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Chymotrypsin (EC 3.4.21.1, chymotrypsins A and B, alpha-chymar ophth, avazyme, chymar, chymotest, enzeon, quimar, quimotrase, alpha-chymar, alpha-chymotrypsin A, alpha-chymotrypsin) is a digestive enzyme component of pancreatic juice acting in the duodenum, where it performs proteolysis, the breakdown of proteins and polypeptides. Chymotrypsin preferentially cleaves peptide amide bonds where the side chain of the amino acid N-terminal to the scissile amide bond (the P1 position) is a large hydrophobic amino acid (tyrosine, tryptophan, and phenylalanine). These amino acids contain an aromatic ring in their side chain that fits into a hydrophobic pocket (the S1 position) of the enzyme. It is activated in the presence of trypsin. The hydrophobic and shape complementarity between the peptide substrate P1 side chain and the enzyme S1 binding cavity accounts for the substrate specificity of this enzyme. Chymotrypsin also hydrolyzes other amide bonds in peptides at slower rates, particularly those containing leucine and methionine at the P1 position.
Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula HOOC-CH-(NH2)-CH2-SH. The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, sometimes the symbol Cyz is used. The deprotonated form can generally be described by the symbol Cym as well. The thiol is susceptible to oxidation to give the disulfide derivative cystine, which serves an important structural role in many proteins. In this case, the symbol Cyx is sometimes used. When used as a food additive, it has the E number E920. It is encoded by the codons UGU and UGC.
In biochemistry, biotinylation is the process of covalently attaching biotin to a protein, nucleic acid or other molecule. Biotinylation is rapid, specific and is unlikely to disturb the natural function of the molecule due to the small size of biotin. Biotin binds to streptavidin and avidin with an extremely high affinity, fast on-rate, and high specificity, and these interactions are exploited in many areas of biotechnology to isolate biotinylated molecules of interest. Biotin-binding to streptavidin and avidin is resistant to extremes of heat, pH and proteolysis, making capture of biotinylated molecules possible in a wide variety of environments. Also, multiple biotin molecules can be conjugated to a protein of interest, which allows binding of multiple streptavidin, avidin or neutravidin protein molecules and increases the sensitivity of detection of the protein of interest. There is a large number of biotinylation reagents available that exploit the wide range of possible labelling methods. Due to the strong affinity between biotin and streptavidin, the purification of biotinylated proteins has been a widely used approach to identify protein-protein interactions and post-translational events such as ubiquitylation in molecular biology.
In chemistry and biology a cross-link is a bond or a short sequence of bonds that links one polymer chain to another. These links may take the form of covalent bonds or ionic bonds and the polymers can be either synthetic polymers or natural polymers.
In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis in living organisms occurs in the opposite direction.
Chemical biology is a scientific discipline spanning the fields of chemistry and biology. The discipline involves the application of chemical techniques, analysis, and often small molecules produced through synthetic chemistry, to the study and manipulation of biological systems. In contrast to biochemistry, which involves the study of the chemistry of biomolecules and regulation of biochemical pathways within and between cells, chemical biology deals with chemistry applied to biology.
A leucine zipper is a common three-dimensional structural motif in proteins. They were first described by Landschulz and collaborators in 1988 when they found that an enhancer binding protein had a very characteristic 30-amino acid segment and the display of these amino acid sequences on an idealized alpha helix revealed a periodic repetition of leucine residues at every seventh position over a distance covering eight helical turns. The polypeptide segments containing these periodic arrays of leucine residues were proposed to exist in an alpha-helical conformation and the leucine side chains from one alpha helix interdigitate with those from the alpha helix of a second polypeptide, facilitating dimerization.
Psoralen is the parent compound in a family of naturally occurring organic compounds known as the linear furanocoumarins. It is structurally related to coumarin by the addition of a fused furan ring, and may be considered as a derivative of umbelliferone. Psoralen occurs naturally in the seeds of Psoralea corylifolia, as well as in the common fig, celery, parsley, West Indian satinwood, and in all citrus fruits. It is widely used in PUVA treatment for psoriasis, eczema, vitiligo, and cutaneous T-cell lymphoma; these applications are typically through the use of medications such as Methoxsalen. Many furanocoumarins are extremely toxic to fish, and some are deposited in streams in Indonesia to catch fish.
In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite strands of double-stranded DNA (interstrand). These adducts interfere with cellular metabolism, such as DNA replication and transcription, triggering cell death. These crosslinks can, however, be repaired through excision or recombination pathways.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.
Methionine aminopeptidase 2 is an enzyme that in humans is encoded by the METAP2 gene.
An expanded genetic code is an artificially modified genetic code in which one or more specific codons have been re-allocated to encode an amino acid that is not among the 22 common naturally-encoded proteinogenic amino acids.
Diazirines are a class of organic molecules consisting of a carbon bound to two nitrogen atoms, which are double-bonded to each other, forming a cyclopropene-like ring, 3H-diazirene. They are isomeric with diazocarbon groups, and like them can serve as precursors for carbenes by loss of a molecule of dinitrogen. For example, irradiation of diazirines with ultraviolet light leads to carbene insertion into various C-H, N-H, and O-H bonds. Hence, diazirines have grown in popularity as small photo-reactive crosslinking reagents. They are often used in photoaffinity labeling studies to observe a variety of interactions, including ligand-receptor, ligand-enzyme, protein-protein, and protein-nucleic acid interactions.
Arsenic biochemistry refers to biochemical processes that can use arsenic or its compounds, such as arsenate. Arsenic is a moderately abundant element in Earth's crust, and although many arsenic compounds are often considered highly toxic to most life, a wide variety of organoarsenic compounds are produced biologically and various organic and inorganic arsenic compounds are metabolized by numerous organisms. This pattern is general for other related elements, including selenium, which can exhibit both beneficial and deleterious effects. Arsenic biochemistry has become topical since many toxic arsenic compounds are found in some aquifers, potentially affecting many millions of people via biochemical processes.
Angelicin is the parent compound in a family of naturally occurring organic compounds known as the angular furanocoumarins. Structurally, it can be considered as benzapyra-2-one fused with a furan moiety in the 7,8-position. Angelicin is commonly found in certain Apiaceae and Fabaceae plant species such as Bituminaria bituminosa. It has a skin permeability coefficient (LogKp) of -2.46. The maximum absorption is observed at 300 nm. The 1HNMR spectrum is available; the infrared and mass spectra of angelicin can be found in this database. The sublimation of angelicin occurs at 120 °C and the pressure of 0.13 Pa. Angelicin is a coumarine.
There are many methods to investigate protein–protein interactions which are the physical contacts of high specificity established between two or more protein molecules involving electrostatic forces and hydrophobic effects. Each of the approaches has its own strengths and weaknesses, especially with regard to the sensitivity and specificity of the method. A high sensitivity means that many of the interactions that occur are detected by the screen. A high specificity indicates that most of the interactions detected by the screen are occurring in reality.
Photoactivatable probes, or caged probes, are cellular players that can be triggered by a flash of light. They are used in biological research to study processes in cells. The basic principle is to bring a photoactivatable agent to cells, tissues or even living animals and specifically control its activity by illumination.
l-Photo-leucine is a synthetic derivative of the l-leucine amino acid that is used as its natural analog and is characterized for having photo-reactivity, which makes it suitable for observing and characterizing protein-protein interactions (PPI). When a protein containing this amino acid (A) is lightened with ultraviolet light while interacting with another protein (B), the complex formed from these two proteins (AB) remains attached and can be isolated for its study.
TDBzcholine is a diazirine analog of acetylcholine that can be used to label the nicotinic acetylcholine receptor.
L-Photo-methionine is a photo-reactive amino acid derivative of L-methionine that was synthetically formed in 2005. Protein are long polymer chains of amino acids; which can range in various structures and sizes. Proteins can interact with each other and with these interactions, affects cellular interactions and pathways. Such interactions; in viral fusion and in growth-factor signaling looked promising for antiviral or anti-cancer drugs, so research must be done to understand the interactions. With that, research has begun to prove that proteins function in supramolecular complexes compared to isolated entities. So, scientists Monika Suchanek, Anna Radzikowski, and Christoph Thiele researched that the direct way to study these interactions in the natural environment better was to create a new way of photo-cross-linking proteins; which led to the synthesis of L-photo-methionine and in that same study, L-photo-leucine.
References
- ↑ Suchanek, M.; Radzikowska, A.; Thiele, C. (2005). "Photo-leucine and photo-methionine allow identification of protein–protein interactions in living cells". Nature Methods. 2 (4): 261–268. doi: 10.1038/nmeth752 . PMID 15782218.
- ↑ Isa, Nur Firdaus; Bensaude, Olivier; Murphy, Shona (2022-02-05). "Amber Suppression Technology for Mapping Site-specific Viral-host Protein Interactions in Mammalian Cells". Bio-protocol. 12 (3): e4315–e4315. doi:10.21769/bioprotoc.4315. PMC 8855090 . PMID 35284605.
- Vila-Perello, M., et al. (2007). Covalent capture of phospho-dependent protein oligomerization by site-specific incorporation of a diazirine photo-cross-linker. J. Am. Chem. Soc., 129(26):8068–69.
- Bomgarden, R. (2008). Studying Protein Interactions in Living Cells. Gen. Eng. News. Vol. 28, No. 7.
- P.-O. Hétu, et al. (2008) Photo-crosslinking of proteins in intact cells reveals a dimeric structure of cyclooxygenase-2 and an inhibitor-sensitive oligomeric structure of microsomal prostaglandin E2 synthase-1. Arch. Biochem. Biophys. doi : 10.1016/j.abb.2008.04.038
- Weaver, M.S., et al. (2008) The copper-binding domain of sparc mediates cell survival in vitro via interaction with integrin beta 1 and activation of integrin-linked kinase. J. Biol. Chem. doi : 10.1074/jbc.M706563200