Buried residues, prediction

Figure 10.9 Tridimensional structure of GM-CSF.148 The tridimensional structure shows that the four methionine residues present on the molecule have different degrees of solvent exposure. The sulfur atoms are either fully exposed (residues M46 and M79), partially exposed (residue M36), or totally buried (residue M80). Forced oxidation experiments described in the text show that residue M80 is unaffected, whereas local structural constraints make M79 less susceptible to oxidation than predicted by the model. 

Interpretation of the electron density maps showed that the large subunit could not be modelled beyond His536 (Fig. 6.10), that is fifteen amino acids short of the 551 residues predicted by the nucleotide sequence (Table 6.2). At about the same time, the cleavage of this fifteen-residue stretch, which is performed by a specific protease, was reported to be an obligatory step for the maturation of the enzyme (Menon et al. 1993). It is also of interest to note that in all [NiFe] hydrogenase crystal structures this buried C-terminal histidine is ligated to a metal atom which is either a magnesium or an iron (see above). 

Rost and Sander (1994b) developed another neural network system to predict the relative solvent accessibility (PHDacc). The one-level network system used the same input information as that in the PHDsec sequence-to-structure network, and mapped it to ten output units coded for ten relative levels of solvent accessibility. PHDacc was superior to other methods in predicting the residues in either of the two states, buried or exposed. Entirely buried residues (<4% accessible) were predicted best. 

Secondary Structure Prediction and the Prediction of Buried Residues From Multiple Sequence Alignment... 

The most common location for an a helix in a protein structure is along the outside of the protein, with one side of the helix facing the solution and the other side facing the hydrophobic interior of the protein. Therefore, with 3.6 residues per turn, there is a tendency for side chains to change from hydrophobic to hydrophilic with a periodicity of three to four residues. Although this trend can sometimes be seen in the amino acid sequence, it is not strong enough for reliable stmctural prediction by itself, because residues that face the solution can be hydrophobic and, furthermore, a helices can be either completely buried within the protein or completely exposed. Table 2.1 shows examples of the amino acid sequences of a totally buried, a partially buried, and a completely exposed a helix. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

However, just considering the individual properties of each amino acid type is not enough to determine its accessibility to the surrounding aqueous environment. There have been many attempts at developing analytical models with predictive value for determining buried or surface accessible amino acids in a folded polypeptide chain. These studies have concluded fractional assignments for each residue that relate to its accessible surface area (ASA) or its solvent exposed area (SEA). 

Fig. 3. An example of fold topologies predicted from the maximization of secondary structure and the minimization of solvent-exposed hydrophobic residues. On the right is the basic three-dimensional packing of the secondary structure elements. Although no restrictions on the connectivity between these elements is shown, maximization of the secondary structure does imply some restrictions, such as those observed in most four-helix bundles and in all a/fi eight barrels. The top view on the right displays, as shaded, the buried hydrophobic sides of the amphipathic a helices and fi sheets.

As has been discussed recently (Murphy etal., 1992), the formalism developed by Lee (1991) predicts not only the convergence behavior discussed by the author (i.e., when the apolar and polar contributions to the enthalpy are identical). For the case in which the buried polar area per residue is constant it also predicts convergence at the point at which the apolar contribution to the enthalpy is zero. In Fig. 3 we have plotted AH0 versus ACp normalized either per residue (Fig. 3a) or per buried total surface area (Fig. 3b), in order to compare the results of the two approaches. It is clear that the linearity is better when the data are normalized to the number of residues than when they are normalized to the buried surface area. This is presumably due to variabilities in the surface area calculation. The slope of the line in Fig. 3a is —72.4, which corresponds to a convergence temperature, Th, of 97.4°C for this set of proteins. If the above analysis is correct, then this temperature corresponds to The value of AH is 1.32kcal (mol res)-1 or 33.6 cal (mol A2)-1 of polar surface area. 

A similar secondary structure is predicted for the 11S globulin. However, differences appear in the tertiary structure as shown by the CD spectrum in the 240-320 nm region. Both tyrosine and tryptophan appear to be buried in the hydrophobic interior of the 11S globulin. CD spectra for both proteins in 0.1 N sodium hydroxide also reveal significant differences in tertiary structure (11). Tyrosine residues in the 7S protein appear to ionize much more readily than in the 11S protein as determined by the magnitude of the positive peak at 253 nm. 

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,... 

Larger molecules such as proteins usually do not fit these predictions, probably because the molecules adopt an ordered three-dimensional structure in which many of the hydrophobic residues are buried within the structure and unavailable for interaction with the reversed phase. As might be expected from the proposed mechanism of separation, the retention of proteins on reversed-phase columns is not related to molecular weight of the sample, but rather the surface polarity of the molecule. Table I shows that there is a correlation of hydrophobicity (measured by mole % of strongly hydrophobic residues) with retention order for seven different proteins. It is unlikely that the retention of all proteins on a reversed-phase column can be correlated in this manner, because many protein structures have few nonpolar residues exposed to the aqueous environment. For example, although the major A and C apolipoproteins are eluted from a ju-Bondapak alkylphenyl column in an order which can be related to the proposed secondary structures, there is little correlation with the content of hydrophobic residues in each protein and the degree of interaction with the stationary phase. A similar lack of correlation be-... 

The results presented here indicate that the two Asn side-chains found on the Max LZ are buried at the interface of the c-Myc-Max heterodimeric LZ. In summary, we have described NOEs between the H8 protons of both Asn side-chains and protons from the residues forming the holes in which they are predicted to pack on the c-Myc LZ. 

A general feature of most of the known membrane protein structures is the occurrence of hydrophobic segments forming a-helices, which are buried in the bilayer. To span the lipid bilayer an a-helix needs about 20 residues. From the amino acid sequence it is therefore possible to predict trans-membrane a-helices. 

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