Protein interior

Less commonly, an a-helix can be completely buried in the protein interior or completely exposed to solvent. Citrate synthase is a dimeric protein in which a-helical segments form part of the subunit-subunit interface. As shown in Figure 6.24, one of these helices (residues 260 to 270) is highly hydrophobic and contains only two polar residues, as would befit a helix in the protein core. On the other hand. Figure 6.24 also shows the solvent-exposed helix (residues 74 to 87) of cahnodulln, which consists of 10 charged residues, 2 polar residues, and only 2 nonpolar residues. 

FIGURE 4.7. A schematic description of the different contributions to the PDLD model. The figure considers the energetics of an ion pair inside a protein interior. The upper part describes the protein permanent dipoles, the middle part describes the induced dipoles of the protein, while the lower part describes the surrounding water molecules and the bulk region, which is represented by a macroscopic continuum model. 

A close analysis of the trimers order in the crystal revealed that the exposed part of neoxanthin molecule is completely free from interactions with any protein or pigment components (Pascal et al., 2005). In addition, an examination of the neoxanthin configuration, taken from the structure of LHCII, points toward strong distortion of the d.v-end of the molecule (Figure 7.9). This fact suggests that the twist most likely occurs within the protein interior, implying that some movement in the LHCII monomer must take place during the transition into dissipative state. Apparently, this movement affects not only lutein 1, as previously discussed, but also neoxanthin. 

Saxena AM, Udgaonkar JB, Krishnamoorthy G (2005) Protein dynamics control proton transfer from bulk solvent to protein interior a case study with a green fluorescent protein. Protein Sci 14 1787-1799... 

NEUTRAL POLAR These side chains are uncharged, but they have groups (-OH, -SH, NH, C=0) that can hydrogen-bond to water. In an unfolded protein, these residues are hydrogen-bonded to water. They prefer to be exposed to water, but if they are found in the protein interior they are hydrogen-bonded to other polar groups. 

Macgregor R. B. and Weber G. (1986) Estimation of the Polarity of the Protein Interior by Optical Spectroscopy, Nature 319, 70-73. 

The detailed study of water structure around proteins is only just beginning, but a number of conclusions can be drawn from the crystallographic and theoretical work that has already been done. Isolated water molecules occur trapped inside protein interiors, where they... 

The surfaces that form subunit-subunit contacts are very much like parts of a protein interior detailed fit of generally hydrophobic side chains, occasional charge pairing, and both side chain and backbone hydrogen bonds. Twofold symmetry is the most common relationship between subunits. The 2-fold is often exact and can be part of the actual crystallographic symmetry, as for the prealbumin dimer in Fig. 62. However, in many cases (e.g., Tulinsky et al., 1973 Blundell et al., 1972) individual side chains very close to the approximate 2-fold axis must take up nonequivalent positions in order to avoid overlapping (see Fig. 63). Conformational nonequivalence can extend further away from the axis and produce such effects as different... 

Electron transfer (ET) is a key reaction in biological processes such as photosynthesis and respiration [1], Photosynthetic and respiratory chain redox proteins contain one or more redox-active prosthetic groups, which may be metal complexes or organic species. Since it is known from crystal structure analyses that the prosthetic groups often are located in the protein interior, it is likely that ET in protein-protein complexes will occur over large molecular distances ( > 10 A) [2-4],... 

The introduced cysteine residues are found in one of three possible environments (1) on the water-accessible surface, (2) within the protein interior, or (3) at the protein-lipid interface (Karbn and Akabas, 1998). 

Protein interior, water exclusion from, HYDROPHOBIC EFFECT PROTEIN KINASE PROTEIN KINASE 0 Protein-ligand interactions,... 

A) The protein conformation does or does not provide access to the protein interior for the surfactant molecules, with implications for the number of available binding sites on each protein. 

C) When charges on surfactant and protein are of similar sign, the electrostatic repulsion between them hinders the penetration of the surfactant head-groups into the protein interior and therefore reduces the probability of polar surfactant-protein interactions. 

These bulky groups of distinctive shapes participate in hydrophobic interactions in protein interiors and in forming binding sites of specific shapes. 

Fn adsorbed on hydrophobic silica, however, fluoresces at 326, suggesting a slight denaturation of the molecule. Fn interactions with the hydrophobic surface may involve some of the apolar residues in the protein interior, suggesting a partial denaturation. Clearly, studies on surfaces of a range of charge, polarity, and apolar character would be of interest. 

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