Hydrophobic bonds in proteins

Nemethy, G., and Scheraga, H. A. The structure of water and hydrophobic bonding in proteins. III. The thermodynamic properties of hydrophobic bonds in proteins. J, Phys. Chem. 66,1773-1789 (1962). 

Scheraga, H. A. Role of hydrophobic bonding in protein structure. Ber. Bunsenges. 63. Hauptversammlung 1964, 838—839. 

G. Nemethy, Curr. Contents, Phys. Chem. Earth Sci., 28(30), 16 (1988). This Week s Citation Classic. G. Nemethy and H. A. Scheraga, J. Phys. Chem., 66, 1773 (1962). The Structure of Wiiter and Hydrophobic Bonds in Proteins. III. The Thermodynamic Properties of Hydrophobic-Bonds in Proteins. 

G. Nemethy and G. H. Scheraga, "Structure of Water and Hydrophobic Bonding in Proteins. I. A Model for< the Thermodynamic Properties of Liquid Water," /. Phys, Chem., 36 3382 (1962). 

G. Nemethy and H. A. Scheraga, Structure of water and hydrophobic bonding in proteins. 1. a model for the thermodynamic properties of liquid water. J. Chem. Phys. 36, 3382-3400 (1962). A. Ben-Naim, Mixture-model approach to the theory of classical fluids. J. Chem. Phys. 56, 2864-2869 (1972). 

Nemethy G., ScheragaH.A. (1962), Structure ofWater and Hydrophobic Bonding in Protein, Part III the Thermodynamic Properties of Hydrophobic Bonds in Proteins Journal of Physical Chemistry, 66,10,1773-89. 

Size Isomers. In solution, hGH is a mixture of monomer, dimer, and higher molecular weight oligomers. Furthermore, there are aggregated forms of hGH found in both the pituitary and in the circulation (16,17). The dimeric forms of hGH have been the most carefully studied and there appear to be at least three distinct types of dimer a disulfide dimer connected through interchain disulfide bonds (8) a covalent or irreversible dimer that is detected on sodium dodecylsulfate- (SDS-)polyacrylamide gels (see Electroseparations, Electrophoresis) and is not a disulfide dimer (19,20) and a noncovalent dimer which is easily dissociated into monomeric hGH by treatment with agents that dismpt hydrophobic interactions in proteins (21). In addition, hGH forms a dimeric complex with ( 2). Scatchard analysis has revealed that two ions associate per hGH dimer in a cooperative... 

The thioredoxin domain (see Figure 2.7) has a central (3 sheet surrounded by a helices. The active part of the molecule is a Pa(3 unit comprising p strands 2 and 3 joined by a helix 2. The redox-active disulfide bridge is at the amino end of this a helix and is formed by a Cys-X-X-Cys motif where X is any residue in DsbA, in thioredoxin, and in other members of this family of redox-active proteins. The a-helical domain of DsbA is positioned so that this disulfide bridge is at the center of a relatively extensive hydrophobic protein surface. Since disulfide bonds in proteins are usually buried in a hydrophobic environment, this hydrophobic surface in DsbA could provide an interaction area for exposed hydrophobic patches on partially folded protein substrates. 

These zinc-dependent endopeptidases (meprin A [EC 3.4.24.18] and meprin B [EC 3.4.24.63] ) are members of the peptidase family M12A. They catalyze the hydrolysis of peptide bonds in proteins and peptide substrates. Meprin A, a membrane-bound enzyme that has been isolated from mouse and rat kidney and intestinal brush borders as well as salivary ducts, acts preferentially on carboxyl side of hydrophobic amino acyl residues. Meprin A and B are insensitive to inhibition by phosphora-midon and thiorphan. 

This zinc-dependent endopeptidase [EC 3.4.24.11] catalyzes the hydrolysis of peptide bonds and exhibits preferential cleavage at the amino group of hydrophobic residues in proteins and polypeptides. Neprilysin is a membrane-bound glycoprotein that is inhibited by phos-phoramidon and thiorphan. 

This endopeptidase [EC 3.4.22.2], a member of the Cl peptidase family hydrolyzes peptide bonds in proteins, exhibiting a broad specificity for those bonds. There is a preference for an amino acyl residue bearing a large hydrophobic side chain at the P2 position and the enzyme does not accept a valyl residue at Pi. 

The same authors [98] have presented a method for the estimation of the number of electroactive disulfide bonds in proteins adsorbed on mercury. The developed approach was based on the assumption that electroactive disulfides are located in more hydrophobic regions of the protein molecule. 

Urea, ranging from 5 to 9 M, is the most common choice of chaotropic agent, and disruption of hydrogen and hydrophobic bonding between proteins is the main mode of action. When used in conjunction with thiourea (from 0 to 2 M), the two can aid solubilization of poorly soluble samples. The use of urea or urea-thiourea mixtures in SD buffers has no effect on the charge of the proteins within the sample. This is ideal for use in separating proteins according to their p in the first... 

Nemethy G, Steinberg IZ, Scheraga HA (1963) The influence of water structure and hydrophobic contacts on the strength of side-chain hydrogen bonds in proteins. Biopolymers 1 43-69... 

The dependence of solubility on temperature varies. We will consider here the range of zero to about 50°C at still higher temperature unfolding may occur. For hydrophilic proteins, the solubility may increase with temperature, by up to 4% per K. For more hydrophobic proteins, solubility decreases with increasing temperature, by up to 10% per K. This is in accordance with the strong temperature dependence of hydrophobic bonds in the range considered (Fig. 3.4). Low temperature may also cause dissociation of quaternary structures. 

---