Hydrophobic contacts tertiary protein structure

The good agreement between the folded and the experimental structure is also evident from Figure (l)(center), which shows the secondary structure alignment of the native and the folded conformations. The good physical alignment of the helices illustrates the importance of hydrophobic contacts to correctly fold this protein. An independent measure to assess the quality of these contacts is to compare the C -C distances (which correspond to the NOE constraints of the NMR experiments that determine tertiary structure) in the folded structure to those of the native structure. We found that 66 % (80 %) of the C/3-C/3 distance distances agree to within one (1.5) standard deviations of the experimental resolution. 

Under certain circumstances however the same proteins can exhibit a markedly hydrophobic character (23.24). This is illustrated in Table 2 in which contact angle measurements have been performed on thin layers of proteins adsorbed onto various polymer surfaces and subsequently exposed to an air interface. This results, due to reorientation and/or structural changes, in a much more hydrophobic tertiary configuration. Thus, when referring to the relative hydrophobicity/hydrophilicity of proteins it is important to bear in mind the environmental conditions under which the experimental data are generated. 

Those simulations beginning from the intermediate structures (rms 5-10 A) also collapsed and became more nativelike in terms of a number of criteria, but they did not refold. The radius of gyration and solvent accessible surface area of the protein in these simulations converged with those values obtained from simulation of the crystal structure at the same temperature. There was preferential burial of hydrophobic groups, some of the native tertiary contacts were formed, but the main-chain contacts characterizing secondary structure... 

We have shown that the morphology of the adsorbed individual molecule and the protein film is dependent upon the surface to which the protein is adsorbed and the wall shear rate at which the protein solution contacts the surface. We have studied the interaction of proteins with surfaces from two approaches the first involved observations of the tertiary structures of individual molecules, and the second involved the use of a flow cell and the exposure of test materials to flowing, dilute, purified human plasma protein solutions. On the hydrophobic surfaces of polystyrene and polycarbonate, albumin and fibrinogen films form networks. On the surface of the hard segment model polyurethane, the morphology of the adsorbed film is very similar to that formed on the hydrophobic polystyrene and polycarbonate surfaces. On the peu-2000, the lowest... 

The amino acid sequence of a protein (as dictated by the nucleotide sequence of the gene) determines the final shape and chemical properties of the protein. Hydrophobic amino adds gravitate toward the center of the amino add chain to avoid contact with water hydrophilic amino acids move outward in search of water. In doing so a hydrophobic central core is created (Fig. 1.3). Positively charged amino acids then seek negatively charged amino acids, and accommodations are made for variances in amino acid shape and size. Subject to these intermolecular forces, the linear amino acid chain folds into a compact, three-dimensional tertiary structure. 

Residues with nonpolar, hydrophobic side chains, such as valine, leucine, isoleucine, methionine, andphenylalanine, are almost always found in the interior of the protein, out of contact with the aqueous solvent. (These hydrophobic interactions are largely responsible for the tertiary structure of proteins that we discuss in Section 24.8B.)... 

From a more "global" perspective, all water-soluble, globular proteins share two important characteristics they are close-packed structures [20], in that they do not possess significant "holes" in their interiors, and they have a laminar structure in which a predominantly hydrophobic core is surrounded by a predominantly hydrophilic shell which constitutes the outer surface of the protein and is in contact with the aqueous solvent environment. Although these characteristics play a role in determining the nature of a protein s tertiary fold and the sequences of amino acids which permit such a fold to exist, other factors have also been shown to be of importance [1,21,22]. 

The tertiary structure of the proteins is the 3D organisation of the proteins, involving the repartition of the secondary structure units of the proteins with respect to each other. The driving force for the folding into tertiary structure is dependent on the physicochemical properties of the medium. In aqueous solutions, the hydro-phobic residues of the proteins are hidden in the core of the proteins in order to minimise contacts with water molecules. The protein tertiary structure is stabilised by hydrophobic interactions, salt bridges, hydrogen bonds and, for some proteins, disulfide bonds. 

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