Carbamoyl phosphate synthetase: a tunnel runs through it Hazel M
... T h e one undeniable fact to emerge from the recent structural investigations of CPS is that the three active sites contained within the (x,~ heterodimer are separated by a linear distance of nearly 100 ~,. T h e carboxyphosphate, ammonia and carbamate intermediates are highly reactive, such that th ...
... T h e one undeniable fact to emerge from the recent structural investigations of CPS is that the three active sites contained within the (x,~ heterodimer are separated by a linear distance of nearly 100 ~,. T h e carboxyphosphate, ammonia and carbamate intermediates are highly reactive, such that th ...
Analytical Ultracentrifugation for Protein Analytical
... 1 Obtained from multi-laboratory, multi-product intermediate precision study (Gabrielson, J.P., et al., (2009). Analytical ...
... 1 Obtained from multi-laboratory, multi-product intermediate precision study (Gabrielson, J.P., et al., (2009). Analytical ...
Supplemental figure legends13092010HM
... Particles were initially centred against a rotationally average total sum and classified using multivariate statistical analysis (MSA) as implemented in IMAGIC-5 (van Heel et al, 1996). Classes were inspected and selected (based on the visual match between the class average and the individual parti ...
... Particles were initially centred against a rotationally average total sum and classified using multivariate statistical analysis (MSA) as implemented in IMAGIC-5 (van Heel et al, 1996). Classes were inspected and selected (based on the visual match between the class average and the individual parti ...
Investigating semantic similarity measures across the
... The terms held within this structure are used to annotate database entries (GO Consortium, 2002b). As they form a standard vocabulary across many biological resources such as SWISS-PROT (Bairoch & Apweiler, 2000), this shared understanding provides a valuable, computationally accessible form of the ...
... The terms held within this structure are used to annotate database entries (GO Consortium, 2002b). As they form a standard vocabulary across many biological resources such as SWISS-PROT (Bairoch & Apweiler, 2000), this shared understanding provides a valuable, computationally accessible form of the ...
Protein sequence databases
... similarity • Most current proteins are thought to be the descendants of no more than 1,000 (structural) ...
... similarity • Most current proteins are thought to be the descendants of no more than 1,000 (structural) ...
STRUCTURAL INSIGHTS INTO NOVEL MICROBIAL METALLOENZYMES
... a metal ion influences both protein stability and function through structural, catalytic or regulatory roles. Discovery of a metal ion cofactor presents new insight into both the structural and functional aspects of a protein and can be essential for the elucidation of the functional and mechanistic ...
... a metal ion influences both protein stability and function through structural, catalytic or regulatory roles. Discovery of a metal ion cofactor presents new insight into both the structural and functional aspects of a protein and can be essential for the elucidation of the functional and mechanistic ...
Prediction of B cell epitopes
... A data set of 75 discontinuous epitopes was compiled from structures of antibodies/protein antigen complexes in the PDB The data set has been used for developing a method for predictions of discontinuous B cell epitopes Since about 30 of the PDB entries represented ...
... A data set of 75 discontinuous epitopes was compiled from structures of antibodies/protein antigen complexes in the PDB The data set has been used for developing a method for predictions of discontinuous B cell epitopes Since about 30 of the PDB entries represented ...
The ATP-Cone: An Evolutionarily Mobile, ATP
... to the well-established relationship among ribonucleotide reductases, the sequence of this domain is statistically significantly similar to 2-phosphoglycerate kinases from archaea and the bacterium Deinococcus radiodurans and a conserved family of small bacterial proteins typified by E. coli YbaD. R ...
... to the well-established relationship among ribonucleotide reductases, the sequence of this domain is statistically significantly similar to 2-phosphoglycerate kinases from archaea and the bacterium Deinococcus radiodurans and a conserved family of small bacterial proteins typified by E. coli YbaD. R ...
Structure, function, and evolution of phosphoglycerate mutases
... this dPGM was located in this area by Winn et al. (1981). There is one active site per monomer located in a crevice at the C-terminal end of the b-sheet and this active site utilizes residues only from this monomer. The active site has, among other amino acids, two histidine residues, His8 and His18 ...
... this dPGM was located in this area by Winn et al. (1981). There is one active site per monomer located in a crevice at the C-terminal end of the b-sheet and this active site utilizes residues only from this monomer. The active site has, among other amino acids, two histidine residues, His8 and His18 ...
From Sequence to Structure
... because its backbone nitrogen is not available for the hydrogen bonding required for helix formation. The aromatic side chain of phenylalanine can sometimes participate in weakly polar interactions. Hydrophilic amino-acid residues are able to make hydrogen bonds to one another, to the peptide backbo ...
... because its backbone nitrogen is not available for the hydrogen bonding required for helix formation. The aromatic side chain of phenylalanine can sometimes participate in weakly polar interactions. Hydrophilic amino-acid residues are able to make hydrogen bonds to one another, to the peptide backbo ...
Overview of tag protein fusions
... (Table 1). Thus, several different strategies have been developed to produce recombinant proteins on a large scale. One approach is to use a very small peptide tag that should not interfere with the fused protein. The most commonly used small peptide tags are poly-Arg-, FLAG-, poly-His-, c-myc-, S-, ...
... (Table 1). Thus, several different strategies have been developed to produce recombinant proteins on a large scale. One approach is to use a very small peptide tag that should not interfere with the fused protein. The most commonly used small peptide tags are poly-Arg-, FLAG-, poly-His-, c-myc-, S-, ...
PowerPoint 演示文稿
... • Each mRNA transcript is read by more than one ribosome. • A second, third, fourth, etc. ribosome starts to read the mRNA transcript before the first ribosome has completed the synthesis of one polypeptide chain. • Multiple ribosomes on a single mRNA transcript are called polyribosomes or polysomes ...
... • Each mRNA transcript is read by more than one ribosome. • A second, third, fourth, etc. ribosome starts to read the mRNA transcript before the first ribosome has completed the synthesis of one polypeptide chain. • Multiple ribosomes on a single mRNA transcript are called polyribosomes or polysomes ...
Diversity in P-loop Structure of A-ATP Synthase
... the concerted main interactions formed by the critical P-loop residues P235, F236 and S238.2 When we superimpose the available P-loop structures from the members of the superfamily of ATP/GTPbinding proteins with the primary sequence of GXXGSGKT, all P-loop structures including the S238 mutant match ...
... the concerted main interactions formed by the critical P-loop residues P235, F236 and S238.2 When we superimpose the available P-loop structures from the members of the superfamily of ATP/GTPbinding proteins with the primary sequence of GXXGSGKT, all P-loop structures including the S238 mutant match ...
Functional implications of the modeled structure of maspin
... insertion but that present in the RSL of a mutant form of a r antichymotrypsin apparently does not (Wei et al., 1994). The evidence for non-insertion also derives from the two published mechanisms by which serpins polymerize. Both rely on the RSL of one molecule being available for insertion into ei ...
... insertion but that present in the RSL of a mutant form of a r antichymotrypsin apparently does not (Wei et al., 1994). The evidence for non-insertion also derives from the two published mechanisms by which serpins polymerize. Both rely on the RSL of one molecule being available for insertion into ei ...
Eukaryotic cells modify their RNA after transcription
... The other parts of the genes are called exons. Exons contain information that appears in the functional mRNA Genes for mRNA have 0 to 60 introns Genes for tRNA have 0 to 1 intron. ...
... The other parts of the genes are called exons. Exons contain information that appears in the functional mRNA Genes for mRNA have 0 to 60 introns Genes for tRNA have 0 to 1 intron. ...
2-D Quant Kit - GE Healthcare Life Sciences
... electrophoresis as well as any sample that contains substances that otherwise interfere with protein quantification. The procedure uses a combination of a unique precipitant and co-precipitant to quantitatively precipitate sample protein while leaving interfering contaminants in solution. The protei ...
... electrophoresis as well as any sample that contains substances that otherwise interfere with protein quantification. The procedure uses a combination of a unique precipitant and co-precipitant to quantitatively precipitate sample protein while leaving interfering contaminants in solution. The protei ...
Accurate Prediction of Contact Numbers for Multi
... residue side chain conformation.13 Traditionally, prediction of the contact numbers for soluble proteins is treated as a two-state (higher or lower than the average contact number) or three-state (much higher, much lower, or close to the average contact number) classification problem.14−16 However, t ...
... residue side chain conformation.13 Traditionally, prediction of the contact numbers for soluble proteins is treated as a two-state (higher or lower than the average contact number) or three-state (much higher, much lower, or close to the average contact number) classification problem.14−16 However, t ...
Carl Woese
... of the relationships between living things, Woese’s analysis had an impact on ribosome biology. Woese realized that one could use RNA sequences to determine the doublehelical folding, or secondary structure, of RNA molecules. Woese and I used this approach to work out the secondary structures of 16S ...
... of the relationships between living things, Woese’s analysis had an impact on ribosome biology. Woese realized that one could use RNA sequences to determine the doublehelical folding, or secondary structure, of RNA molecules. Woese and I used this approach to work out the secondary structures of 16S ...
Spinalin, a new glycine- and histidine
... 254 amino acids beginning at nucleotide 126. The start codon ATG is immediately followed by a G residue and preceded at position −3 by an A, which is in agreement with the consensus sequence for eukaryotic translation initiation sites (Kozak, 1987). No homology to other proteins in the database (SWI ...
... 254 amino acids beginning at nucleotide 126. The start codon ATG is immediately followed by a G residue and preceded at position −3 by an A, which is in agreement with the consensus sequence for eukaryotic translation initiation sites (Kozak, 1987). No homology to other proteins in the database (SWI ...
The Right Whey Protein
... Cooking Denatures Protein Cooking reduces the biological value of protein. Exposure to high-heat ruptures the bonds that hold peptides together causing a cross-linking effect. Few of us eat wild, raw animal protein, which is actually alkaline forming, high in bioactive micronutrient and enzyme value ...
... Cooking Denatures Protein Cooking reduces the biological value of protein. Exposure to high-heat ruptures the bonds that hold peptides together causing a cross-linking effect. Few of us eat wild, raw animal protein, which is actually alkaline forming, high in bioactive micronutrient and enzyme value ...
RNA processing #1
... Where is the catalytic activity in RNase P? RNase P is composed of a 375 nucleotide RNA and a 20 kDa protein. The protein component will NOT catalyze cleavage on its own. The RNA WILL catalyze cleavage by itself !!!! The protein component aids in the reaction but is not required for catalysis. Thus ...
... Where is the catalytic activity in RNase P? RNase P is composed of a 375 nucleotide RNA and a 20 kDa protein. The protein component will NOT catalyze cleavage on its own. The RNA WILL catalyze cleavage by itself !!!! The protein component aids in the reaction but is not required for catalysis. Thus ...
Predictable Alteration of Sequence Recognition by RNA
... Recombinant CLB19 Binds Specifically to the clpP and rpoA Editing Sites The Arabidopsis plastid protein CLB19 consists of 10 PPR motifs and is required for editing of two plastid transcripts, clpP and rpoA (Chateigner-Boutin et al., 2008). Alignments of CLB19 to both RNA targets show a mismatch and fi ...
... Recombinant CLB19 Binds Specifically to the clpP and rpoA Editing Sites The Arabidopsis plastid protein CLB19 consists of 10 PPR motifs and is required for editing of two plastid transcripts, clpP and rpoA (Chateigner-Boutin et al., 2008). Alignments of CLB19 to both RNA targets show a mismatch and fi ...
Proteins and their Ligands: Their Importance and how to Crystallize
... 2) Ligand soaking to obtain the ligand bound state The second method, which can be used to obtain a ligand bound protein structure, is ligand soaking. Soaking crystals with ligands is often the method of choice to obtain crystals of protein-ligand complexes owing to the ease of the method. However, ...
... 2) Ligand soaking to obtain the ligand bound state The second method, which can be used to obtain a ligand bound protein structure, is ligand soaking. Soaking crystals with ligands is often the method of choice to obtain crystals of protein-ligand complexes owing to the ease of the method. However, ...
Structural Features of Angiotensin-I Converting Enzyme Catalytic Sites
... fragments. Angiotensin-I Converting Enzyme bears the sequence and topology characteristics of the well-known gluzincins, a sub-family of zincins metallopeptidases and these similarities are exploited in order to reveal common structural elements among these enzymes. 3D homology models are also built ...
... fragments. Angiotensin-I Converting Enzyme bears the sequence and topology characteristics of the well-known gluzincins, a sub-family of zincins metallopeptidases and these similarities are exploited in order to reveal common structural elements among these enzymes. 3D homology models are also built ...
power-point slides
... The problem is analogous to the problems of representing the surface of the earth on a two-dimensional map Reduction of the dimensions leads to distortions of scales, ...
... The problem is analogous to the problems of representing the surface of the earth on a two-dimensional map Reduction of the dimensions leads to distortions of scales, ...
Structural alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.