Buried surfaces

The slow rate of hydration for buried surfaces is desirable from a service point of view, but makes the study and evaluation of the durability of surface treatments difficult unless wedge tests (ASTM D3762) or similar tests are used to accelerate the degradation. As for the wedge test, the stress at the crack tip, together with the presence of moisture at the tip, make this a more severe test than soaked lap shear specimens or similar types and therefore a better measure of relative durability. 

Fig. 8. Calculated values of (top) /(0), (center) /(75), and (bottom) J (653) for acid-unfolded apoMb, pH 2.3, 25°C. The horizontal lines show the mean values of J (75) (0.19 ns rad-1) and /(653) (0.020 ns rad-1), and the 10% trimmed mean value of J (0) (0.97 ns rad-1). The average buried surface area, calculated using the values of Rose and co-workers (Rose et al., 1985) and averaged over a seven-residue window, is also shown in the center figure (solid line, no data points, right-hand scale). Black bars indicate the positions of the helices in the folded structure of myoglobin.

In the PPA-a-AI 1 complex, a flexible loop of the enzyme, which would normally contact the substrate, is pushed outward to allow entry of the inhibitor, and one of the key aspartate residues is held in a conformation similar to that observed in the free enzyme. Therefore, some changes relative to the carbohydrate complex are required in order to accommodate the inhibitor. The structurally mimetic interactions within the catalytic site are supplemented by other specific protein-protein interactions, with a substantial buried surface area at the interface, involving 50 residues of the enzyme [171]. 

Ding J, Jacobo-Molina A, Tantillo C, Lu X, Nanni RG, Arnold E. Buried surface analysis of HIV-1 reverse transcriptase p66/p51 heterodimer and its interaction with dsDNA template/primer. J Mol Recognition 1994 7 157-161. 

It has been found experimentally that the hydrophobic effect is proportional to buried surface area for the transfer of small molecules to hydrophobic solvents. The energy of transfer is 80-100 kJ/mol per A2 of solute surface area that becomes buried (20-25 cal/mol/A2).20-23... 

The residues at positions a and d make up the hydrophobic core (Scheme 2). A portion of the buried surface area also comes from residues at positions e and g. Thus, interchain electrostatic attractions, for example, Lys at position g forming an i to i + 5 interaction with Glu at position e, cross the hydrophobic core, further burying these residues. The hydro-phobic interface includes residues a, d, e, and g (Scheme 2). An excellent colored spacefilling model of a two-stranded coiled coil showing these features is shown in a published review.114 These interchain and intrachain electrostatic attractions have been shown to contribute to protein stability (refs125,29,301 and references cited therein). 

In contrast to the relatively constant number of hydrogen bonds per residue, a set of proteins must bury variable amounts of apolar surface area in order to show convergence (Murphy and Gill, 1991). At the temperature at which the apolar contribution to AH° is zero, no variation would be observed in AH° per residue and the constant polar contribution is all that should be observed. The breakdown into polar and apolar interactions can also be viewed in terms of buried surface area. Proteins bury an increasing amount of surface area per residue with increasing size, but the increase is due to increased burial of apolar surface, whereas the polar surface buried remains constant. This is illustrated in Fig. 2 for 12 globular proteins that show convergence of AH°. These proteins bury a constant 39 2 A2 of polar... 

The value of AH can also be compared to the helix unfolding AH0 of Scholtz et al. (1991). The buried surface area, relative to the extended chain, was calculated for a 50-residue alanine a helix. An average of 19.5 A2 of polar surface is buried per residue and an average of 3.2 A2 of apolar surface is overexposed (i.e., is less accessible in the extended chain than in the helix). Using the fundamental parameters for the polar and apolar ACP described above, a value of — 6.5 cal K-1 (mol res)-1 is estimated for ACp for the helix denatur-ation. At 100°C the extrapolated value of AH0 is about 1.0 kcal (mol res)-1, again in reasonable agreement with the value of AH of 1.35 kcal (mol res)-1. These results strongly support the assertion that the apolar contribution to AH0 is close to zero at 7h. 

It is important to note, however, that although group additivity with a constant component will always lead to convergence temperatures, the presence of convergence temperatures may not require this condition. Recently Lee (1991) proposed an alternative explanation of the protein convergence temperatures. In the analysis Lee showed that if the protein data are normalized to the total amount of buried surface area, the variable fraction of the total buried surface that is apolar will lead to a convergence temperature at which the apolar and polar AH0 contributions are the same on a per square angstrom basis. 

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. 

The change in both polar and apolar buried surface area on de-naturation can be estimated from the difference between the polar or apolar ASA of the folded protein and of the extended chain, respectively (Eisenberg and McLachlan, 1986 Ooi etal., 1987 Spolar et al., 1989). Although the denatured protein may not be a random coil, it has been argued that globular proteins behave experimentally... 

L144M buried, surface loop 3 Reorients helix 6, which stabilizes the 265-275 loop. Interacts with loops also affected by... 

Other computational studies of static structures seek to analyze the contributions to the thermodynamic stability of the native state. These studies include the detection of hydrogen bonds, packing patterns, and analysis of buried surface area. 

Only residues contributing more than 5A of surface area to the interface are included in the summaries. B.S., buried surface MC, number of mainchain hydrogen bonds MC/SC, number of mainchain/sidechain hydrogen bonds, T, total number of interactions. 

Fig. 14. Residues that form the IL-IO/IL-IORI interface. IL-lORl and IL-IO are shown as ribbon diagrams. The position of each IL-IORI and IL-IO residue that buries surface area in to the interface is shown as a sphere corresponding to the Ca atom for each residue.

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