Hydrophobic sidechains

Within the cellulosome complex, type I dockerin domain is responsible for incorporating its associated glycosyl hydrolase in the bacterial cellulosome via interaction with a reception domain, the cohesin domain. The three-dimensional solution structure of the 69-residue dockerin domain from the thermophilic Clostridium thermocellum (Topt = 55-65 °C) was solved by NMR and was found to consist of two Ca " -binding loop-helix motifs connected by a linker. Each Ca " -binding subdomain is stabilized by a cluster of buried hydrophobic sidechains. Recently, the NMR sequence-specific resonance assignment of type II cohesin module from C. thermocellum has been published. ... 

Currently available BAS include cholestyramine, colestipol and colesevelam hydrochloride (colestimide). Cholestyramine comprises a long-chain polymer of styrene with divinylbenzene trimethylbenzylammonium groups, whereas colestipol is a long-chain polymer of l-chloro-2,3-epoxypropane with diethylenetriamine. Colesevelam HCl is poly(allylamine hydrochloride) cross-linked with epichlorohydrin and alkylated with 1-bromodecane and 6-bromo-hexyl-trimethylammonium bromide. Bile-acid binding is enhanced and stabilised in the latter compound by long hydrophobic sidechains, increased density of primary amines, and quaternary amine sidechains. For this reason, colesevelam HCl exhibits increased affinity, specificity and capacity to bind bile acids compared with the other BAS. Colesevelam HCl also binds dihydroxy and trihydroxy bile acids with equal affinity, contrasting with cholestyramine and colestipol that preferentially bind dihydroxy bile acids (CDCA and deoxycholic acid). The latter BAS can lead to an imbalance towards trihydroxy bile acids and a more hydrophilic bile-acid pool. 

A host of carriers, with a wide variety of ion selectivities, have been proposed for this task. Most of them have been used for the recognition of alkali and alkaline metal cations (e.g., clinically relevant electrolytes). A classical example is the cyclic depsipeptide valinomycin (Fig. 5.13), used as the basis for the widely used ISE for potassium ion (38). This doughnut-shaped molecule has an electron-rich pocket in the center into which potassium ions are selectively extracted. For example, the electrode exhibits a selectivity for K+ over Na+ of approximately 30,000. The basis for the selectivity seems to be the fit between the size of the potassium ion (radius 1.33 A) and the volume of the internal cavity of the macrocyclic molecule. The hydrophobic sidechains of valinomycin stretch into the lipophilic part of the membrane. In addition to its excellent selectivity, such an electrode is well behaved and has a wide working pH range. Strongly acidic media can be employed because the electrode is 18,000 times more responsive to K+ than to H+. A Nernstian response to potassium ion activities, with a slope of 59mV/pK+, is commonly observed... 

Figure 5 Structural features of bacteriocin AS-48. (a) Structural ensemble representing the solution structure of AS-48 (PDB code 1E68). (b) Packing of hydrophobic sidechains in the core of AS-48. Residues with less than 20% surface exposure are shown and labelled with residue numbers, (c) Ribbon diagram illustrating the orientation of the five helices and comparison to the saposin fold represented by (d) the solution structure of NK-lysin (PDB code 1NKL).

One could investigate the polar and steric effects of the hydrophobe sidechain using the appropriate substituent constants and equation 6 ... 

The relative values of c" and "d" suggest that polar effects have a greater effect on the cmc value than steric effects of linear alkyl hydrophobe sidechains. Molecular models suggest that the steric effect of the sidechain is limited to the closest 2-5 EO groups of the 6-12 member EO chain. Even for the longest hydrophobe sidechains a substantial portion of the hydrophile chain is uninfluenced by steric effects. However, inductive effects, while weak, could still be transmitted through the chemical bonds of the hydrophile chain for much of its length. 

The direction of activity for disubsdtuted aryl ring compounds was reasonably predicted by averaging the there is no large interactions between the ring substitutents. With the optimum aryl substituent in hand, the hydrophobic sidechain (quadrant II) was re-investigated. Table IV lists the results which verified that the para-chlarophenyl, butyl substituted compound was one of the best Some further verification of the substituent scheme was conducted by preparing other mixed quadrant I, quadrant II variants. The best compounds were subjected to additional studies, including systemic and curative tests, and within the scope of alkyl and alkenyl sidechains, myclobutanil, was determined to be the best compound, overall. 

Hydropathy plots are used to predict buried and exposed regions of a protein. Use of these plots was first demonstrated by Rose and Rose and Roy. Hydropathy plots are based on Chothia s " observation that hydro-phobic residues (amino acid residues with hydrophobic sidechains) tend to be buried when the protein exists in its native conformation. More than one set of hydropathy values is available. The best known hydropathy indexing methodology is that of Kyte and Doolittle. 

Gramicidin A. Gramicidin A (gA) is a small 15-residue antibiotic peptide formed as a dimer in a head-to-head (HH) or a double-helical (DH) conformation. " Because of its simplicity and reduced dimensions, the gA structure has been studied extensively and simulated as a model for ion channels,and has emerged as a benchmark for simulation approaches. " The structure exposes its hydrophobic sidechains to the lipid membrane that embeds the protein. The molecular structure of gA has been known for three decades,and has been recently resolved with NMR spectroscopyThe relation of the structure seen spectroscopically to that... 

Figure 1 Atomic stracture of a (a) double-helical (Imic.pdb ) and (b) head-to-head (Imag.pdb ) conformation of Gramicidin A. The pictures to the left show the backbone representation perpendicular to the pore. The pictures to the right show a view parallel to the channel that includes the hydrophobic sidechains. The pictures were generated with VMD. ...

The sidechain of methionine-192 plays an important role in a-chymotrypsin, being implicated in both the activation of the enzyme from its zymogen and the binding and orientation of a-chymotrypsin substrates during catalysis. X-ray diffraction studies reveal that the sidechain may act as a lid over a hydrophobic sidechain binding pocket known as the tosyl hole. Modification of the sidechain of Met-192 therefore has kinetic consequences thus the addition of an aromatic moiety allows it to bind in the tosyl pocket and to compete for this site with substrate or inhibitor. The behavior of such an aromatic moiety may conveniently be followed via... 

Cyclosporine A (16) is a natural product which serves as the quintessential Beyond Rule-of-5 macrocycle, able to overcome the disadvantages of high MW (1203 Daltons) and polarity (11 amide bonds) and achieve excellent absorption (Fa = 0.86). It appears able to do this by a combination of N-methylation (seven Ai-methylated amides), intramolecular hydrogen bonding (four observed in the crystal structure), a compact 3D structure incorporating p turns, and a preponderance of hydrophobic sidechains. This same feature set is seen in many of the designed orally bioavailable macrocycles in Tables 10.7 and 10.8 and perhaps most closely adopted in the design of 24. 

Polyacrylic acid and polyacrylamide are typical water-soluble polymers that can be functionalized by the addition of hydrophobic sidechains that turn them into amphiphilic materials. The usual processes would include esterification and amida-tion of the carboxyl groups. Similar results can be obtained by preparing copolymers of acrylic and methacryhc acid with the desired preformed esters. A third alternative is the formation of polyacrylate or polymethacrylate esters followed by controlled saponification or hydrolysis to a desired degree of free carboxyl groups. The derivitization of acrylics is also an essentially random process, so that the exact characteristics of the final product may be somewhat variable. Close process control can, again, ensure a functionally reproducible product. 

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