Polypeptides examples

Remember that, by convention, the NH2 group of each amino acid is written at the left the COOH group is at the right Other reagents split the chain at different points. By correlating the results of different hydrolysis experiments, it is possible to deduce the primary structure of the protein (or polypeptide). Example 23.10 shows how this is done in a particularly simple case. 

Carbodiimides are widely used to mediate the attachment of biomarkers to polypeptides. Examples include carbodiimides with ferrocenyl substituents. Also, peptides are covalently modified with ferrocenecarboxylic acid using EDCCl and N-hydroxy-succinimide to promote the coupling to surface lysines. They also mediate the attachment of substituents to single walled nanotubes (SWNTs) and multiwalled nanotubes (MWNTs). Also, microdots are attached to virus molecules using a water soluble carbodiimide. The attachment of viral DNA to gold particles is used in the manufacture of a new type of vaccine. 

In a non-polypeptide example, Gu, et al. [39] attempted to use four proteases (chymotrypsin, trypsin, subtilisin, and papain) to polymerize water-soluble polyamides from dimethyl adipate and diethylene triamine. However, only oligoamides were obtained. 

D-and L-Poly(lysine) both occur in a helical conformation in aqueous solution above pH 10. A 1 1 mixture of both helices in water precipitates in the form of regular, silk-like P-sheets (Fig. 9.5.3). This is a polypeptide example of the chiral bilayer effect. It demonstrates the importance of chiral uniformity not only for noncovalent, soft-membrane systems, but also for covalent polyamides. Helical fibers in aqueous gels do not survive the addition of enantiomeric fibers with the single exception of DNA (see Fig. 8.6.1). The precipitation of enantiomeric peptides containing more than one kind of amino acid has, however, not been reported so far. 

The polymers described so far have relatively flexible main chains which can result in complex confonnations. In some cases, tliey can double back and cross over tliemselves. There are also investigations on polymers which are constrained to remain in a confonnation corresponding, at least approximately, to a straight line, but which have amphiphilic properties tliat ensure tliat tliis line is parallel to tire water surface. Chiral molecules are one example and many polypeptides fall into tliis class [107]. Another example is cofacial phtlialocyanine polymers (figure C2.4.9). 

Example Crippen and Snow reported their success in developing a simplified potential for protein folding. In their model, single poin Ls rep resell t am in o acids. For th e avian pan creatic polypeptide, th c n ative structure is not at a poten tial m in imum. However, a global search fotin d that the most stable poten tial m in im urn h ad only a 1.8, An gstrom root-m ean-square deviation from thenative structu re. 

A polymer is a macromolecule that is constructed by chemically linking together a sequent of molecular fragments. In simple synthetic polymers such as polyethylene or polystyrer all of the molecular fragments comprise the same basic unit (or monomer). Other poly me contain mixtures of monomers. Proteins, for example, are polypeptide chains in which eac unit is one of the twenty amino acids. Cross-linking between different chains gives rise to j-further variations in the constitution and structure of a polymer. All of these features me affect the overall properties of the molecule, sometimes in a dramatic way. Moreover, or... 

For example, a polypeptide is synthesized as a linear polymer derived from the 20 natural amino acids by translation of a nucleotide sequence present in a messenger RNA (mRNA). The mature protein exists as a weU-defined three-dimensional stmcture. The information necessary to specify the final (tertiary) stmcture of the protein is present in the molecule itself, in the form of the specific sequence of amino acids that form the protein (57). This information is used in the form of myriad noncovalent interactions (such as those in Table 1) that first form relatively simple local stmctural motifs (helix... 

CeUs synthesize and secrete multiple hormones. Eor example, some ceUs in the anterior pituitary have the capacity to secrete both polypeptide hormones, ESH and LH. CeUs also can secrete different chemical classes of hormone, eg, ceUs in the adrenal meduUa synthesize and secrete the... 

Disulfides. The introduction of disulfide bonds can have various effects on protein stability. In T4 lyso2yme, for example, the incorporation of some disulfides increases thermal stability others reduce stability (47—49). Stabili2ation is thought to result from reduction of the conformational entropy of the unfolded state, whereas in most cases the cause of destabili2ation is the introduction of dihedral angle stress. In natural proteins, placement of a disulfide bond at most positions within the polypeptide chain would result in unacceptable constraint of the a-carbon chain. 

Arachin, the counterpart of glycinin in peanuts, consists of subunits of 60,000—70,000 mol wt which on reduction with 2-mercaptoethanol yield polypeptides of 41,000—48,000 and 21,000 mol wt (17) analogous to the behavior of glycinin. In addition to the storage proteins, oilseeds contain a variety of minor proteins, including trypsin inhibitors, hemagglutinins, and enzymes. Examples of the last are urease and Hpoxygenase in soybeans. 

The side groups of the amino acids vary markedly in size and chemical nature and play an important role in the chemical reactions of the fiber. For example, the basic groups (hisidine, arginine, and lysine) can attract acid (anionic) dyes, and in addition the side chains of lysine and hisidine are important sites for the attachment of reactive dyes. The sulfur-containing amino acid cysteine plays a very important role, because almost all of the cysteine residues in the fiber are linked in pairs to form cystine residues, which provide a disulfide bridge —S—S— between different polypeptide molecules or between segments of the same molecules as shown ... 

Although current matrix diffusional systems are most suitable for small-molecule compounds, it has been demonstrated (84) that soHd hydrophobic polymers allow dispersed powdered macromolecules of nearly any size, for example, ethylene—vinyl acetate copolymers containing dispersed polypeptides, to be released for periods exceeding 100 days. 

Until the early 1960s, laboratory iavestigators rehed on dialysis for the separation, concentration, and purification of a wide variety of biologic fluids. Examples iaclude removal of a buffer from a proteia solution or concentrating a polypeptide with hyperosmotic dialysate. Speciali2ed fixtures were sometimes employed alternatively, dialysis tubes, ie, cylinders of membrane about the si2e of a test tube and sealed at both ends, were simply suspended ia a dialysate bath. In recent years, dialysis as a laboratory operation has been replaced largely by ultrafiltration and diafiltration. 

Figure 2.14 shows examples of both cases, an isolated ribbon and a p sheet. The isolated ribbon is illustrated by the structure of bovine trypsin inhibitor (Figure 2.14a), a small, very stable polypeptide of 58 amino acids that inhibits the activity of the digestive protease trypsin. The structure has been determined to 1.0 A resolution in the laboratory of Robert Huber in Munich, Germany, and the folding pathway of this protein is discussed in Chapter 6. Hairpin motifs as parts of a p sheet are exemplified by the structure of a snake venom, erabutoxin (Figure 2.14b), which binds to and inhibits... 

Protein molecules that have only one chain are called monomeric proteins. But a fairly large number of proteins have a quaternary structure, which consists of several identical polypeptide chains (subunits) that associate into a multimeric molecule in a specific way. These subunits can function either independently of each other or cooperatively so that the function of one subunit is dependent on the functional state of other subunits. Other protein molecules are assembled from several different subunits with different functions for example, RNA polymerase from E. coli contains five different polypeptide chains. 

The fundamental unit of tertiary structure is the domain. A domain is defined as a polypeptide chain or a part of a polypeptide chain that can fold independently into a stable tertiary structure. Domains are also units of function. Often, the different domains of a protein are associated with different functions. For example, in the lambda repressor protein, discussed in Chapter 8, one domain at the N-terminus of the polypeptide chain binds DNA, while a second domain at the C-terminus contains a site necessary for the dimerization of two polypeptide chains to form the dimeric repressor molecule. 

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