Leucine relative hydrophobicity

Figure 3.S Schematic diagram of packing side chains In the hydrophobic core of colled-coll structures according to the "knobs In holes" model. The positions of the side chains along the surface of the cylindrical a helix Is pro-jected onto a plane parallel with the heUcal axis for both a helices of the coiled-coil. (a) Projected positions of side chains in helix 1. (b) Projected positions of side chains in helix 2. (c) Superposition of (a) and (b) using the relative orientation of the helices In the coiled-coil structure. The side-chain positions of the first helix, the "knobs," superimpose between the side-chain positions In the second helix, the "holes." The green shading outlines a d-resldue (leucine) from helix 1 surrounded by four side chains from helix 2, and the brown shading outlines an a-resldue (usually hydrophobic) from helix 1 surrounded by four side chains from helix 2.

The results of kinetic and X-ray crystallographic experiments on mutant carbonic anhydrases II, in which side-chain alterations have been made at the residue comprising the base of the hydrophobic pocket (Val-143), illuminate the role of this pocket in enzyme-substrate association. Site-specific mutants in which smaller hydrophobic amino acids such as glycine, or slightly larger hydrophobic residues such as leucine or isoleucine, are substituted for Val-143 do not exhibit an appreciable change in CO2 hydrase activity relative to the wild-type enzyme however, a substitution to the bulky aromatic side chain of phenylalanine diminishes activity by a factor of about 10 , and a substitution to tyrosine results in a protein which displays activity diminished by a factor of about 10 (Fierke et o/., 1991). 

Irreversible insolubilization of proteins may occur mainly through formation of both intermolecular disulfide and hydrophobic bonds. The product can be quite different depending on the relative contribution of these two types of bonds. The hydrophobic bonds are formed among the hydrophobic amino acid side chains contributed by valine, leucine, isoleucine, phenylalanine, etc. 

The term lyophobic interactions is intended to generalize the expres sion hydrophobic interactions to other solvents than water. Hydro-phobic interactions have been prominently implicated in determining the native configuration of proteins in aqueous solution. These interactions are actually not of a single relatively well-defined character, as are electrostatic or hydrogen bond interactions, but are rather a set of interactions responsible for the immiscibility of nonpolar substances and water. Proteins contain a substantial proportion of amino acids such as phenylalanine, valine, leucine, etc., with nonpolar side-chain residues. These nonpolar groups should tend, therefore, other factors permitting, to cluster on the... 

Polymers of the naturally occurring amino acids alanine, leucine, and methionine all show interactions which depend on the relative directions of the backbones. In contrast, poly(L-norleucine) shows less specific interactions clearly for the hydrophobic regions of proteins to function in a precise manner the natural amino acids are most suitable. 

Effects of amino acids The effects of 18 kinds of amino acids on crystal appearance are summarized in table 4. Among these amino acids tested, only leucine and tryptophan affected the change in crystal form from pillars to thin plates at concentrations relative to Lmore than 3%. These two amino acids are hydrophobic, so they might interact with the Lrphenylalanine skeleton in the crystal structure of di-L-phenylalanine sulfate monohydrate and are supposed to suppress growth in the a-axis direction. Isoleucine, valine and tyrosine which are analogous... 

The thermodynamic stability, the aggregation state, and the relative orientation of the helical strands in such peptides were shown to depend largely on the identity of the amino acid residues at positions a, d, e, and g. The use of leucine and valine at the hydrophobic core (positions a and glutamic acid and lysine at the e and g positions were shown to control equilibrium between dimeric and trimeric coiled-coil aggregation states." Peptide sequences that allow interconversion between dimeric and trimeric parallel coiled coils were found as productive templates to enhance substrate selectivity, catalytic efficiency, and turnover and were commonly used in peptide-replicating systems. 

Several other conserved amino acid residues are found in the vicinity of the conserved central His residue in both the a and yS-polypeptides. There is usually a leucine (a-polypeptide) or large aromatic residue (fi-polypeptide) located at His +4 (numbered relative to the conserved His, considered as position 0) and, located about one or-helix turn away at His -4, a small hydrophobic residue (Brunisholz et al., 1984 Theiler Zuber, 1984). Conserved tyrosine or tryptophan residues are found at positions His +4, +6 and +9 in the LHl, or His +9 in the LH2 yS-poly-peptides and at position His +11 in the LHl and His +9 and +14 in the LH2 -polypeptides (Zuber Cogdell, 1995). These aromatic amino acid residues create a particular microenvironment for the His-bound Bchl molecules, thereby influencing their spectral characteristics (Fowler et al., 1992 Sturgis et al., 1995). The structures of the LH2 and RC-LHl complexes are described in detail below. 

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