Hydrophobic side chain burying

An essential feature of proteins is that they spontaneously fold into well-defined, three-dimensional structures. The single most important contributor to protein folding is the hydrophobic effect. It is imperative that amino acids such as leucine and valine, which have hydrophobic side chains, bury those side chains in the core of the protein, away from the aqueous environment of the cell. This hydrophobic collapse is a key early event in the process... 

Figure 3.6 Four-helix bundles frequently occur as domains in a proteins. The arrangement of the a helices is such that adjacent helices in the amino acid sequence are also adjacent in the three-dimensional structure. Some side chains from all four helices are buried in the middle of the bundle, where they form a hydrophobic core, (a) Schematic representation of the path of the polypeptide chain in a four-helrx-bundle domain. Red cylinders are a helices, (b) Schematic view of a projection down the bundle axis. Large circles represent the main chain of the a helices small circles are side chains. Green circles are the buried hydrophobic side chains red circles are side chains that are exposed on the surface of the bundle, which are mainly hydrophilic.

Hydrophobic interactions are the single most important stabilizing influence of protein native structure. The hydrophobic effect refers to the tendency of non-polar substances to minimize contact with a polar solvent such as water. Non-polar amino acid residues constitute a significant proportion of the primary sequence of virtually all polypeptides. These polypeptides will fold in such a way as to maximize the number of such non-polar residue side chains buried in the polypeptide s interior, i.e. away from the surrounding aqueous environment. This situation is most energetically favourable. 

Various efforts have been made to develop scales of hydrophobicity that can be used to predict the probability of finding a given amino acid side chain buried within a protein or in a surface facing water.59 73 A new approach has been provided by the study of mutant proteins. For example, deletion of a single -CH2- group from an interior hydrophobic region of a protein was observed to decrease the stability of the protein by 4.6 kj/mol.74... 

It can be seen from these data that the larger hydrophobic side chains are the most buried with the exception that cystine also tends to be quite inaccessible with 26, 72, 84, and 110 completely buried. All of the alanines are exposed, three of the four prolines are very exposed, three of the valines are completely buried as are Met 30, Phe 46, and Ser 90. Phenylalanine 8 is only accessible via a tunnel from the surface which is in fact occupied and blocked by one well-defined solvent molecule. The various residues of each polar amino acid have a wide range of exposure, but the larger residues tend to be most accessible with the exception of the tyrosines, which are quite variable. Residues in the active site region, 11, 12, 41, 43, 44, 45, 119, 120, 121, and 123, tend to be the extremes within each residue type but it should be noted that the motion of His 119 to the active position proposed later (Section VI) would increase the exposure of 11, 12, 41, and 44 and decrease the exposure of 121 and 109 in particular. The hydrophilic residues and especially the hydrophilic portions of these residues are generally ex-... 

The processes of both denaturation and renaturation are intimately related to the structures of native proteins. Alpha helices and g-pleated sheets constitute the main structures in most all native proteins. How the helices and sheets pack together depends on the geometrical characteristics of their surfaces. Contacts may exist on all sides and, although nonpolar (hydrophobic) side chains are buried inside, water may be present in crevices as well as in pools on the surface. It is through the disarrangement and rearrangement of all these, and more, structures that the pathways of denaturation and renaturation are directed. 

When the first soluble protein structures were revealed, it was immediately obvious that there was a striking preference for hydrophobic side chains in the interior and polar side chains on the surface (Perutz et al., 1965). This simple observation has had a powerful impact on our ability to predict structural features of soluble proteins (Eisenberg and McLachlan, 1986 Bowie et at, 1990, 1991). An examination of the first membrane protein structures found a much more subtle contrast between interior and surface residues. Rees et al. (1989a) found that the interiors of membrane proteins are about as hydrophobic as the interiors of soluble proteins, but the lipid facing residues were somewhat more apolar. Thus, residue preferences for buried or surface environments are much weaker for TM helices than for soluble proteins. A number of more recent surveys have noted a preference for small residues at helix interfaces (Javadpour et al., 1999 Jiang and Vakser,... 

This behavior can be seen as complementary to another aspect of protein folding the withdrawal of hydrophobic side chains from solvent. The latter minimizes perturbation by burying those portions of the polypeptide for which water is the poorest solvent. The former minimizes perturbation of solvent by what remains exposed. Not all biological macromolecules show so small an effect. Nucleic acids require for their hydration about twice the amount of water required by globular proteins (for heat capacity measurements comparing protein and tRNA, see Rupley and Siemankowski, 1986). It may be signihcant that DNA, with an extensive hydration shell, undergoes facile hydration-dependent conformational transitions, which are not found for proteins. 

The four-helix bundle is a common motif in which (usually) antiparallel a helices are packed side by side. It is found in myohemerythrin, various cytochromes, and a number of other proteins. A viral example is the coat protein of tobacco mosaic virus (TMV) (Bloomer et al, 1978). TMV represents the most common type, in which the helix axes are nearly antiparallel, off by 18°, coiled with a left-handed superhelical twist (Fig. 5 see Color Insert). The slight misalignment of the individual helix axes allows the side chains to interdigitate efficiently, burying internal hydrophobic side chains. 

Two highly conserved phenylalanines are located on /8D and /3E in the gap region (Phe-64 and Phe-70 of ALBP). They are visible in Fig. 7 and will be discussed in more detail below. The two rings have a similar orientation and appear to be stacked one on the other. These side chains, along with several other hydrophobic side chains (Val-49 and Ile-84 of ALBP), form a hydrophobic patch located near the bottom of the gap between the two strands. A similar small cluster of hydrophobic residues is observed in all six of the seven refined structures. This is adjacent to a buried residue that has a high preference for a glutamic acid at residue 72. The carboxylate of Glu-72 is involved in the formation of several hydrogen bonds to the side chains of residues 93 and 95. 

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