Amino acids hydrophobic side chains

Hydrophobicity scales measure the degree of hydrophobicity of different amino acid side chains... 

SNARE motifs spontaneously assemble into SNARE complexes. These consist of a bundle of four intertwined a-helices that are connected by a total of 16 layers of mostly hydrophobic amino acid side chains. In the middle of the bundle, there is a highly conserved and polar 0-layer consisting of three glutamine and one arginine residue. These residues are among the most conserved in the SNARE superfamily and led to a classification of SNAREs into Q- and R-SNAREs, respectively. Different fusion steps require different sets of SNAREs but some SNAREs can participate in different complexes, and some fusion steps involve several SNARE complexes that appear to operate in parallel and independently. 

Higher orders of protein structure are stabilized primarily—and often exclusively—by noncovalent interactions. Principal among these are hydrophobic interactions that drive most hydrophobic amino acid side chains into the interior of the protein, shielding them... 

Interaction with a lipid bilayer driven by a potential difference and by polar and/or hydrophobic forces between the amino acid side chains of the pardaxin tetramers and the polar membrane lipid head group triggers insertion from a "raft" like structure. 

Imately 65 X 55 X 50 It Is composed of four polypeptide chains each resembling quite closely the myoglobin chain The three dimensional structure of the subunits Is held together by weak noncovalent bonds The polar amino acid side chains are In contact with the solvent, and the nonpolar residues are located In the Interior of the molecule or In regions which form the contacts between chains The heme group Is located In a pocket In each chain residues In contact with heme are Invariable ( e are the same In different mammalian hemoglobins) and the bonds between heme and chain are hydrophobic Interactions Contacts between like chains (a-a are... 

Fig. 3. (A) Model of the proposed pore forming part of K channel subunits. Segments S5 and S6 are possibly membrane-spanning helices. The helices are connected by a hydrophobic segment H5 which may be tucked into the lipid bilayer [48]. H5 is flanked by two proline residues P. Adjacent to these proline residues are amino acid side chains ( ) important for external TEA binding [45,46]. Approximately halfway between these two proline residues are amino acid side chains ( ) affecting internal TEA binding [46,47] and K channel selectivity [48]. (B) Mutations are indicated which affect in Shaker channels external TEA (TEAe) or internal TEA (TEA,) binding. Concentrations of TEA for half block of the wild-type and mutant K channels are given at the right-hand side of the corresponding sequence. Data have been compiled from [45-47].

Proteins represent another major group of membrane components. They play structural roles and/or are involved in many cellular processes, which are strictly coupled to membranes. Proteins can be either entirely embedded within the bilayer, or they might be firmly anchored (e.g. by a hydrophobic transmembrane segment composed of hydrophobic amino acid side-chains or as lipoprotein), or they can be just associated with the surface. 

The precise chemical interactions between an adhesin and its receptor are also important. For example, direct- and water-mediated hydrogen bonds are the most important interactions within the carbohydrate-recognition domain in carbohydrate-binding adhesins on the host cell surface (Weis and Drickamer, 1996). Nonpolar van der Waals interactions and hydrophobic "stacking of the receptor oligosaccharide rings with aromatic amino acid side chains of the bacterial adhesin protein also contribute to oligosaccharide-protein interactions. X-ray structural... 

Let s go back to the classification of the amino acid side chains (chapter 10). Several of these are hydrocarbons greasy, fat-like side chains. Look at the side chains of leucine, isoleucine, valine, and phenylalanine as examples. Eats and water do not mix. Eats are termed hydrophobic, water-hating. It follows that these side chains will try to do what they can to get out of contact with water. The obvious way to do this is to hide in the center of the protein structure, where they may enjoy the company of like-minded amino acid side chains and avoid that of water molecules—sort of a molecular ethnic cleansing. 

We encountered the properties of hydrophilic and hydrophobic molecules in our thoughts about driving forces for formation of three-dimensional protein structures. Specifically, proteins fold in a way that puts most of the hydrophobic amino acid side chains into the molecular interior, where they can enjoy each other s company and avoid the dreaded aqueous environment. At the same time, they fold to get the hydrophilic amino acid side chains onto the molecular surface, where they happily interact with that enviromnent. The same ideas are important for the double-stranded helical structure of DNA. The hydrophobic bases are localized within the double hehx, where they interact with each other, and the strongly hydrophilic sugar and phosphate groups are exposed on the exterior of the double helix to the water environment. Now, we need to understand something more about structural features that control these properties. 

The H-site is formed of clusters ofnon-polar amino acid side chains which provide a highly hydrophobic surface, which, in the absence of a drug substrate is open to bulk solvent Binding of substrates to this site has been shown to relate to increased lipophilicity for substrates (4-hydroxyalkenes). The actual conjugation reaction, with the thiolate anion acting as a nucleophile proceeds via an SN2-type mechanism yielding the deactivated product... 

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