The goal of protein structure prediction by threading is to find a best
... Most threading approaches do not use the physical full-atom free energy functions commonly used by macromolecular modeling software. Instead, most threading objective functions are determined empirically by statistical analysis of the 3D data deposited in the Protein Data Bank (PDB). Thus they are o ...
... Most threading approaches do not use the physical full-atom free energy functions commonly used by macromolecular modeling software. Instead, most threading objective functions are determined empirically by statistical analysis of the 3D data deposited in the Protein Data Bank (PDB). Thus they are o ...
Secondary structure of proteins - Home
... β Turns are often found at sites where the peptide chain changes direction. β-Bends reverse the direction of a polypeptide chain, helping it to form a compact, globular shape. They are usually found on the surface of protein molecules These are sections in which four amino acid residues are ...
... β Turns are often found at sites where the peptide chain changes direction. β-Bends reverse the direction of a polypeptide chain, helping it to form a compact, globular shape. They are usually found on the surface of protein molecules These are sections in which four amino acid residues are ...
The role of cytosolic proteins in the insertion of tail
... which distinguish between true transmembrane integration of TA proteins and their salt-resistant association to the cytosolic leaflet of the bilayer (Brambillasca et al., 2005), has led to important advances in our understanding of the mechanisms used by this class of proteins to insert into the ER ...
... which distinguish between true transmembrane integration of TA proteins and their salt-resistant association to the cytosolic leaflet of the bilayer (Brambillasca et al., 2005), has led to important advances in our understanding of the mechanisms used by this class of proteins to insert into the ER ...
Bacterial Ribosomes and Protein Synthesis
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
Bacterial Ribosomes and Protein Synthesis
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
... bacterial cell contains 10,000 or more ribosomes and makes perhaps 1000 different proteins, and it is important to know whether or not different proteins can be made on the same ribosome or whether a specific kind of ribosome is needed for each specific protein. If DNA in the nucleus transmits ‘info ...
Structural biology and drug design
... • Virtual screening requires a known 3D structure of the target protein • The aim of virtual HTS screening (docking) is to evaluate the fit between • a set of small molecules in a library and the drug target • To calculate interaction energies, surface contacts and steric volume complementarity the ...
... • Virtual screening requires a known 3D structure of the target protein • The aim of virtual HTS screening (docking) is to evaluate the fit between • a set of small molecules in a library and the drug target • To calculate interaction energies, surface contacts and steric volume complementarity the ...
The method SPrOS (Specificity Projection On Sequence)
... The method SPrOS (Specificity Projection On Sequence) is developed to analyze the amino acid sequences related to the same protein family in order to recognize the sites responsible for the specificity of separated subclasses within this family. Comparing the sequences within a protein family, one c ...
... The method SPrOS (Specificity Projection On Sequence) is developed to analyze the amino acid sequences related to the same protein family in order to recognize the sites responsible for the specificity of separated subclasses within this family. Comparing the sequences within a protein family, one c ...
LETTERS MtArt: A New Model of Amino Acid Replacement for Arthropoda
... was not included in the original training data set used to stimate the MtREV/MtMam matrices and/or because it is the only protein-coding gene encoded on the L-strand of the vertebrate mt-genomes and hence may be subjected to particular compositional biases. In the case of Atp8, these results are lik ...
... was not included in the original training data set used to stimate the MtREV/MtMam matrices and/or because it is the only protein-coding gene encoded on the L-strand of the vertebrate mt-genomes and hence may be subjected to particular compositional biases. In the case of Atp8, these results are lik ...
`Hybrid Protein Model`for optimally defining 3D protein structure
... Published by Oxford University Press ...
... Published by Oxford University Press ...
III. - Sugars and Polysaccharides
... The basic carbohydrate units are called monosaccharides. They differ in their number of carbon atoms and in the arrangement of the H and O atoms attached to the carbons. Many of these compounds are synthesized from simpler substances in a process named gluconeogenesis. Others are the products of pho ...
... The basic carbohydrate units are called monosaccharides. They differ in their number of carbon atoms and in the arrangement of the H and O atoms attached to the carbons. Many of these compounds are synthesized from simpler substances in a process named gluconeogenesis. Others are the products of pho ...
Exam #3 2 Problem 1. (25 points) You study ligand binding to two
... 5. Which of these constants (KT, KR, L, L’) will be affected by a mutation of the proximal His to Ala? All of them. (1) Mutation of the proximal His will change the coordination of Fe ion, hence it will affect heme binding properties: KT, KR (2) Proximal His is directly involved in the translation o ...
... 5. Which of these constants (KT, KR, L, L’) will be affected by a mutation of the proximal His to Ala? All of them. (1) Mutation of the proximal His will change the coordination of Fe ion, hence it will affect heme binding properties: KT, KR (2) Proximal His is directly involved in the translation o ...
`N17` region of huntingtin protein
... Where exactly Huntingtin’s final destination in the cell is, plays an important role in the progression of Huntington’s disease. Huntingtin does different things in different places. In some locations, it may be less dangerous than in others. Exactly where huntingtin is found inside cells can have a ...
... Where exactly Huntingtin’s final destination in the cell is, plays an important role in the progression of Huntington’s disease. Huntingtin does different things in different places. In some locations, it may be less dangerous than in others. Exactly where huntingtin is found inside cells can have a ...
Domain organization of human cleavage factor Im 1 Distinct
... CF!Im68 identified members of the SR family of splicing factors, suggesting that CF!Im may contribute to the coordination of splicing and 3’!end formation. Furthermore, we investigated the subcellular localization of CF!Im. We found that CF!Im subunits are localized to the nucleus and accumulate wit ...
... CF!Im68 identified members of the SR family of splicing factors, suggesting that CF!Im may contribute to the coordination of splicing and 3’!end formation. Furthermore, we investigated the subcellular localization of CF!Im. We found that CF!Im subunits are localized to the nucleus and accumulate wit ...
The three-dimensional structure of the interleukin
... found that IL-18 (green) bound to IL-18 receptor α (light blue) as it was surrounded by the receptor, and IL-18 receptor β (blue) lay side by side with IL-18 receptor α and bound to IL-18 (figure below left). In addition, we also measured the effects of amino acids located on the interaction surface ...
... found that IL-18 (green) bound to IL-18 receptor α (light blue) as it was surrounded by the receptor, and IL-18 receptor β (blue) lay side by side with IL-18 receptor α and bound to IL-18 (figure below left). In addition, we also measured the effects of amino acids located on the interaction surface ...
Analysis of High Accuracy, Quantitative Proteomics Data in the
... difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addr ...
... difficult to avoid contamination of databases with low quality peptide identifications, to control for the inflation in false positive identifications when combining data sets, and to integrate quantitative data. Although, for example, the contamination with low quality identifications has been addr ...
Dissecting the protein–RNA interface
... As of 11 November 2010, the PDB listed 824 structures of protein–RNA complexes that had been solved using X-ray crystallography (5). From this data set, 344 complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleot ...
... As of 11 November 2010, the PDB listed 824 structures of protein–RNA complexes that had been solved using X-ray crystallography (5). From this data set, 344 complexes were selected based on the following criteria: (i) structural resolution better than 3.0 Å and (ii) polypeptides and polyribonucleot ...
Mass Spectrometry in Viral Proteomics
... FIGURE 4. Probing protein structure and protein/protein interactions using proteolysis and MALDI-MS. Schematic view (left) of key concepts. Two cleavage sites are accessible for the protein of interest alone (top, left), yielding fragments after limited digestion. In the complex with protein X, one ...
... FIGURE 4. Probing protein structure and protein/protein interactions using proteolysis and MALDI-MS. Schematic view (left) of key concepts. Two cleavage sites are accessible for the protein of interest alone (top, left), yielding fragments after limited digestion. In the complex with protein X, one ...
Know Your Feed Terms - Alberta Agriculture and Forestry
... hail, frost or high levels of nitrogen fertilization. Feeds containing high levels of nitrate (greater than 1 per cent) can be toxic to ruminants. ...
... hail, frost or high levels of nitrogen fertilization. Feeds containing high levels of nitrate (greater than 1 per cent) can be toxic to ruminants. ...
NFX1-123 Increases HTERT Post-Transcriptionally in HPV 16E6
... Background: E6 induces telomerase activity through upregulation of hTERT, the catalytic subunit of telomerase. Full activation of hTERT by 16E6 in keratinocytes (HFKs) requires the endogenous protein NFX1-123. NFX1-123 contains a PAM2 motif, to which cytoplasmic poly(A) binding proteins (PABPCs) bin ...
... Background: E6 induces telomerase activity through upregulation of hTERT, the catalytic subunit of telomerase. Full activation of hTERT by 16E6 in keratinocytes (HFKs) requires the endogenous protein NFX1-123. NFX1-123 contains a PAM2 motif, to which cytoplasmic poly(A) binding proteins (PABPCs) bin ...
Function and specificity of 14-3-3 proteins in the regulation of
... reduced in vitro by 5¢-AMP which interacts with 14-3-3s and directly reduces their binding to target ligands (Kaiser and Spill, 1991; Athwal et al., 1998b). It is noteworthy that there is evidence for an AMP binding site in a spinach 14-3-3 isoform. Thus 14-3-3 protein activity might also be under m ...
... reduced in vitro by 5¢-AMP which interacts with 14-3-3s and directly reduces their binding to target ligands (Kaiser and Spill, 1991; Athwal et al., 1998b). It is noteworthy that there is evidence for an AMP binding site in a spinach 14-3-3 isoform. Thus 14-3-3 protein activity might also be under m ...
吴冬茵
... Latent semantic analysis (LSA) is a theory and method for extracting and representing the contextual-usage meaning by statistical computations applied to a large corpus of text. LSA analysis the relationships between a set of documents and the terms they contain by producing a set of concepts re ...
... Latent semantic analysis (LSA) is a theory and method for extracting and representing the contextual-usage meaning by statistical computations applied to a large corpus of text. LSA analysis the relationships between a set of documents and the terms they contain by producing a set of concepts re ...
Leukaemia Section t(11;14)(q23;q32) Atlas of Genetics and Cytogenetics in Oncology and Haematology
... Protein 3969 amino acids; 431 kDa; contains two DNA binding motifs (a AT hook and a CXXC domain), a DNA methyl transferase motif, a bromodomain. MLL is cleaved by taspase 1 into 2 proteins before entering the nucleus, called MLL-N and MLL-C. The FYRN and a FRYC domains of native MLL associate MLL-N ...
... Protein 3969 amino acids; 431 kDa; contains two DNA binding motifs (a AT hook and a CXXC domain), a DNA methyl transferase motif, a bromodomain. MLL is cleaved by taspase 1 into 2 proteins before entering the nucleus, called MLL-N and MLL-C. The FYRN and a FRYC domains of native MLL associate MLL-N ...
Cloning, Purification, and Partial Characterization of the
... and its integration site [5,6] clearly suggest that it is an intein. The intein is inserted in the middle of the Walker-A motif [7], a highly conserved motif which is found in all members of the AAA+ family of ATPases [8,9]. The sequence of the motif in Halobacterium MCM is GDPGTGKS and the intein i ...
... and its integration site [5,6] clearly suggest that it is an intein. The intein is inserted in the middle of the Walker-A motif [7], a highly conserved motif which is found in all members of the AAA+ family of ATPases [8,9]. The sequence of the motif in Halobacterium MCM is GDPGTGKS and the intein i ...
The Logic Linking Protein Acetylation and Metabolism
... CDKs to drive the cell cycle under these conditions. More generally, phosphorylation-based signaling pathways may impinge on sirtuins to exert an additional layer of control over protein acetylation. How will the flow of carbon provide acetyl-CoA for acetylation of cytosolic/ nuclear proteins under ...
... CDKs to drive the cell cycle under these conditions. More generally, phosphorylation-based signaling pathways may impinge on sirtuins to exert an additional layer of control over protein acetylation. How will the flow of carbon provide acetyl-CoA for acetylation of cytosolic/ nuclear proteins under ...
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.