Covalent bonds, proteins

Small tfbiquitin-like modifier represents a family of evolutionary conserved proteins that are distantly related in amino-acid sequence to ubiquitin, but share the same structural folding with ubiquitin proteins. SUMO proteins are covalently conjugated to protein substrates by an isopeptide bond through their carboxyl termini. SUMO addition to lysine residues of target proteins, termed SUMOylation, mediates post-transla-tional modification and requires a set of enzymes that are distinct from those that act on ubiquitin. SUMOylation regulates the activity of a variety of tar get proteins including transcription factors. 

Some proteins contain covalent disulfide (S— S) bonds that link the sulfhydryl groups of cysteinyl residues. Formation of disulfide bonds involves oxidation of the cysteinyl sulfhydryl groups and requires oxygen. Intrapolypeptide disulfide bonds further enhance the stability of the folded conformation of a peptide, while interpolypeptide disulfide bonds stabilize the quaternary structure of certain oligomeric proteins. 

Functionalization of CNTs with Proteins via Covalent or Non-Covalent Bond... 

Bonds and Forces - These properties are the mediators affecting the changes in size and conformation. Van der Waal forces, ionic bonds, hydrogen bonds, covalent bonds, and hydrophobic bonds all play a part in the original protein structure as well as in the modifications leading to altered functionality. Adequate correlations of these with functional properties are the subjects of "Functional Evaluations" 3). 

For high-performance lAC, the preferred solid support is a glass bead solid support coated wilh either protein-A or protein-A covalently linked with the antibody through a carbodiimide bond (165, 166). In either case, protein-A binds to the Fc portion of the antibody so that the combining sites are oriented to the mobile phase. Once the protein is attached, the lAC matrix is packed into the column either as a slurry or dry. Pump-slurry techniques use buffers with a low salt content, such as Tris or 0.01 M phosphate buffer to minimize friction and denaturation of the immobilized antibody (16). If the solid support consists of glass beads, the packing can be freeze-dried after antibody attachment and packed dry. 

Aggregation. Protein aggregation has two forms non-covalent (involving the interaction of two or more denatured proteins) and covalent (e.g., disulfide bond formation and/or peptide condensation reactions). 

The most common source of aflatoxins is moldy food, particularly nuts, some cereal grains, and oil seeds. The most notorious of the aflatoxins is aflatoxin B1( for which the structural formula is shown in Figure 19.1. Produced by Aspergillus niger, it is a potent liver toxin and liver carcinogen in some species. It is metabolized in the liver to an epoxide (see Section 7.3). The product is electrophilic with a strong tendency to bond covalently to protein, DNA, and RNA. Other common aflatoxins produced by molds are those designated by the letters B2, G1( G2, and M,. 

DNA adducts comprise nucleotides where chemical mutagenic substances are covalently bound. The common property of the chemical mutagenic substances is their electrophilic nature. Electrophilic sites (electron deficiency) bind to the nucleophilic sites of DNA or the proteins inducing covalent bonding leading to adduct formation, resulting in DNA conformation distortion, and replication and transcription blockage (Esaka etal. 2003). 

The structure of cytochrome c determined by Dickerson and his colleagues (23, 24, 25, 26) is depicted in Figure 1. The heme group, which lies in a crevice of the essentially globular protein, is covalently bonded to the protein by thioether bridges between the porphyrin ring and two cysteine residues in the peptide chain. The iron atom is situated... 

Radicals generated during peroxidation of lipids and proteins show reactivity similar to that of the hydroxyl radical however, their oxidative potentials are lower. It is assumed that the reactive alkoxyl radicals rather than the peroxyl radicals play a part in protein fragmentation secondary to lipid peroxidation process, or protein exposure to organic hydroperoxides (DIO). Reaction of lipid radicals produces protein-lipid covalent bonds and dityrosyl cross-links. Such cross-links were, for example, found in dimerization of Ca2+-ATPase from skeletal muscle sarcoplasmic reticulum. The reaction was carried out in vitro by treatment of sarcoplasmic reticulum membranes with an azo-initiator, 2,2/-azobis(2-amidinopropane) dihydrochloride (AAPH), which generated peroxyl and alkoxyl radicals (V9). 

In many of the haemoproteins we shall be discussing, the protoporphyrin IX group is held to the polypeptide chain only by hydrogen bonding, Van der Wools forces and iron-protein bonds. In several other cases, notably in cytochrome-c and its related compounds, the haem is covalently linked to the protein via substituents at the pyrrole carbon atoms. Cyto-chrome-c can be regarded as an iron protoporphyrin IX group with the addition of a protein cysteine side-chain across the vinyl double bonds giving two thio-ether links (Fig. 3). 

The overall shape of the protein, long and narrow or globular, is called its tertiary structure and is maintained by several different types of interactions hydrogen bonding, dipole-dipole interactions, ionic bonds, covalent bonds, and London dispersion forces between nonpolar groups. These bonds, which represent all the bonding types discussed in this text, are summarized in Fig. 22.25. 

Further analysis of the cross-linked intermediate showed that lysine at position 250 of one capsid subunit was covalently linked to the identical amino acid on a second subunit. In a model of the nucleocapsid derived from both cryoelectron microscopy (cryo-EM) analysis and X-ray analysis of the nucleocapsid protein, the covalent bond connects a pentamer of coat proteins with a hexamer of coat proteins, that is, it is an intercapsomer contact rather than an intracapsomer contact. This finding was unexpected because a possible assembly model proposed preassembly of pentameric and hexameric units that would recruit RNA for assembly into the final structure. In light of the new data, however, this scenario is unlikely. Instead, the initial assembly intermediate appears to be a coat protein dimer bound to RNA and the dimer spans the intercapsomere space. 

Whereas many coenzymes form noncovalent complexes with their respective apoenzymes, various flavoenzymes are characterized by covalently bound FMN (25) or FAD (Fig. 3). Covalent linkage involves the position 8a methyl group or the benzenoid carbon atom 6 of the flavin and a cysteine or histidine residue of the protein. The covalent CN or CS bond can be formed by autoxidation of the noncovalent apoen-zyme/coenzyme precursor complex as shown in detail for nicotine oxidase (59). 

From a purely chemical point of view, the fundamental fact is that proteins contain covalent bonds which are split by rather drastic means and more labile, noncovalent bonds which may be split or at least altered by denaturation alone. Two types of covalent structures exist, involving peptide bonds and disulfide bridges respectively. Both structures should be clearly differentiated since they are destroyed by quite different chemical treatments (hydrolysis for the first, oxidation or reduction for the second). They will be called for this reason, respectively, the primary and the secondary structures. Conversely, several inter- or intrachain, noncovalent... 

A molecule is formed when two or more atoms bond covalently. The carbohydrates and simple sugars you eat the proteins, fats, and DNA found in your body and the wool, cotton, and synthetic fibers in the clothes you wear all consist of molecules formed from covalently bonded atoms. 

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