Buried residues

The proteins thus adapt to mutations of buried residues by changing their overall structure, which in the globins involves movements of entire a helices relative to each other. The structure of loop regions changes so that the movement of one a helix is not transmitted to the rest of the structure. Only movements that preserve the geometry of the heme pocket are accepted. Mutations that cause such structural shifts are tolerated because many different combinations of side chains can produce well-packed helix-helix interfaces of similar but not identical geometry and because the shifts are coupled so that the geometry of the active site is retained. 

The globin fold has been used to study evolutionary constraints for maintaining structure and function. Evolutionary divergence is primarily constrained by conservation of the hydrophobicity of buried residues. In contrast, neither conserved sequence nor size-compensatory mutations in the hydrophobic core are important. Proteins adapt to mutations in buried residues by small changes of overall structure that in the globins involve movements of entire helices relative to each other. 

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. 

In addition, for solid samples or peptides in nonaqueous solvents, the amide II (primarily in-plane NH deformation mixed with C—N stretch, -1500-1530 cm-1) and the amide A (NH stretch, -3300 cm-1 but quite broad) bands are also useful added diagnostics of secondary structure 5,15-17 Due to their relatively broader profiles and complicated by their somewhat weaker intensities, the frequency shifts of these two bands with change in secondary structure are less dramatic than for the amide I yet for oriented samples their polarization properties remain useful 18 Additionally, the amide A and amide II bands are highly sensitive to deuteration effects. Thus, they can be diagnostic of the degree of exchange for a peptide and consequently act as a measure of protected or buried residues as compared to those fully exposed to solvent 9,19,20 Amide A measurements are not useful in aqueous solution due to overlap with very intense water transitions, but amide II measurements can usefully be measured under such conditions 5,19,20 The amide III (opposite-phase NH deformation plus C—N stretch combination) is very weak in the IR and is mixed with other local modes, but has nonetheless been the focus of a few protein-based studies 5,21-26 Finally, other amide modes (IV-VII) have been identified at lower frequencies, but have been the subject of relatively few studies in peptides 5-8,18,27,28 ... 

Hydrogen bonding in buried residues places severe constraints on substitutions, but a variety of changes can be made to surface residues. For example, Ser — Ala may remove the hydrogen-bonding potential of the —OH group, but water may be able to take its place. 

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. 

The k and FI values give different views of residue accessibility in a protein, n values, because of the nature of the measurement, reflect a state in proportion to its equilibrium population. Thus, rare fluctuations in the protein structure that transiently expose a buried residue will not be seen. On the other hand, the covalent reaction of 4-PDS with a buried cysteine during a fluctuation will trap the state, and the event will be counted and added to previous such events. Thus, the sulfhydryl reactivity method is an integrating method that can reveal low-frequency fluctuations much like hydrogen exchange. A comparison of relative n and k values thus may provide information on the existence of low-frequency structural fluctuations (Altenbach et aL, 1999a,b), and this point will be discussed further below. 

Figure 1. Schematic presentation of p-sheet 2 of the N-domain and amino-terminal residues or P-sheet 4 of the C-domain and the proximal C-terminal extension. Interface residues with large accessibility change in the interface are open circles and buried residues are filled circles. Other residues of the P-sheet are always accessible to the water probe and ate shown by squares, while buried residues are shown as filled squares. Residues with large accessibility change are labelled vl-v8 for the variable region, and cl-c7 for the interface residues included in the 3-layer packing of P-sheets (the constant region). The main chain pathways and virtual interstrand connections of up/down equivalent Ca-atoms are shown by solid and interrupted lines, respectively.

The carboxy-terminal domain of T4 lysozyme (residues 81-164) is composed of seven helices and includes the largest contiguous set of buried residues in the protein. Side-chains were considered to be part of the core if they have less than 10% solvent accessible surface. 

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. 

Merritt EA, Sarfaty S, Pizza M, et al. (1995) Mutation of a buried residue causes loss of activity, but no conformational change in the heat-labile enterotoxin of Escherichia coli. In Struct. Biol. 2 269-272. 

Fig. 5.2 Thermal average of the average number of hydrogen bond partnerships, T, for water molecules located within the desolvation domain of each residue in the DNA-binding domain of p53. If no water is found in the desolvation domain (buried residue), the bulk water value T =4 is adopted. Reprinted with permission from [19] copyright 2007 American Chemical Society...

Although the arrangements of the helices in the globins are topologically similar, changes in the volumes of the buried residues cause shifts in the relative... 

Fitch, C.A., Karp, D.A., Lee, K.K., Stites, W.E., Lattman, E.E., Garcia-Moreno, E.B. Experimental pK(a) values of buried residues Analysis with continuum methods and role of water penetration. Biophys. J. 2002, 82,3289-304. 

Indole ring Ring environment sharp intense line for buried residue intensity diminished on exposure or environmental change 48, 49... 

The factors influencing water erosion, according to McCalla and Army (1961), are chiefly intensity, amount and duration of rainfall amount and velocity of surface flow nature of the soil and its cover and slope of the land. Organic matter in the form of residues on the surface are more effective in erosion prevention than are buried residues, or thoroughly decomposed organic matter that is a part of the soil mass. 

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

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