Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides which have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides.
A hemeprotein, or heme protein, is a protein that contains a heme prosthetic group. They are a very large class of metalloproteins. The heme group confers functionality, which can include oxygen carrying, oxygen reduction, electron transfer, and other processes. Heme is bound to the protein either covalently or noncovalently or both.
Post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes translating mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.
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.
Nonribosomal peptides (NRP) are a class of peptide secondary metabolites, usually produced by microorganisms like bacteria and fungi. Nonribosomal peptides are also found in higher organisms, such as nudibranchs, but are thought to be made by bacteria inside these organisms. While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as discussed in this article.
In mathematical knot theory, the Hopf link is the simplest nontrivial link with more than one component. It consists of two circles linked together exactly once, and is named after Heinz Hopf.
Protein tags are peptide sequences genetically grafted onto a recombinant protein. Tags are attached to proteins for various purposes. They can be added to either end of the target protein, so they are either C-terminus or N-terminus specific or are both C-terminus and N-terminus specific. Some tags are also inserted at sites within the protein of interest; they are known as internal tags.
DNA supercoiling refers to the amount of twist in a particular DNA strand, which determines the amount of strain on it. A given strand may be "positively supercoiled" or "negatively supercoiled". The amount of a strand’s supercoiling affects a number of biological processes, such as compacting DNA and regulating access to the genetic code. Certain enzymes, such as topoisomerases, change the amount of DNA supercoiling to facilitate functions such as DNA replication and transcription. The amount of supercoiling in a given strand is described by a mathematical formula that compares it to a reference state known as "relaxed B-form" DNA.
The heat shock proteins HslV and HslU are expressed in many bacteria such as E. coli in response to cell stress. The hslV protein is a protease and the hslU protein is an ATPase; the two form a symmetric assembly of four stacked rings, consisting of an hslV dodecamer bound to an hslU hexamer, with a central pore in which the protease and ATPase active sites reside. The hslV protein degrades unneeded or damaged proteins only when in complex with the hslU protein in the ATP-bound state. HslV is thought to resemble the hypothetical ancestor of the proteasome, a large protein complex specialized for regulated degradation of unneeded proteins in eukaryotes, many archaea, and a few bacteria. HslV bears high similarity to core subunits of proteasomes.
In polymer chemistry and materials science, the term "polymer" refers to large molecules whose structure is composed of multiple repeating units. Supramolecular polymers are a new category of polymers that can potentially be used for material applications beyond the limits of conventional polymers. By definition, supramolecular polymers are polymeric arrays of monomeric units that are connected by reversible and highly directional secondary interactions–that is, non-covalent bonds. These non-covalent interactions include van der Waals interactions, hydrogen bonding, Coulomb or ionic interactions, π-π stacking, metal coordination, halogen bonding, chalcogen bonding, and host–guest interaction. The direction and strength of the interactions are precisely tuned so that the array of molecules behaves as a polymer in dilute and concentrated solution, as well as in the bulk.
Bissulfosuccinimidyl suberate (BS3) is a crosslinker used in biological research. It is a water-soluble version of disuccinimidyl suberate.
Self-assembling peptides are a category of peptides which undergo spontaneous assembling into ordered nanostructures. Originally described in 1993, these designer peptides have attracted interest in the field of nanotechnology for their potential for application in areas such as biomedical nanotechnology, tissue cell culturing, molecular electronics, and more.
Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar. Nucleic acid structure is often divided into four different levels: primary, secondary, tertiary, and quaternary.
Peptide amphiphiles (PAs) are peptide-based molecules that self-assemble into supramolecular nanostructures including; spherical micelles, twisted ribbons, and high-aspect-ratio nanofibers. A peptide amphiphile typically comprises a hydrophilic peptide sequence attached to a lipid tail, i.e. a hydrophobic alkyl chain with 10 to 16 carbons. Therefore, they can be considered a type of lipopeptide. A special type of PA, is constituted by alternating charged and neutral residues, in a repeated pattern, such as RADA16-I. The PAs were developed in the 1990s and the early 2000s and could be used in various medical areas including: nanocarriers, nanodrugs, and imaging agents. However, perhaps their main potential is in regenerative medicine to culture and deliver cells and growth factors.
In molecular biology, the cerato-platanin family of proteins includes the phytotoxin cerato-platanin (CP) produced by the Ascomycete Ceratocystis platani. CP homologs are also found in both the Ascomycota and the Basidiomycota branches of Dikarya. This toxin causes the severe plant disease: canker stain. This protein occurs in the cell wall of the fungus and is involved in the host-pathogen interaction and induces both cell necrosis and phytoalexin synthesis which is one of the first plant defense-related events. CP, like other fungal surface proteins, is able to self-assemble in vitro. CP is a 120 amino acid protein, containing 40% hydrophobic residues. It is one of the rare examples of protein in which contains a Hopf link. The link is formed by covalent loops - the pieces of protein backbone closed by two disulphide bonds. The N-terminal region of CP is very similar to cerato-ulmin, a phytotoxic protein produced by the Ophiostoma species belonging to the hydrophobin family, which also self-assembles.
Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends. When a knotted protein is “pulled” from both termini, it does not get disentangled. Knotted proteins are very rare, making up only about one percent of the proteins in the Protein Data Bank, and their folding mechanisms and function are not well understood. Although there are experimental and theoretical studies that hint to some answers, systematic answers to these questions have not yet been found.
Ribosomally synthesized and post-translationally modified peptides (RiPPs), also known as ribosomal natural products, are a diverse class of natural products of ribosomal origin. Consisting of more than 20 sub-classes, RiPPs are produced by a variety of organisms, including prokaryotes, eukaryotes, and archaea, and they possess a wide range of biological functions.
A stapled peptide is a short peptide, typically in an alpha-helical conformation, that is constrained by a synthetic brace ("staple"). The staple is formed by a covalent linkage between two amino acid side-chains, forming a peptide macrocycle. Staples, generally speaking, refer to a covalent linkage of two previously independent entities. Peptides with multiple, tandem staples are sometimes referred to as stitched peptides. Among other applications, peptide stapling is notably used to enhance the pharmacologic performance of peptides.
Polymer-protein hybrids are a class of nanostructure composed of protein-polymer conjugates. The protein component generally gives the advantages of biocompatibility and biodegradability, as many proteins are produced naturally by the body and are therefore well tolerated and metabolized. Although proteins are used as targeted therapy drugs, the main limitations—the lack of stability and insufficient circulation times still remain. Therefore, protein-polymer conjugates have been investigated to further enhance pharmacologic behavior and stability. By adjusting the chemical structure of the protein-polymer conjugates, polymer-protein particles with unique structures and functions, such as stimulus responsiveness, enrichment in specific tissue types, and enzyme activity, can be synthesized. Polymer-protein particles have been the focus of much research recently because they possess potential uses including bioseparations, imaging, biosensing, gene and drug delivery.
Coiled-coil drug delivery systems refer to drug delivery systems utilizing coiled-coil motifs capable of delivering disease-treating therapies, imaging agents, and vaccines to patients systemically or specifically. These systems are a form of peptide therapeutics and are capable of being engineered and finely tuned into different types of drug delivery vehicles based on the specific application required. The goal of a coiled-coil drug delivery system is to deliver cargo such as medication, imaging agents, biological molecules, or vaccines efficiently and specifically, in order to maximize the therapeutic efficacy and minimize unwanted side effects. This is achieved through fine-tuning the factors affecting the coiled coil’s oligomerization, resulting in modular systems that are highly specific for the intended application.
