Hydrophobic residue

The sequence space of proteins is extremely dense. The number of possible protein sequences is 20. It is clear that even by the fastest combinatorial procedure only a very small fraction of such sequences could have been synthesized. Of course, not all of these sequences will encode protein stmctures which for functional purjDoses are constrained to have certain characteristics. A natural question that arises is how do viable protein stmctures emerge from the vast sea of sequence space The two physical features of folded stmctures are (l)in general native proteins are compact but not maximally so. (2) The dense interior of proteins is largely made up of hydrophobic residues and the hydrophilic residues are better accommodated on the surface. These characteristics give the folded stmctures a lower free energy in comparison to all other confonnations. 

Water-soluble globular proteins usually have an interior composed almost entirely of non polar, hydrophobic amino acids such as phenylalanine, tryptophan, valine and leucine witl polar and charged amino acids such as lysine and arginine located on the surface of thi molecule. This packing of hydrophobic residues is a consequence of the hydrophobic effeci which is the most important factor that contributes to protein stability. The molecula basis for the hydrophobic effect continues to be the subject of some debate but is general considered to be entropic in origin. Moreover, it is the entropy change of the solvent that i... 

Reversed-phase chromatography rehes on significantly stronger-hydrophobic interactions than in HIC, which can result in unfolding and exposure of the interior hydrophobic residues, i.e., leads to protein denaturation and irreversible inactivation as such, RPC depends... 

An off-lattice minimalist model that has been extensively studied is the 46-mer (3-barrel model, which has a native state characterized by a four-stranded (3-barrel. The first to introduce this model were Honeycutt and Thirumalai [38], who used a three-letter code to describe the residues. In this model monomers are labeled hydrophobic (H), hydrophilic (P), or neutral (N) and the sequence that was studied is (H)9(N)3(PH)4(N)3(H)9(N)3(PH)5P. That is, two strands are hydrophobic (residues 1-9 and 24-32) and the other two strands contain alternating H and P beads (residues 12-20 and 36-46). The four strands are connected by neutral three-residue bends. Figure 3 depicts the global minimum confonnation of the 46-mer (3-barrel model. This (3-barrel model was studied by several researchers [38-41], and additional off-lattice minimalist models of a-helical [42] and (3-sheet proteins [43] were also investigated. 

Figure 3 The mimmum energy conformation of the off-lattice 46-mer P-baiTel model. Hydrophobic residues are in gray, hydrophilic residues in black, and neutral residues are white. (Adapted from Ref. 44.)...

The first sequence is from the enzyme citrate synthase, residues 260-270, which form a buried helix the second sequence is from the enzyme alcohol dehydrogenase, residues 355-365, which form a partially exposed helix and the third sequence is from troponin-C, residues 87-97, which form a completely exposed helix. Charged residues are colored red, polar residues ate blue, and hydrophobic residues are green. 

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

Lesk and Chothia did find, however, that there is a striking preferential conservation of the hydrophobic character of the amino acids at the 59 buried positions, but that no such conservation occurs at positions exposed on the surface of the molecule. With a few exceptions on the surface, hydrophobic residues have replaced hydrophilic ones and vice versa. However, the case of sickle-cell hemoglobin, which is described below, shows that a charge balance must be preserved to avoid hydrophobic patches on the surface. In summary, the evolutionary divergence of these nine globins has been constrained primarily by an almost absolute conservation of the hydro-phobicity of the residues buried in the helix-to-helix and helix-to-heme contacts. 

In barrels the hydrophobic side chains of the a helices are packed against hydrophobic side chains of the p sheet. The a helices are antiparallel and adjacent to the p strands that they connect. Thus the barrel is provided with a shell of hydrophobic residues from the a helices and the p strands. 

There is one exception to the rule that requires bulky hydrophobic residues to fill the interior of eight-stranded a/p barrels in order to form a tightly packed hydrophobic core. The coenzyme Biz-dependent enzyme methylmalonyl-coenzyme A mutase, the x-ray structure of which was determined by Phil Evans and colleagues at the MRC Laboratory of Molecular... 

Leucine residues 2, 5, 7, 12, 20, and 24 of the motif are invariant in both type A and type B repeats of the ribonuclease inhibitor. An examination of more than 500 tandem repeats from 68 different proteins has shown that residues 20 and 24 can be other hydrophobic residues, whereas the remaining four leucine residues are present in all repeats. On the basis of the crystal structure of the ribonuclease inhibitor and the important structural role of these leucine residues, it has been possible to construct plausible structural models of several other proteins with leucine-rich motifs, such as the extracellular domains of the thyrotropin and gonadotropin receptors. 

Figure S.4 The binding site for retinol inside the RBP barrel is lined with hydrophobic residues. They provide a hydrophobic surrounding for the hydrophobic part of the retinol molecule.

Figure S.S Amino acid sequence of p strands 2 3 4 in human plasma retinol-binding protein. The sequences are listed in such a way that residues which point into the barrel are aligned. These hydrophobic residues are arrowed and colored green. The remaining residues are exposed to the solvent.

Dimerization of the Ce-zinc cluster transcription factors involves an a-helical coiled coil in the dimerization region. Coiled coils, often called leucine zippers, are also found in a large group of transcription factors that do not contain zinc. The leucine zipper is made up of two a helices in a coiled coil with every seventh residue leucine or some other large hydrophobic residue, such as isoleucine or valine. Leucine zipper transcription factors (b/zip) include factors characterized by heterodimerization, for example Fos and Jun. The a-helical DNA-binding motifs of the heterodimers recognize quite different base sequences and are continous with the a helices of the zipper. 

Gram-negative bacteria are surrounded by two membranes, an inner plasma membrane and an outer membrane. These are separated by a periplasmic space. Most plasma membrane proteins contain long, continuous sequences of about 20 hydrophobic residues that are typical of transmembrane a helices such as those found in bacteriorhodopsin. In contrast, most outer membrane proteins do not show such sequence patterns. 

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. 

This pair of chlorophyll molecules, which as we shall see accepts photons and thereby excites electrons, is close to the membrane surface on the periplasmic side. At the other side of the membrane the symmetry axis passes through the Fe atom. The remaining pigments are symmetrically arranged on each side of the symmetry axis (Figure 12.15). Two bacteriochlorophyll molecules, the accessory chlorophylls, make hydrophobic contacts with the special pair of chlorophylls on one side and with the pheophytin molecules on the other side. Both the accessory chlorophyll molecules and the pheophytin molecules are bound between transmembrane helices from both subunits in pockets lined by hydrophobic residues from the transmembrane helices (Figure 12.16). 

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