Amino functional side chains

A series of fluorene copolymers with amino-functionalized side chains 373 and 374 has been prepared by the same group (Chart 2.92). Upon quaternization, they gave copolymers 375 and 376, which were soluble in polar solvents (methanol, DMF, DMSO) [439]. Devices from the... 

Much of protein engineering concerns attempts to explore the relationship between protein stmcture and function. Proteins are polymers of amino acids (qv), which have general stmcture +H3N—CHR—COO , where R, the amino acid side chain, determines the unique identity and hence the stmcture and reactivity of the amino acid (Fig. 1, Table 1). Formation of a polypeptide or protein from the constituent amino acids involves the condensation of the amino-nitrogen of one residue to the carboxylate-carbon of another residue to form an amide, also called peptide, bond and water. The linear order in which amino acids are linked in the protein is called the primary stmcture of the protein or, more commonly, the amino acid sequence. Only 20 amino acid stmctures are used commonly in the cellular biosynthesis of proteins (qv). 

Through combined effects of noncovalent forces, proteins fold into secondary stmctures, and hence a tertiary stmcture that defines the native state or conformation of a protein. The native state is then that three-dimensional arrangement of the polypeptide chain and amino acid side chains that best facihtates the biological activity of a protein, at the same time providing stmctural stabiUty. Through protein engineering subde adjustments in the stmcture of the protein can be made that can dramatically alter its function or stabiUty. 

Other immobilization methods are based on chemical and physical binding to soHd supports, eg, polysaccharides, polymers, glass, and other chemically and physically stable materials, which are usually modified with functional groups such as amine, carboxy, epoxy, phenyl, or alkane to enable covalent coupling to amino acid side chains on the enzyme surface. These supports may be macroporous, with pore diameters in the range 30—300 nm, to facihtate accommodation of enzyme within a support particle. Ionic and nonionic adsorption to macroporous supports is a gentle, simple, and often efficient method. Use of powdered enzyme, or enzyme precipitated on inert supports, may be adequate for use in nonaqueous media. Entrapment in polysaccharide/polymer gels is used for both cells and isolated enzymes. 

Amino acids undergo reactions characteristic of the amino group (e.g., amide formation) and the carboxyl group (e.g., esterification). Amino acid side chains undergo reactions characteristic of the functional groups they contain. 

Proteins are the indispensable agents of biological function, and amino acids are the building blocks of proteins. The stunning diversity of the thousands of proteins found in nature arises from the intrinsic properties of only 20 commonly occurring amino acids. These features include (1) the capacity to polymerize, (2) novel acid-base properties, (3) varied structure and chemical functionality in the amino acid side chains, and (4) chirality. This chapter describes each of these properties, laying a foundation for discussions of protein structure (Chapters 5 and 6), enzyme function (Chapters 14-16), and many other subjects in later chapters. 

FIGURE4.il Reactions of amino acid side-chain functional groups. 

Evolution has provided the cell with a repertoire of 20 amino acids to build proteins. The diversity of amino acid side chain properties is enormous, yet many additional functional groups have been selectively chosen to be covalently attached to side chains and this further increases the unique properties of proteins. Diese additional groups play a regulatory role allowing the cell to respond to changing cellular conditions and events. Known covalent modifications of proteins now include phosphorylation, methylation, acetylation, ubi-quitylation, hydroxylation, uridylylation and glycosyl-ation, among many others. Intense study in this field has shown the addition of a phosphate moiety to a protein... 

The structural versatility of pseudopoly (amino acids) can be increased further by considering dipeptides as monomeric starting materials as well. In this case polymerizations can be designed that involve one of the amino acid side chains and the C terminus, one of the amino acid side chains and the N terminus, or both of the amino acid side chains as reactive groups. The use of dipeptides as monomers in the manner described above results in the formation of copolymers in which amide bonds and nonamide linkages strictly alternate (Fig. 3). It is noteworthy that these polymers have both an amino function and a carboxylic acid function as pendant chains. This feature should facilitate the attachment of drug molecules or crosslinkers,... 

In the Boc protection approach, benzyl groups are used to protect the reactive amino acid side-chain functionalities because they are more acid-stable than the Boc groups. Trifluoroacetic acid (TFA) is sufficient to remove the Boc groups while leaving the benzyl groups intact (Fig. 3). 

An alternative to modifying the functional group attached to fibrils is to utilise the chemistry present in the amino acid side chains. Furthermore, as peptides often undergo specific modification by enzymes in vivo, these could be harnessed for synthetic purposes. Qll (Ac-QQKFQFQFEQQ-Am, a fibril-forming peptide based on Pi 1-2), was coupled to lysine-based molecules by treatment with an enzyme (tissue transglutaminase, TGase) which results in a reaction between lysine and glutamine side chains [72] (Fig. 32). 

An affinity label is a molecule that contains a functionality that is chemically reactive and will therefore form a covalent bond with other molecules containing a complementary functionality. Generally, affinity labels contain electrophilic functionalities that form covalent bonds with protein nucleophiles, leading to protein alkylation or protein acylation. In some cases affinity labels interact selectively with specific amino acid side chains, and this feature of the molecule can make them useful reagents for defining the importance of certain amino acid types in enzyme function. For example, iodoacetate and A-ethyl maleimide are two compounds that selectively modify the sulfur atom of cysteine side chains. These compounds can therefore be used to test the functional importance of cysteine residues for an enzyme s activity. This topic is covered in more detail below in Section 8.4. 

The crystallographic structure of rubredoxin from Clostridium pasteurianum at 2.5 A, a resolution sufficient to reveal the sequence of several of the bulky amino acid side chains, shows the iron coordinated to two pairs of cysteine residues located rather near the termini of the polypeptide chain (Fig. 1). A related rubredoxin, with a three times larger molecular weight, from Pseudomonas oleovorans is believed to bind iron in a similar fashion. This conclusion is based on physical probes, especially electron paramagnetic resonance spectroscopy, all of which indicate that the iron is in each case situated in a highly similar environment however, the proteins display some specificity in catalytic function. 

Seebach, D., Sifferlen, T., Mathieu, P. A., Hane, A. M., Krell, C. M., Bierbaum, D. J., and Abele, S. (2000). CD spectra in methanol of /3-oligopeptides consisting of /3-amino acids with functionalized side chains, with alternating configuration, and with geminal backbone substituents. Fingerprints of new secondary structures Helv. Chim. Acta 83, 2849-2864. 

The amino acid side chains and enzymes cofactors provide functional groups that are used to make the reaction go faster by providing new pathways and by making existing pathways faster. 

The chiral distinction capability of cinchonan carbamate CSPs for underivatized amino acids has not been fully elucidated yet, in contrast to the large embodiment of A-acylated and A-arylated amino acid derivatives vide infra). However, it seems that chiral amino acids can be successfully resolved into enantiomers if the amino acid side chain R residue) contains a functionality that represents a strongly interactive binding site with the selector such as an extended aromatic ring system like in thyroxin (T4). 

Figure 16 (a) Structures of adenylation domain intermediates and inhibitors aminoacyl-sulfamoyl adenosine (AMS) and cisoid -like macrocyclic inhibitor, (b) Alkyne-functionalized chemical probe for NRPS A and PCP domains, (c) Structure of aminoacyl PCP, SNAC substrate analogue, and hydrolytically stable phosphopantetheinyl analogue, (d) Structure of vinylsulfonamide probe. R represents a peptide component and R an amino acid side chain. 

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