Hydrophobic contact

Similarly to the concept of the Catalyst software package [35, 40], hydrophobic areas are implemented in the form of spheres located in the center of hydro-phobic atom chains, branches or groups. First, a hydrophobicity scoring function pursuant to the Catalyst definition is implemented. As a next step, the algorithm checks if an ensemble of adjacent atoms is able to attain a sufficient overall hydrophobicity score. If this condition is met and a hydrophobic area in the macromolecule exists, a level 4 feature consisting of a sphere with a tolerance 

Positive ionizable areas are represented by atoms or groups of atoms that are likely to be protonated at a physiological pH. These are summarized in Table 

---

SH Bryant, LM Amzel. Coirectly folded proteins make twice as many hydrophobic contacts. Int J Peptide Protein Res 29 46-52, 1987. 

This pair of chlorophyll molecules, which as we shall see accepts photons and thereby excites electrons, is close to the membrane surface on the periplasmic side. At the other side of the membrane the symmetry axis passes through the Fe atom. The remaining pigments are symmetrically arranged on each side of the symmetry axis (Figure 12.15). Two bacteriochlorophyll molecules, the accessory chlorophylls, make hydrophobic contacts with the special pair of chlorophylls on one side and with the pheophytin molecules on the other side. Both the accessory chlorophyll molecules and the pheophytin molecules are bound between transmembrane helices from both subunits in pockets lined by hydrophobic residues from the transmembrane helices (Figure 12.16). 

The two peptides form a symmetrical dimer stabilized by four hydrogen bonds (red dashes) and hydrophobic contacts. The two monomers form a four-stranded, anti-parallel pleated sheet. 

Aryloxyphosphazene polymers, such as compound 1 or its mixed-substituent analogs, are also hydrophobic (contact angles in the region of 100°). These too show promise as inert biomaterials on the basis of preliminary in vivo tissue compatibility tests (13). 

Hydrophobicity is found to be the single most important parameter for this data set, which shows that at all the parts where substituents have been entered, hydrophobic contacts have been made. The Unear Clog P model suggests that the highly hydrophobic molecules will be more active. Although this is a very small data set it is the best model and explains 97.5% of the variance in log 1/C. 

FIGURE 1.4 Ligand-binding plots showing hydrogen-bonding interactions and distances and hydrophobic contacts for (a) the sucrose molecule in the A. maxima OCP structure and (b) the 3 -hydroxyechinenone molecule. Residues labeled in bold are absolutely conserved in the primary structure of the OCP. (From Wallace, A.C. et al., Protein Eng., 8, 127, 1995.)... 

Hydrophobicity (contact angle with water) 82° 82° 0° hydrophilic ... 

At least three regions of the receptor participate in the process of dimer formation. One of them is unspecific and is made up of the sequences of hydrophobic amino acids of the LBD. These form hydrophobic contact surfaces that facilitate, in a general way, the interactions among proteins. The other two are specific sequences of amino acids. One of them is situated immediately after the DBD. It is comprised of a group of some 20 amino acids, and its capacity to intervene in the dimer is independent of binding to the hormone. The other dimerization region is found inside the LBD. It is poorly located, and it is possible that noncontiguous sequences of amino acids participate in it. It is exhibited only when the receptor has been already bound to a hormone. 

Apart from the hydrogen bond potential at the bottom of the pTyr pocket, the phenol ring of pTyr makes a number of hydrophobic contacts with the SH2... 

Peptides larger than 10 to 20 residues adopt conformations in solution through the interplay of hydrogen bonding, electrostatic and hydrophobic interactions, positioning of polar residues on the solvated surface of the polypeptide, and sequestering of hydrophobic residues in the nonpolar interior. Protein shape is dynamic, changing continuously in response to the solvent environment. The retention process in RPLC is initiated as the protein approaches the stationary-phase surface. Structured water associated at the phase surface and adjacent to hydrophobic contact surfaces on the polypeptide is released into the bulk mobile... 

Proper protein folding is a concern in the production of a bioactive protein therapeutic, and it is of interest to verify that the conformation of a recombinant protein is the same as the wild-type molecule. Because retention in RPLC depends on the surface hydrophobic contact area, comparable chromatographic behavior of a recombinant protein with that of the wild-type molecule provides evidence of similar 3-D structure.17 38... 

HIC, like IEC, is performed under conditions that preserve protein shape and activity. It is used in preparative applications to obtain a selectivity complimentary to IEC and akin to RPLC but without the denaturing properties of the latter technique. Although HIC and RPLC share a mechanism based on hydro-phobic partitioning, the actual peak spacing and elution order of the two techniques can be different. This arises from the different hydrophobic contact points presented by the protein under native (HIC) and denaturing (RPLC) conditions. Although not widely used for analytical separations, HIC can be used to answer questions about accessible hydrophobic surface area that cannot be addressed by RPLC.44... 

The protease conformation of DegP is still elusive as crystallization of a substratelike inhibitor complex has failed and maintenance of a stably folded protein precludes long-term experimentation at elevated temperatures where it displays protease activity. We propose a profound rearrangement of the LA -L1-L2 loop triad into the canonical conformation of active serine proteases competent for substrate binding. This may be initiated by a collapse of the hydrophobic LA platforms and an enlargement of the hydrophobic contacts caused at high temperature. 

Structural mimicry of the substrate is also observed in the complex between PPA and the proteinaceous inhibitor tendamistat [173]. Again, the inhibitor extends into the catalytic site, but contacts only one of the catalytic residues, the glutamate residue. The sequence of three residues of the inhibitor, WRY (Trp-18 to Tyr-20) is positioned in the active site, with the arginine residue forming hydrogen bonds with the catalytic Glu-233. The WRY sequence and residues Thr-55, Gly-59 and Tyr-60 make hydrophobic contacts with the active site which are similar to those of acarbose and of a-All. 

---