Support vector machines for protein function prediction
... • A protein is classified as either belong (+) or not belong (-) to a functional family • By screening against all families, the function of this protein can be identified (example: SVMProt) ...
... • A protein is classified as either belong (+) or not belong (-) to a functional family • By screening against all families, the function of this protein can be identified (example: SVMProt) ...
A Acidic amino acids: Those whose side chains can carry a negative
... Endopeptidase: Enzyme that can cleave peptide bonds within the body of a protein chain. Enzyme: Proteins with ability to catalyse the chemical reactions necessary in living organisms. Typically, enzymes are no smaller than 100 amino acid residues. Epitope: Part of a protein’s surface area liable to ...
... Endopeptidase: Enzyme that can cleave peptide bonds within the body of a protein chain. Enzyme: Proteins with ability to catalyse the chemical reactions necessary in living organisms. Typically, enzymes are no smaller than 100 amino acid residues. Epitope: Part of a protein’s surface area liable to ...
Tentative exam questions on Food Biochemistry part - e
... Protein modification to alter their functional properties: removal or replacement of positive charge of lysine; write reactions Explain the role of protein hydrolysis in modification of protein functional properties. Explain the utilization of peptidyl-glutaminase in modification of protein function ...
... Protein modification to alter their functional properties: removal or replacement of positive charge of lysine; write reactions Explain the role of protein hydrolysis in modification of protein functional properties. Explain the utilization of peptidyl-glutaminase in modification of protein function ...
ORGANELLE-SPECIFIC PROTEIN QUALITY CONTROL SYSTEMS
... are associated with variations in the PARKIN, UCHL1, DJ-1, or PINK1 genes. These genes code for components involved in the ubiquitination and turnover of α-synuclein, and it is speculated that the pathogenesis includes a loss of PQC function, leading to α-synuclein aggregation in addition to general ...
... are associated with variations in the PARKIN, UCHL1, DJ-1, or PINK1 genes. These genes code for components involved in the ubiquitination and turnover of α-synuclein, and it is speculated that the pathogenesis includes a loss of PQC function, leading to α-synuclein aggregation in addition to general ...
Document
... Protein degradation rate varies 100x Most have motifs marking them for polyubiquitination: taken to proteosome & destroyed Other signals for selective degradation include PEST & KFERQ • PEST : found in many rapidly degraded proteins • Deletion increases t1/2 10x, adding PEST drops t1/2 10x • Sometim ...
... Protein degradation rate varies 100x Most have motifs marking them for polyubiquitination: taken to proteosome & destroyed Other signals for selective degradation include PEST & KFERQ • PEST : found in many rapidly degraded proteins • Deletion increases t1/2 10x, adding PEST drops t1/2 10x • Sometim ...
Preferentially biotinylate N-terminal α
... Biotinylation reagents containing N-hydroxysuccinimide (NHS) esters are widely used to label proteins at primary amino groups (-NH2), which exist in the side chain of lysine residues and at the N-terminus of each polypeptide. With large proteins, labeling of several lysine residues and the N-terminu ...
... Biotinylation reagents containing N-hydroxysuccinimide (NHS) esters are widely used to label proteins at primary amino groups (-NH2), which exist in the side chain of lysine residues and at the N-terminus of each polypeptide. With large proteins, labeling of several lysine residues and the N-terminu ...
Structural Genomics
... Peptide chains can be cross-linked by disulfides, Zinc, heme or other liganding compounds. Zinc has a complete d orbital , one stable oxidation state and forms ligands with sulfur, nitrogen and oxygen. Proteins refold very rapidly and generally in only one stable conformation. ...
... Peptide chains can be cross-linked by disulfides, Zinc, heme or other liganding compounds. Zinc has a complete d orbital , one stable oxidation state and forms ligands with sulfur, nitrogen and oxygen. Proteins refold very rapidly and generally in only one stable conformation. ...
Role of the ubiquitinselective CDC48UFD1/NPL4 chaperone
... 2000). They become activated by two ubiquitin-dependent events. In the ®rst step, SPT23 forms a homodimer at the membrane in which one molecule (processing substrate) is cleaved off the membrane by regulated ubiquitin/proteasome-dependent processing (RUP) (Hoppe et al., 2000; Rape et al., 2001). SPT ...
... 2000). They become activated by two ubiquitin-dependent events. In the ®rst step, SPT23 forms a homodimer at the membrane in which one molecule (processing substrate) is cleaved off the membrane by regulated ubiquitin/proteasome-dependent processing (RUP) (Hoppe et al., 2000; Rape et al., 2001). SPT ...
chains - TeacherWeb
... Protein-protein’s another chemical chain Made of amino acids, a thousand links long Repeat that peptide bond, never get it wrong. ...
... Protein-protein’s another chemical chain Made of amino acids, a thousand links long Repeat that peptide bond, never get it wrong. ...
Structural Genomics - University of Houston
... Peptide chains can be cross-linked by disulfides, Zinc, heme or other liganding compounds. Zinc has a complete d orbital , one stable oxidation state and forms ligands with sulfur, nitrogen and oxygen. Proteins refold very rapidly and generally in only one stable conformation. ...
... Peptide chains can be cross-linked by disulfides, Zinc, heme or other liganding compounds. Zinc has a complete d orbital , one stable oxidation state and forms ligands with sulfur, nitrogen and oxygen. Proteins refold very rapidly and generally in only one stable conformation. ...
New construction kit for designing new proteins
... On the level of basic research, Höcker hopes that her work will also contribute to finding out why proteins fold the way they do. "I would like to understand how the sequence determines the structure," said Höcker. The database will connect all structural knowledge and additional important informati ...
... On the level of basic research, Höcker hopes that her work will also contribute to finding out why proteins fold the way they do. "I would like to understand how the sequence determines the structure," said Höcker. The database will connect all structural knowledge and additional important informati ...
biological process
... Simple motifs include transmembrane domains and phosphorylation sites. These do not imply homology when found in a group of proteins. PROSITE (www.expasy.org/prosite) is a dictionary of motifs (there are currently 1600 entries). In PROSITE, a pattern is a qualitative motif description (a protein eit ...
... Simple motifs include transmembrane domains and phosphorylation sites. These do not imply homology when found in a group of proteins. PROSITE (www.expasy.org/prosite) is a dictionary of motifs (there are currently 1600 entries). In PROSITE, a pattern is a qualitative motif description (a protein eit ...
Concept review: Chromatography (applied to protein purification)
... • 1. Cell disruption should be performed at cold temperatures. Keep the sample on ice as much as possible and use chilled solutions. This will decrease the activity of the proteases for the simple reasons that all chemical reactions occur more slowly at low temperature. • 2. Add protease inhibitors ...
... • 1. Cell disruption should be performed at cold temperatures. Keep the sample on ice as much as possible and use chilled solutions. This will decrease the activity of the proteases for the simple reasons that all chemical reactions occur more slowly at low temperature. • 2. Add protease inhibitors ...
protein
... _____________________________ _____________________________ _____________________________ _____________________________ It also contains small amounts of: _____________________________ _____________________________ What is the chemical composition of protein? F&N-Protein-Year 9 ...
... _____________________________ _____________________________ _____________________________ _____________________________ It also contains small amounts of: _____________________________ _____________________________ What is the chemical composition of protein? F&N-Protein-Year 9 ...
A. Collagen
... are found at lungs, wall of blood vessels and elastic ligaments. Elastin can be stretched to several times their normal length but recoil to their original shape when the stretching force is relaxed Structure of elastin Amino acid composition Elastin is composed primarily of small, non-polar amino ...
... are found at lungs, wall of blood vessels and elastic ligaments. Elastin can be stretched to several times their normal length but recoil to their original shape when the stretching force is relaxed Structure of elastin Amino acid composition Elastin is composed primarily of small, non-polar amino ...
ready for
... folding process as the strands. there can be a smooth transition to a right-handed loop with the helix unwinding slightly at the ends. • In this case, the preference for righthandedness depends on the righthandedness of the a-helix, combined with the fact that it is much more likely for the backbone ...
... folding process as the strands. there can be a smooth transition to a right-handed loop with the helix unwinding slightly at the ends. • In this case, the preference for righthandedness depends on the righthandedness of the a-helix, combined with the fact that it is much more likely for the backbone ...
Acetylation of Ribosomal Proteins in Regenerating Rat Liver
... any possible contamination by lipids, nucleotides and cytoplasmic protein, the radioactivity still remained in these proteins. When the [’Hlacetate-labelled ribosomal proteins were hydrolysed in strong acid at 110°C overnight, more than 50% of the radioactivity was removed. These results are regarde ...
... any possible contamination by lipids, nucleotides and cytoplasmic protein, the radioactivity still remained in these proteins. When the [’Hlacetate-labelled ribosomal proteins were hydrolysed in strong acid at 110°C overnight, more than 50% of the radioactivity was removed. These results are regarde ...
Chapter 3
... domain) also may be encoded within a single polypeptide chain, as illustrated in Fig. 3.11. Domains still perform their standard functions although fused together in a longer polypeptide (e.g., DNA binding and ATPase domains of a transcription factor). The modular domain structure of many proteins h ...
... domain) also may be encoded within a single polypeptide chain, as illustrated in Fig. 3.11. Domains still perform their standard functions although fused together in a longer polypeptide (e.g., DNA binding and ATPase domains of a transcription factor). The modular domain structure of many proteins h ...
The Role of F-Box Proteins during Viral Infection
... known to compete with FBPs for the SCF’s active site, avoiding the self-ubiquitination of F-box proteins by the SFC complex [22]. Some FBPs can also be regulated by the interaction with small molecules to be able to bind to the SCF complex [16]. The diverse functions of FBPs act through the SCF comp ...
... known to compete with FBPs for the SCF’s active site, avoiding the self-ubiquitination of F-box proteins by the SFC complex [22]. Some FBPs can also be regulated by the interaction with small molecules to be able to bind to the SCF complex [16]. The diverse functions of FBPs act through the SCF comp ...
PHM 142 UNIT 9B Mitochondrial function in neurodegenerative
... preliminary studies suggestive of general impairment of mitochondrial function by unknown causes. Now we will examine mitochondrial function in neurodegenerative disorders where mitochondrial stress can cause nerve cell death. In some cases, such as Parkinson’s disease, the molecular mechanisms ...
... preliminary studies suggestive of general impairment of mitochondrial function by unknown causes. Now we will examine mitochondrial function in neurodegenerative disorders where mitochondrial stress can cause nerve cell death. In some cases, such as Parkinson’s disease, the molecular mechanisms ...
structure_property
... but they are always short and frequently occur at the termini of regular alpha-helices. The name 310 arises because there are three residues per turn and ten atoms enclosed in a ring formed by each hydrogen bond (note the hydrogen atom is included in this count). There are main chain hydrogen bonds ...
... but they are always short and frequently occur at the termini of regular alpha-helices. The name 310 arises because there are three residues per turn and ten atoms enclosed in a ring formed by each hydrogen bond (note the hydrogen atom is included in this count). There are main chain hydrogen bonds ...
Formation of Lys63-linked polyubiquitin chains on Gap1p permease
... promote both basal and ligand-induced internalization of a Cterminally truncated form of Ste2p (Terrel et al., 1998). Although ligand binding to full-length Ste2p leads to formation of di-and tri-ubiquitinated Ste2p conjugates, there is evidence that this may mainly reflect addition of single Ub moi ...
... promote both basal and ligand-induced internalization of a Cterminally truncated form of Ste2p (Terrel et al., 1998). Although ligand binding to full-length Ste2p leads to formation of di-and tri-ubiquitinated Ste2p conjugates, there is evidence that this may mainly reflect addition of single Ub moi ...
Protein Architecture and Structure Alignment
... “The three-dimensional structure of a native protein in its normal physiological milieu (solvent, pH, ionic strength, presence of other components such as metal ions or prosthetic groups, temperature, etc.) is the one in which the Gibbs free energy of the whole system is lowest; that is, that the na ...
... “The three-dimensional structure of a native protein in its normal physiological milieu (solvent, pH, ionic strength, presence of other components such as metal ions or prosthetic groups, temperature, etc.) is the one in which the Gibbs free energy of the whole system is lowest; that is, that the na ...
The role of different positively and negatively charged ions on the
... Nucleosomes are the basic building blocks of the chromatins and the fundamental repeating units in the cell nucleus. Its crystal structure has been identified by the Richmond Group initially at 2.8 Å atomic resolution (Luger et al., 1997) using X-ray diffraction experiments, which they subsequently ...
... Nucleosomes are the basic building blocks of the chromatins and the fundamental repeating units in the cell nucleus. Its crystal structure has been identified by the Richmond Group initially at 2.8 Å atomic resolution (Luger et al., 1997) using X-ray diffraction experiments, which they subsequently ...
Ubiquitin
Ubiquitin is a small (8.5 kDa) regulatory protein that has been found in almost all tissues (ubiquitously) of eukaryotic organisms. It was discovered in 1975 by Goldstein and further characterized throughout the 1970s and 1980s. There are four genes in the human genome that produce ubiquitin: UBB, UBC, UBA52 and RPS27A.The addition of ubiquitin to a substrate protein is called ubiquitination or ubiquitylation. Ubiquitination can affect proteins in many ways: It can signal for their degradation via the proteasome, alter their cellular location, affect their activity, and promote or prevent protein interactions. Ubiquitination is carried out in three main steps: activation, conjugation, and ligation, performed by ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s), respectively. The result of this sequential cascade binds ubiquitin to lysine residues on the protein substrate via an isopeptide bond or to the amino group of the protein's N-terminus via a peptide bond.The protein modifications can be either a single ubiquitin protein (monoubiquitination) or a chain of ubiquitin (polyubiquitination). The ubiquitination bonds are always formed with one of the seven lysine residues from the ubiquitin molecule. These 'linking' lysines are represented by a ""K"" (which is the one-letter amino acid notation of lysine) and a number, referring to its position in the ubiquitin molecule. First, a ubiquitin molecule is bonded by its C-terminus to a specific lysine residue (e.g. K48, K29, K63,...) on the target protein. Poly-ubiquitination occurs when the C-terminus of another ubiquitin, will be linked again to a lysine residue (for example again K48 or K29) on the previously added ubiquitin molecule, forming a chain. This process repeats several times, leading to the addition of several ubiquitins. Only poly-ubiquitination on defined lysines, mostly on K48 and K29, is related to degradation with the proteasome (referred to as the ""molecular kiss of death""), while other polyubiquitinations (e.g. on K63, K11, K6) and monoubiquitinations may regulate processes such as endocytic trafficking, inflammation, translation and DNA repair.Lysine 48-linked chains have been much-studied. They are the forms of chains that signal proteins to the proteasome, which destroys and recycles proteins. This discovery won the Nobel Prize for chemistry in 2004.