Deciphering the molecular basis of the specificity of protein
... determine their amino acid preferences. Two datasets have been examined. Firstly, one composed of non-covalently bound carbohydrates ligands. The results of this analysis is compared to the second dataset, obtained from the study of the spatial vicinity of the monosaccharides that form the common st ...
... determine their amino acid preferences. Two datasets have been examined. Firstly, one composed of non-covalently bound carbohydrates ligands. The results of this analysis is compared to the second dataset, obtained from the study of the spatial vicinity of the monosaccharides that form the common st ...
Metabolism of BCAAs
... equilibrium, with both substrate and product concentrations being at or below their Km values. This allows BCAT isozymes to quickly respond to changes in tissue concentrations of substrate or product, which allows BCAAs to be an ideal reserve for both carbon skeletons and nitrogen for glutamate synt ...
... equilibrium, with both substrate and product concentrations being at or below their Km values. This allows BCAT isozymes to quickly respond to changes in tissue concentrations of substrate or product, which allows BCAAs to be an ideal reserve for both carbon skeletons and nitrogen for glutamate synt ...
Strain in Protein Structures as Viewed Through Nonrotameric Side
... 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 rotameric side chains can deviate in each of the 1 and 2 angles by no more than 20° from the closest associated ro ...
... 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 rotameric side chains can deviate in each of the 1 and 2 angles by no more than 20° from the closest associated ro ...
Classification of pseudo pairs between nucleotide bases and amino
... extracted from the PDB (1 March 2011 release). Since the PDB contains many identical protein structures obtained in different crystallization conditions or those with amino acid mutations, proteins with >30% sequence identity were removed from our data set to minimize redundancy. In this study, a to ...
... extracted from the PDB (1 March 2011 release). Since the PDB contains many identical protein structures obtained in different crystallization conditions or those with amino acid mutations, proteins with >30% sequence identity were removed from our data set to minimize redundancy. In this study, a to ...
Structure of L‑Serine Dehydratase from Legionella
... by the Midwest Center for Structural Genomics, revealed that its fold had a molecular architecture similar to that of the “allosteric substrate binding” or “ASB” domain observed in some D-3-phosphoglycerate dehydrogenases.14 The D-3-phosphoglycerate dehydrogenases function in metabolism by catalyzin ...
... by the Midwest Center for Structural Genomics, revealed that its fold had a molecular architecture similar to that of the “allosteric substrate binding” or “ASB” domain observed in some D-3-phosphoglycerate dehydrogenases.14 The D-3-phosphoglycerate dehydrogenases function in metabolism by catalyzin ...
Biochemical and physiological bases for utilization
... be synthesized in the body are termed nutritionally dispensable or nonessential, including alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine. NEAA and their metabolites have many physiological functions (Table 2). Cysteine, glutamate, glutamine, g ...
... be synthesized in the body are termed nutritionally dispensable or nonessential, including alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, and tyrosine. NEAA and their metabolites have many physiological functions (Table 2). Cysteine, glutamate, glutamine, g ...
Regulation of transcript encoding the 43K
... Materials and methods). The sequence of the cDNA was determined and both the nucleic acid and deduced amino acid sequences were compared to that for the Torpedo 43K protein (Figs 1 and 2). Xen 43.1 cDNA is 1403 bp long, contains 205 bp of the 5' untranslated region and 1198 bp of protein-coding regi ...
... Materials and methods). The sequence of the cDNA was determined and both the nucleic acid and deduced amino acid sequences were compared to that for the Torpedo 43K protein (Figs 1 and 2). Xen 43.1 cDNA is 1403 bp long, contains 205 bp of the 5' untranslated region and 1198 bp of protein-coding regi ...
Representations of 3D Structures
... A b-strand is distinguished by strong CaHi-NHi+1contacts and long range nOes connecting the strands. A long range nOe connects residues more than 5 residues apart in the chain. ...
... A b-strand is distinguished by strong CaHi-NHi+1contacts and long range nOes connecting the strands. A long range nOe connects residues more than 5 residues apart in the chain. ...
Comparative Analysis of Prothrombin Activators
... possessing either group C or D prothrombin activators. The overall domain arrangement in these proteins was highly conserved between all elapids and with the corresponding mammalian clotting factors. The deduced protein sequence for the factor X–like protease precursor, identified in elapids contain ...
... possessing either group C or D prothrombin activators. The overall domain arrangement in these proteins was highly conserved between all elapids and with the corresponding mammalian clotting factors. The deduced protein sequence for the factor X–like protease precursor, identified in elapids contain ...
OptCDR: a general computational method for the design
... 2000) method and then expanded to include amino acids with similar chemical properties. When these sequence-based rules were not sufficient (25% of cases), the framework of the antibody variable region was aligned to a consensus framework and structural analysis was used to identify the CDRs. Throu ...
... 2000) method and then expanded to include amino acids with similar chemical properties. When these sequence-based rules were not sufficient (25% of cases), the framework of the antibody variable region was aligned to a consensus framework and structural analysis was used to identify the CDRs. Throu ...
Accurate Prediction of Contact Numbers for Multi
... Generation of Data Set. The data set of HMPs with known structures used in the current study was retrieved from the OPM (Orientation of Proteins in the Membrane) database.24 Peripheral HMPs and peptides were removed to obtain a set of “true” HMPs. Further refinement was carried out by removing thylak ...
... Generation of Data Set. The data set of HMPs with known structures used in the current study was retrieved from the OPM (Orientation of Proteins in the Membrane) database.24 Peripheral HMPs and peptides were removed to obtain a set of “true” HMPs. Further refinement was carried out by removing thylak ...
Translocation Arrest by Reversible Folding of a Precursor Protein
... these procedures render the mature protein part of the precursor incompetent for translocation by conferring a more stably folded structure. The topology of the intermediates formed was characterized, on one hand as accesgibile to the processing peptidase in the matrix, cleaving off the amino-termin ...
... these procedures render the mature protein part of the precursor incompetent for translocation by conferring a more stably folded structure. The topology of the intermediates formed was characterized, on one hand as accesgibile to the processing peptidase in the matrix, cleaving off the amino-termin ...
NIH Public Access
... elucidate the determinants of activation in SIRT1, we screened for SIRT1 mutant proteins lacking activation (Fig. 2C). The ability of SIRT1 to be activated by resveratrol was attenuated in one mutant that substituted a lysine for a glutamate at position 230 (E230K), whether an AMC-tagged substrate ( ...
... elucidate the determinants of activation in SIRT1, we screened for SIRT1 mutant proteins lacking activation (Fig. 2C). The ability of SIRT1 to be activated by resveratrol was attenuated in one mutant that substituted a lysine for a glutamate at position 230 (E230K), whether an AMC-tagged substrate ( ...
Interaction of Urea with Amino Acids: Implications for Urea
... Urea is a widely used protein denaturant. Despite its widespread use, however, the molecular mechanism underlying urea-induced denaturation is not well understood. Two classes of interaction models are distinguished in the literature. In the first, direct interactions between urea and the protein ar ...
... Urea is a widely used protein denaturant. Despite its widespread use, however, the molecular mechanism underlying urea-induced denaturation is not well understood. Two classes of interaction models are distinguished in the literature. In the first, direct interactions between urea and the protein ar ...
How flexible is α-actinin`s rod domain?
... Force required for stretching of Loops and Protein Unfolding : Another interesting observation of our simulation is the similarity in magnitude of force required to unfold the loops and the magnitude of the force required to unfold the protein. The percent extension of two sample loops and two sampl ...
... Force required for stretching of Loops and Protein Unfolding : Another interesting observation of our simulation is the similarity in magnitude of force required to unfold the loops and the magnitude of the force required to unfold the protein. The percent extension of two sample loops and two sampl ...
EF-Tu (elongation factor thermo unstable)
... The active site of the protein is the site of the hydrolysis of GTP to GDP, which occurs to release the aatRNA molecule. The protein and its interacting amino acids along with the Mg2+ metal stabilize this active site. Without stability in the active site the hydrolysis of GTP to GDP would not be ab ...
... The active site of the protein is the site of the hydrolysis of GTP to GDP, which occurs to release the aatRNA molecule. The protein and its interacting amino acids along with the Mg2+ metal stabilize this active site. Without stability in the active site the hydrolysis of GTP to GDP would not be ab ...
Nucleoside Phosphoramidate Monoesters: Potential
... charging of tRNAs with amino acids 1. tRNA synthetases must link tRNAs with their correct amino acids. 2. tRNA synthetases recognize correct amino acids by specific binding to the active site and proofreading. 3. tRNA synthetases recognize correct tRNAs via by interacting with specific regions of tR ...
... charging of tRNAs with amino acids 1. tRNA synthetases must link tRNAs with their correct amino acids. 2. tRNA synthetases recognize correct amino acids by specific binding to the active site and proofreading. 3. tRNA synthetases recognize correct tRNAs via by interacting with specific regions of tR ...
Johansson L, Gafvelin G, Arnér ES. Selenocysteine in proteins
... Selenocysteine (Sec), the 21st amino acid, exists naturally in all kingdoms of life as the defining entity of selenoproteins. Sec is a cysteine (Cys) residue analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group in Cys. The selenium atom gives Sec quite diff ...
... Selenocysteine (Sec), the 21st amino acid, exists naturally in all kingdoms of life as the defining entity of selenoproteins. Sec is a cysteine (Cys) residue analogue with a selenium-containing selenol group in place of the sulfur-containing thiol group in Cys. The selenium atom gives Sec quite diff ...
P6060Datasheet-Lot0151208
... Recognition Determinants: The minimal recognition motif for phosphorylation by CaMKII is RXXS/T. A more recent report suggests the presence of positive determinants at the -5, -2 and +1 positions in addition to the -3R. Thus, CaMKII preferentially phosphorylates substrates with motifs: HydXRXXS/T an ...
... Recognition Determinants: The minimal recognition motif for phosphorylation by CaMKII is RXXS/T. A more recent report suggests the presence of positive determinants at the -5, -2 and +1 positions in addition to the -3R. Thus, CaMKII preferentially phosphorylates substrates with motifs: HydXRXXS/T an ...
A Loop Unique to Ferredoxin-Dependent Glutamate Synthases is
... shown), in both the visible and near UV regions, of the loopless variant were very similar to those measured for the wild-type enzyme. Thus, although the presence of small conformational differences produced by deletion of the 27 amino acids of the loop cannot be ruled out, the CD data allow us to c ...
... shown), in both the visible and near UV regions, of the loopless variant were very similar to those measured for the wild-type enzyme. Thus, although the presence of small conformational differences produced by deletion of the 27 amino acids of the loop cannot be ruled out, the CD data allow us to c ...
Additional file 1
... Vacuolar sequestration of flavonoids, efflux of toxic compounds etc Transportation of amino acids during seed germination and grain filling ...
... Vacuolar sequestration of flavonoids, efflux of toxic compounds etc Transportation of amino acids during seed germination and grain filling ...