Collagen is the main structural protein in the extracellular matrix found in the body's various connective tissues. As the main component of connective tissue, it is the most abundant protein in mammals, making up from 25% to 35% of the whole-body protein content. Collagen consists of amino acids bound together to form a triple helix of elongated fibril known as a collagen helix. It is mostly found in connective tissue such as cartilage, bones, tendons, ligaments, and skin.
Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion.
Trypsin is an enzyme in the first section of the small intestine that starts the digestion of protein molecules by cutting long chains of amino acids into smaller pieces. It is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins. Trypsin is formed in the small intestine when its proenzyme form, the trypsinogen produced by the pancreas, is activated. Trypsin cuts peptide chains mainly at the carboxyl side of the amino acids lysine or arginine. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or trypsinization, and proteins that have been digested/treated with trypsin are said to have been trypsinized. Trypsin was discovered in 1876 by Wilhelm Kühne and was named from the Ancient Greek word for rubbing since it was first isolated by rubbing the pancreas with glycerin.
Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process often occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product. PTMs are important components in cell signaling, as for example when prohormones are converted to hormones.
Proteinogenic amino acids are amino acids that are incorporated biosynthetically into proteins during translation. The word "proteinogenic" means "protein creating". Throughout known life, there are 22 genetically encoded (proteinogenic) amino acids, 20 in the standard genetic code and an additional 2 that can be incorporated by special translation mechanisms.
Elastin is a protein that in humans is encoded by the ELN gene. Elastin is a key component of the extracellular matrix in gnathostomes. It is highly elastic and present in connective tissue allowing many tissues in the body to resume their shape after stretching or contracting. Elastin helps skin to return to its original position when it is poked or pinched. Elastin is also an important load-bearing tissue in the bodies of vertebrates and used in places where mechanical energy is required to be stored.
DD-transpeptidase is a bacterial enzyme that catalyzes the transfer of the R-L-αα-D-alanyl moiety of R-L-αα-D-alanyl-D-alanine carbonyl donors to the γ-OH of their active-site serine and from this to a final acceptor. It is involved in bacterial cell wall biosynthesis, namely, the transpeptidation that crosslinks the peptide side chains of peptidoglycan strands.
Elastic fibers are an essential component of the extracellular matrix composed of bundles of proteins (elastin) which are produced by a number of different cell types including fibroblasts, endothelial, smooth muscle, and airway epithelial cells. These fibers are able to stretch many times their length, and snap back to their original length when relaxed without loss of energy. Elastic fibers include elastin, elaunin and oxytalan.
A peptide library is a tool for studying proteins. The Peptide libraries contain a great number of peptides that have a systematic combination of amino acids. Usually, the peptide library is synthesized on a solid phase, mostly on resin, which can be made as a flat surface or beads. The peptide library provides a powerful tool for drug design, protein–protein interactions, and other biochemical and pharmaceutical applications.
An isopeptide bond is a type of amide bond formed between a carboxyl group of one amino acid and an amino group of another. An isopeptide bond is the linkage between the side chain amino or carboxyl group of one amino acid to the α-carboxyl, α-amino group, or the side chain of another amino acid. In a typical peptide bond, also known as eupeptide bond, the amide bond always forms between the α-carboxyl group of one amino acid and the α-amino group of the second amino acid. Isopeptide bonds are rarer than regular peptide bonds. Isopeptide bonds lead to branching in the primary sequence of a protein. Proteins formed from normal peptide bonds typically have a linear primary sequence.
Lysyl oxidase (LOX), also known as protein-lysine 6-oxidase, is an enzyme that, in humans, is encoded by the LOX gene. It catalyzes the conversion of lysine residues into its aldehyde derivative allysine. Allysine form cross-links in extracellular matrix proteins. Inhibition of lysyl oxidase can cause osteolathyrism, but, at the same time, its upregulation by tumor cells may promote metastasis of the existing tumor, causing it to become malignant and cancerous.
Allysine is a derivative of lysine that features a formyl group in place of the terminal amine. The free amino acid does not exist, but the allysine residue does. It is produced by aerobic oxidation of lysine residues by the enzyme lysyl oxidase. The transformation is an example of a post-translational modification. The semi-aldehyde form exists in equilibrium with a cyclic derivative.
Isodesmosine is a lysine derivative found in elastin. Isodesmosine is an isomeric pyridinium-based amino acid resulting from the condensation of four lysine residues between elastin proteins by lysyl-oxidase. These represent ideal biomarkers for monitoring elastin turnover because these special cross-links are only found in mature elastin in mammals.
Galactosidase, beta 1, also known as GLB1, is a protein which in humans is encoded by the GLB1 gene.
Pyridinoline, also known as Hydroxylysylpyridinoline, is a fluorescent cross-linking compound of collagen fibers. Crosslinks in collagen and elastin are derived from lysyl and hydroxylysyl residues, a process catalyzed by lysyl oxidase. Fujimoto and colleagues first described the isolation and characterization of a fluorescent material in bovine Achilles tendon collagen and termed it pyridinoline. It is reported to be present in collagen of bone and cartilage, but is absent in collagen of skin. It is not present in newly synthesized collagen and is formed from aldimine cross-links during maturation of collagen fibers.
Copper peptide GHK-Cu is a naturally occurring copper complex of the tripeptide glycyl-L-histidyl-L-lysine. The tripeptide has strong affinity for copper(II) and was first isolated from human plasma. It can be found also in saliva and urine.
In biochemistry, non-coded or non-proteinogenic amino acids are distinct from the 22 proteinogenic amino acids which are naturally encoded in the genome of organisms for the assembly of proteins. However, over 140 non-proteinogenic amino acids occur naturally in proteins and thousands more may occur in nature or be synthesized in the laboratory. Chemically synthesized amino acids can be called unnatural amino acids. Unnatural amino acids can be synthetically prepared from their native analogs via modifications such as amine alkylation, side chain substitution, structural bond extension cyclization, and isosteric replacements within the amino acid backbone. Many non-proteinogenic amino acids are important:
Lysine carboxypeptidase is an enzyme. This enzyme catalyses the following chemical reaction:
Elastin-like polypeptides (ELPs) are synthetic biopolymers with potential applications in the fields of cancer therapy, tissue scaffolding, metal recovery, and protein purification. For cancer therapy, the addition of functional groups to ELPs can enable them to conjugate with cytotoxic drugs. Also, ELPs may be able to function as polymeric scaffolds, which promote tissue regeneration. This capacity of ELPs has been studied particularly in the context of bone growth. ELPs can also be engineered to recognize specific proteins in solution. The ability of ELPs to undergo morphological changes at certain temperatures enables specific proteins that are bound to the ELPs to be separated out from the rest of the solution via experimental techniques such as centrifugation.
