Abgent
Encyclopedia
Abgent is a San Diego biotechnology
company that develops tools to profile post-translational modifications related to cellular function and disease. Abgent's antibodies cover targeting protein kinases (kinome
), phosphatases, methyl and acetyl transferases, ubiquitin
and SUMO
, glycosylases and other protein modification enzymes.
Technology, Drug Discovery
Features and The Scientist's cell signaling
feature Full list of citations.
Abgent specializes in FMOC solid-phase synthesis
of peptide
s using pseudoproline
to improve the quality of synthetic peptides. Pseudoproline dipeptides have been shown to increase the success rate for synthesizing both long and difficult peptides. Pseudoproline
dipeptides can be introduced in the same manner as other amino acid
derivatives
. The routine use of pseudoproline
(oxazolidine
) dipeptides in the FMOC solid phase pepdide sysnthesis (SPPS) of serine
- and threonine
-containing peptides has been shown to improve the quality and yield of crude products and helps avoid unnecessary repeat synthesis of failed sequences. Pseudoproline
dipeptides have also been shown to be effective in the synthesis of intractable peptides, long peptides/small proteins, and cyclic peptides, enabling in many cases the production of peptides that are otherwise difficult to produce. The dipeptides are used by substituting a serine
or threonine
residue together with the preceding amino acid
residue in the peptide
sequence with the appropriate pseudoproline dipeptide
. The native sequence is regenerated on cleavage and deprotection.
conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate
specificity appears to be derived directly from Ubc9 and the respective substrate motif. SUMOplot predicts the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot score system is based on two criteria: 1) direct amino acid match to the SUMO-CS observed and shown to bind Ubc9, and 2) substitution of the consensus amino acid
residues with amino acid residues exhibiting similar hydrophobicity. SUMOplot has been used in the past to predict Ubc9 dependent sites.
Biotechnology
Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...
company that develops tools to profile post-translational modifications related to cellular function and disease. Abgent's antibodies cover targeting protein kinases (kinome
Kinome
In molecular biology, the kinome of an organism is the set of protein kinases in its genome. Kinases are enzymes that catalyze phosphorylation reactions and fall into several groups and families, e.g., those that phosphorylate the amino acids serine and threonine, those that phosphorylate tyrosine...
), phosphatases, methyl and acetyl transferases, ubiquitin
Ubiquitin
Ubiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. Among other functions, it directs protein recycling.Ubiquitin can be attached to proteins and label them for destruction...
and SUMO
SUMO protein
Small Ubiquitin-like Modifier or SUMO proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function...
, glycosylases and other protein modification enzymes.
Peer review
Abgent's was listed as a selected supplier in Nature Magazine, AntibodyAntibody
An antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
Technology, Drug Discovery
Drug discovery
In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which drugs are discovered or designed.In the past most drugs have been discovered either by identifying the active ingredient from traditional remedies or by serendipitous discovery...
Features and The Scientist's cell signaling
Cell signaling
Cell signaling is part of a complex system of communication that governs basic cellular activities and coordinates cell actions. The ability of cells to perceive and correctly respond to their microenvironment is the basis of development, tissue repair, and immunity as well as normal tissue...
feature Full list of citations.
Core business
Solid-phase synthesis
In chemistry, solid-phase synthesis is a method in which molecules are bound on a bead and synthesized step-by-step in a reactant solution; compared with normal synthesis in a liquid state, it is easier to remove excess reactant or byproduct from the product. In this method, building blocks are...
of peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
s using pseudoproline
Pseudoproline
Pseudoproline derivatives are artificially created dipeptides to minimize aggregation during FMOC solid-phase synthesis of peptides.-Introduction:...
to improve the quality of synthetic peptides. Pseudoproline dipeptides have been shown to increase the success rate for synthesizing both long and difficult peptides. Pseudoproline
Pseudoproline
Pseudoproline derivatives are artificially created dipeptides to minimize aggregation during FMOC solid-phase synthesis of peptides.-Introduction:...
dipeptides can be introduced in the same manner as other amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
derivatives
Derivative (chemistry)
In chemistry, a derivative is a compound that is derived from a similar compound by some chemical or physical process. In the past it was also used to mean a compound that can be imagined to arise from another compound, if one atom is replaced with another atom or group of atoms, but modern...
. The routine use of pseudoproline
Pseudoproline
Pseudoproline derivatives are artificially created dipeptides to minimize aggregation during FMOC solid-phase synthesis of peptides.-Introduction:...
(oxazolidine
Oxazolidine
Oxazolidine is a five-membered ring compound consisting of three carbons, a nitrogen, a hydrogen, and an oxygen. The oxygen and NH are the 1 and 3 positions, respectively. In oxazolidine derivatives, there is always a carbon between the oxygen and the nitrogen . All of the carbons in oxazolidines...
) dipeptides in the FMOC solid phase pepdide sysnthesis (SPPS) of serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
- and threonine
Threonine
Threonine is an α-amino acid with the chemical formula HO2CCHCHCH3. Its codons are ACU, ACA, ACC, and ACG. This essential amino acid is classified as polar...
-containing peptides has been shown to improve the quality and yield of crude products and helps avoid unnecessary repeat synthesis of failed sequences. Pseudoproline
Pseudoproline
Pseudoproline derivatives are artificially created dipeptides to minimize aggregation during FMOC solid-phase synthesis of peptides.-Introduction:...
dipeptides have also been shown to be effective in the synthesis of intractable peptides, long peptides/small proteins, and cyclic peptides, enabling in many cases the production of peptides that are otherwise difficult to produce. The dipeptides are used by substituting a serine
Serine
Serine is an amino acid with the formula HO2CCHCH2OH. It is one of the proteinogenic amino acids. By virtue of the hydroxyl group, serine is classified as a polar amino acid.-Occurrence and biosynthesis:...
or threonine
Threonine
Threonine is an α-amino acid with the chemical formula HO2CCHCHCH3. Its codons are ACU, ACA, ACC, and ACG. This essential amino acid is classified as polar...
residue together with the preceding amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residue in the peptide
Peptide
Peptides are short polymers of amino acid monomers linked by peptide bonds. They are distinguished from proteins on the basis of size, typically containing less than 50 monomer units. The shortest peptides are dipeptides, consisting of two amino acids joined by a single peptide bond...
sequence with the appropriate pseudoproline dipeptide
Dipeptide
A dipeptide is a molecule consisting of two amino acids joined by a single peptide bond.Dipeptides are produced from polypeptides by the action of the hydrolase enzyme dipeptidyl peptidase. Dietary proteins are digested to dipeptides and amino acids, and the dipeptides are absorbed more rapidly...
. The native sequence is regenerated on cleavage and deprotection.
SUMOplot
Most SUMO-modified proteins contain the tetrapeptide motif B-K-x-D/E where B is a hydrophobic residue, K is the lysineLysine
Lysine is an α-amino acid with the chemical formula HO2CCH4NH2. It is an essential amino acid, which means that the human body cannot synthesize it. Its codons are AAA and AAG....
conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
specificity appears to be derived directly from Ubc9 and the respective substrate motif. SUMOplot predicts the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot score system is based on two criteria: 1) direct amino acid match to the SUMO-CS observed and shown to bind Ubc9, and 2) substitution of the consensus amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residues with amino acid residues exhibiting similar hydrophobicity. SUMOplot has been used in the past to predict Ubc9 dependent sites.
See also
- SUMO proteinSUMO proteinSmall Ubiquitin-like Modifier or SUMO proteins are a family of small proteins that are covalently attached to and detached from other proteins in cells to modify their function...
- SUMO pathway
- UbiquitinUbiquitinUbiquitin is a small regulatory protein that has been found in almost all tissues of eukaryotic organisms. Among other functions, it directs protein recycling.Ubiquitin can be attached to proteins and label them for destruction...
- PseudoprolinePseudoprolinePseudoproline derivatives are artificially created dipeptides to minimize aggregation during FMOC solid-phase synthesis of peptides.-Introduction:...
- Aurora inhibitorsAurora inhibitorsAurora kinases regulate cell cycle transit from G2 through cytokinesis and, thus, are targets in cancer therapy. There are three mammalian aurora kinase genes, encoding aurora A, B and C. Intense investigation has focused on aurora A and B as they appear to play a role in oncogenesis with aurora A...
- KinomeKinomeIn molecular biology, the kinome of an organism is the set of protein kinases in its genome. Kinases are enzymes that catalyze phosphorylation reactions and fall into several groups and families, e.g., those that phosphorylate the amino acids serine and threonine, those that phosphorylate tyrosine...
- Diet and cancerDiet and cancerDiet and cancer are associated. While it is not yet possible to provide quantitative estimates of the overall risks, it has been estimated that 35 percent of cancer deaths may be related to dietary factors. Almost all cancers are caused by environmental factors, and of these, 30–40% of cancers are...
- PRMT4 pathwayPRMT4 pathwayProtein arginine N-methyltransferase-4 methylation of arginine residues within proteins plays a critical key role in transcriptional regulation . PRMT4 binds to the classes of transcriptional activators known as p160 and CBP/p300. The modified forms of these proteins are involved in stimulation of...