Hydrophilic side chains

Both in situ cross-linking of partially hydroly2ed polyacrylamides (69) and injection of quaternary ammonium salt polymers having long hydrophilic side chains (70) have been used to reduce the permeabiUty of water-producing 2ones adjacent to production wells. This permeabiUty reduction decreases the produced water oil ratio as does injection of polyacrylamide in high hardness brine to reduce permeabiUty (71). 

Figure 4.4 Schematic diagram of the structure of the a/p-barrel domain of the enzyme methylmalonyl-coenzyme A mutase. Alpha helices are red, and p strands are blue. The inside of the barrel is lined by small hydrophilic side chains (serine and threonine) from the p strands, which creates a hole in the middle where one of the substrate molecules, coenzyme A (green), binds along the axis of the barrel from one end to the other. (Adapted from a computer-generated diagram provided by P. Evans.)...

Since the outside of the barrel faces hydrophobic lipids of the membrane and the inside forms the solvent-exposed channel, one would expect the P strands to contain alternating hydrophobic and hydrophilic side chains. This requirement is not strict, however, because internal residues can be hydrophobic if they are in contact with hydrophobic residues from loop regions. The prediction of transmembrane p strands from amino acid sequences is therefore more difficult and less reliable than the prediction of transmembrane a helices. 

The most likely way for pardaxin molecules to insert across the membrane in an antiparallel manner is for them to form antiparallel aggregates on the membrane surface that then insert across the membrane. We developed a "raft"model (data not shown) that is similar to the channel model except that adjacent dimers are related to each other by a linear translation instead of a 60 rotation about a channel axis. All of the large hydrophobic side chains of the C-helices are on one side of the "raft" and all hydrophilic side chains are on the other side. We postulate that these "rafts" displace the lipid molecules on one side of the bilayer. When two or more "rafts" meet they can insert across the membrane to form a channel in a way that never exposes the hydrophilic side chains to the lipid alkyl chains. The conformational change from the "raft" to the channel structure primarily involves a pivoting motion about the "ridge" of side chains formed by Thr-17, Ala-21, Ala-25, and Ser-29. These small side chains present few steric barriers for the postulated conformational change. 

C13-0078. Assign each amino acid in Problem as possessing hydrophobic or hydrophilic side chains. Explain... 

Fig. 6.3 7-Transmembrane GPCR and extra-cellular view of odourant molecule shown in putative binding position hydrophobic and hydrophilic side-chains (O) shown for protein segments 3, 4 and 5 (from Sharon, 1998).

Chen R, Yue Z, Eccleston ME et al (2005) Modulation of cell membrane disruption by pH-responsive pseudo-peptides through grafting with hydrophilic side chains. J Control Release 108 63-72... 

Polyesters Having Reactive (Hydrophilic) Side-Chain Groups... 

To design amphiphilic and/or reactive copolymers containing aliphatic polyesters, one of the most promising approaches is copolymerization with functional monomers having protected reactive side-chain groups. Some kinds of monomers having reactive (hydrophilic) side-chain groups have been reported (Fig. 3). Recently, the synthesis of various types of functional polyesters has been reviewed [15-19],... 

Copolymers of a-hydroxy acids and a-amino acids are one type of poly(ester-amide)s and are called polydepsipeptides (PDPs) [17]. Since some of natural occurring a-amino acids, typically Asp, Glu, lysine (Lys), cysteine (Cys), serine (Ser), and threonine (Thr), possess reactive (hydrophilic) side-chain groups, PDPs... 

The amino acids can be classified as either hydrophobic or hydrophilic, depending on the ease ith which their side chains interact with water. In general, proteins fold so that amino adds ith hydrophobic side chains are in the interior of the molecule where they are protected from water and those with hydrophilic side chains are on the surface. 

Water-soluble PPEs have been made by the suitable choice of ionic and highly hydrophilic side chains. These PPEs will play a role in bio-type sensing applications (vide infra). A clever example is Schanze s synthesis of a sulfonato-substituted PPE [40, 41]. The NaOH-promoted reaction of [1, 2]oxathiolane-2,2-dioxide with 2,5-diiodohydroquinone gives a bis-sulfonate that can be coupled (Pd-catalyzed) to 1,4-diethynylbenzene to form a water-soluble PPE (Scheme 4) Table 6, entry 1). In a similar approach, Schanze et al. [42] made a... 

Hydrophilic side chain Salts, HP04 are P-sheet, Also Product from high pH, high temperature is P-sheet... 

AG1002 has rather low inhibitory potency with a binding constant of 0.55 pMThe low binding constant most likely reflects the absence of the group, the free energy required for desolvation of the hydrophilic side chains, and the charged N- and C-termini as well as entropic effects caused by the flexible nature of the heptapeptide. 

Drugs that cause phospholipidosis are cationic amphiphiles they contain a hydrophobic ring structure and a hydrophilic side chain with a positively charged amine group. Such chemicals can interact with either the ionic (e.g., chlorophentermine) or hydrophobic (e.g., amiodarone) moieties of phospholipids. 

It seems that for drugs to cause accumulation of phospholipids, the necessary physicochemical characteristic is the presence of both hydrophilic and lipophilic parts to the molecule, as exemplified by chlorphentermine (see chap. 3) (chap. 5, Fig. 1). They contain a hydrophobic ring structure and a hydrophilic side chain with a positively charged (cationic) amine group. Such molecules are known as cationic amphipathic drugs or CADs. Other drugs, all in use, known to cause phospholipidosis are amiodarone, chloroquine (chap. 5, Fig. 1), tafenoquine, and gentamycin. 

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