Proline properties

Consider, for example, the protein shown in Figure 15.7. The bottom left-hand amino acid is valine, which is linked to proline. Suppose for the sake of argument that we wanted to treat this valine quantum-mechanically and the rest of the protein chain according to the methods of molecular mechanics. We would have to draw a QM/MM boundary somewhere between valine and the rest of the protein. The link atoms define the boundary between the QM and the MM regions. A great deal of care has to go into this choice of boundary. The boundary should not give two species whose chemical properties are quite different from those implied by the structural formulae on either side of this boundary. 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

Schobert, B. and Tschesche, H., Unusual solution properties of proline and its interaction with proteins, Biochem. Biophys. Acta, 541, 270, 1978. 

The most advanced PDF inhibitor to emerge thus far from this collaboration is LBM-415 (12) (also called NVP PDF-713 or VIC-104959), an V-formyl-V-hydroxylamine compound still containing a proline residue at P2. The activity, PK properties, and in vivo efficacy data of (12) were presented at the 14th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) (2004) and the structure of this... 

T. P. Creamer (unpublished results). A plot of estimated (ASA) against %PPII content is given in Figure 5. At first glance, it would appear that there is little correlation between the two properties. However, three residues—proline, glycine, and glutamine—can be considered outliers, each for a specific reason. Proline has a high %PPII content in the polyproline-based host peptide used by Kelly et al. (2001) as a result of its unique properties as an imine. As discussed above, a proline that is followed in sequence by a second proline is restricted to the PPII conformation by steric interactions. 

A different strategy for measuring protease activity is based on the property of xanthene dyes to form H-type dimers (see Sect. 6.2.3) when they are in close proximity. These dimers are accompanied with a characteristic quenching of their fluorescence and, particularly for rhodamines, with a blue shift in the absorption spectrum [121, 122]. The probe D-NorFES-D designed to measure activity of elastase in HL-60 cells consists of an undecapeptide derivatized with one tetramethylrhodamine dye on each side. The sequence contains proline residues to create a bent structure and bring the two fluoro-phores in close proximity. Intact D-NorFES-D shows 90% of its fluorescence quenched plus a blue shift of the absorption spectrum. After addition of the serine protease elastase, an increase in the fluorescence and a bathochromic shift of the absorption spectrum is observed, resulting in an increase in the emission ratio [80],... 

Two structurally unrelated immunosuppressant drugs, cyclosporin A and FK506, have been shown to bind to separate proteins, which have in common the ability to catalyse the interconversion (8) of the cis and trans rotamers of peptidyl-proline bonds of peptide substrates. A profound change in the conformation, and hence the shape and binding properties of the protein, may result. The mechanism of this isomerization appears, on the basis of recent work (Rosen et al., 1990 Van Duyne et al., 1993 Albers et al., 1990), to involve simple twisting about the amide bond, rather than such alternatives as conversion to a C-N single bond by addition of a nucleophile to C=0.y The proteins which catalyse the reaction may be... 

The major side reaction associated with the use of mixed anhydrides is aminolysis at the carbonyl of the carbonate moiety (Figure 7.4, path B). The product is a urethane that resembles the desired protected peptide in properties, except that the amino-terminal substituent is not cleaved by the usual deprotecting reagents. Hence, its removal from the target product is not straightforward. The problem is serious when the residues activated are hindered (Val, lie, MeXaa), where the amounts can be as high as 10%. Other residues generate much less, but the reaction cannot be avoided completely, with the possible exception of activated proline (see Section 7.22). This is one reason why mixed anhydrides are not employed for solid-phase synthesis. 

From the fore gut of Laccophilus minutus, a Bacillus pumilus strain was isolated which produced maculosin, the diketopiperazine formed from proline and tyrosine [103] 24, phenyl malonate 25, N-acetylphenylalanine 26, N-acetyl-tryptophane 27 and 3,4-dihydroxybenzoic acid [ 103]. Maculosin which has also been isolated from several microorganisms and sponges shows phytotoxic and cytotoxic properties [103], 3,4-dihydroxybenzoic acid shows antioxidant properties and was already found in pygidial defensive glands of several dytis-cid beetles. 

Cytochrome c possesses three phyllogenetically-conserved proline residues that are presumably involved in the correct folding of the protein to form the native structure. The effects of substitutions at one of these sites, Pro-71 (Fig. 4), on the equilibrium and kinetics of yeast iso-2-cytochrome c unfolding have been studied by Nall and co-workers through comparison of the properties of a Thr... 

Seto B, Stadtman TC. 1976. Purification and properties of proline reductase from Clostridium sticklandii. J Biol Chem 251 2435-9. 

Stadtman TC, Elliott P. 1957. Studies on the Enzymatic Reduction of amino acids II. Purification and properties of ao-proline reductase and a prohne racemase from Clostridium sticklandii. 1 Biol Chem 228 983-97. 

Vitamin C is essential for the formation of collagen, the principal structural protein in skin, bone, tendons, and ligaments, being a cofactor in the hydroxylation of the amino acids proline to 4-hydroxyproline, and of lysine to 5-hydroxylysine. These hydroxyamino acids account for up to 25% of the collagen structure. Vitamin C is also associated with some other hydroxylation reactions, e.g. the hydroxylation of tyrosine to dopa (dihydroxyphenylalanine) in the pathway to catecholamines (see Box 15.3). Deficiency leads to scurvy, a condition characterized by muscular pain, skin lesions, fragile blood vessels, bleeding gums, and tooth loss. Vitamin C also has valuable antioxidant properties (see Box 9.2), and these are exploited commercially in the food industries. 

Robust peptide-derived approaches aim to identify a small drug-like molecule to mimic the peptide interactions. The primary peptide molecule is considered in these approaches as a tool compound to demonstrate that small molecules can compete with a given interaction. A variety of chemical, 3D structural and molecular modeling approaches are used to validate the essential 3D pharmacophore model which in turn is the basis for the design of the mimics. The chemical approaches include in addition to N- and C-terminal truncations a variety of positional scanning methods. Using alanine scans one can identify the key pharmacophore points D-amino-acid or proline scans allow stabilization of (i-turn structures cyclic scans bias the peptide or portions of the peptide in a particular conformation (a-helix, (i-turn and so on) other scans, like N-methyl-amino-acid scans and amide-bond-replacement (depsi-peptides) scans aim to improve the ADME properties." ... 

This approach has been extended to cyclic 1,3-dicarbonyls for the synthesis of tetrahydrobenzopyrane derivatives, also known as tetrahydrochromenes, which have attracted much attention due to their wide range of biological properties. Thus, a mixture of an aromatic aldehyde, dimedone, and malonitrile in aqueous media catalyzed either by (5)-proline [123] or tetramethylammoniura hydroxide (TMAH) [124] gave the bicyclic heterocycle in excellent yields (Scheme 35). 

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