within the cell was first elucidated by studies of the import of secre ...
The maize ID1 flowering time regulator is a zinc finger protein with
... Full-length cDNA clones for VEG7 or VEG9, cloned into the pBSK± vector, were used as templates for ampli®cation of VEG7 and VEG9 fragments. The VEG7 fragment was ampli®ed using forward primer VEG7KKKRBF (5¢GCGGATCCAAGAAGAAGAGGAACCAG-3¢) and reverse primer VEG7SAQT7 (5¢-GCCTCGAGTCAACCCATTTGCTGTCCACCA ...
... Full-length cDNA clones for VEG7 or VEG9, cloned into the pBSK± vector, were used as templates for ampli®cation of VEG7 and VEG9 fragments. The VEG7 fragment was ampli®ed using forward primer VEG7KKKRBF (5¢GCGGATCCAAGAAGAAGAGGAACCAG-3¢) and reverse primer VEG7SAQT7 (5¢-GCCTCGAGTCAACCCATTTGCTGTCCACCA ...
Inherited metabolic disorders Factfile
... is taken between 72 and 120 hours following birth. HPA is inherited as an autosomal recessive disorder, ie. both parents are carriers. With each pregnancy there is a 25% chance of the child inheriting the condition. There are now over 400 mutations described at the phenylalanine hydroxylase gene. Th ...
... is taken between 72 and 120 hours following birth. HPA is inherited as an autosomal recessive disorder, ie. both parents are carriers. With each pregnancy there is a 25% chance of the child inheriting the condition. There are now over 400 mutations described at the phenylalanine hydroxylase gene. Th ...
Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae
... (residues 394±511) with ®ve twisted parallel b-strands (S16±S20), but with a 2-3-1-4-5 topology. This structural classi®cation reveals its close relationship to the superfamily of P-loop-containing nucleotide triphosphate hydrolases and the family of nucleotide kinases, indicating a common evolution ...
... (residues 394±511) with ®ve twisted parallel b-strands (S16±S20), but with a 2-3-1-4-5 topology. This structural classi®cation reveals its close relationship to the superfamily of P-loop-containing nucleotide triphosphate hydrolases and the family of nucleotide kinases, indicating a common evolution ...
Passenger Protein Determines Translocation Versus Retention in
... lumen, integral membrane proteins embed in the ER membrane through one or more of their transmembrane segments. Furthermore, N-glycosylation and signal peptide cleavage are cotranslational modifications of proteins in the ER, performed by oligosaccharyltransferase (OST) and signal peptidase complex, ...
... lumen, integral membrane proteins embed in the ER membrane through one or more of their transmembrane segments. Furthermore, N-glycosylation and signal peptide cleavage are cotranslational modifications of proteins in the ER, performed by oligosaccharyltransferase (OST) and signal peptidase complex, ...
Cellular responses of Prochilodus lineatus hepatocytes after
... Cylindrospermopsin is a potent toxicant for eukaryotic cells produced by several cyanobacteria. Recently, primary hepatocyte cultures of Neotropical fish have been established, demonstrating to be a quite efficient in vitro model for cellular toxicology studies. In the current study, a protocol for cu ...
... Cylindrospermopsin is a potent toxicant for eukaryotic cells produced by several cyanobacteria. Recently, primary hepatocyte cultures of Neotropical fish have been established, demonstrating to be a quite efficient in vitro model for cellular toxicology studies. In the current study, a protocol for cu ...
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.