Flexibility of polypeptides

In order to check the flexibility of polypeptide helix predicted by these considerations, we may utilize various conformation-dependent properties. The most tangible way will be to examine the chain-length dependence of 1/2, which ought to be linear for a series of rigid rods of constant diameter. 

In spite of the above drawbacks. Equations 6.1 and 6.2 are popular mainly due to their simple form and have been used to estimate Me of protein (e.g., egg, gelatin) and other gels from shear modulus-concentration data (Table 6-2) (Fu, 1998). Its successful application to protein gels initially has been attributed to the greater flexibility of polypeptide chains in comparison to polysaccharide chains that are relatively stiff. In addition, the inability to employ low strain rates in early experimental studies on polysaccharide gels could be another reason. 

Balazs, A. 1991. Notes on the Local Flexibility of the Polypeptide Backbone Part I. Mean amplitudes of thermal motions in the dipeptide model. J. Mol. Struct. 245, 111-117. 

The rational synthesis of peptide-based nanotubes by self-assembling of polypeptides into a supramolecular structure was demonstrated. This self-organization leads to peptide nanotubes, having channels of 0.8 nm in diameter and a few hundred nanometer long (68). The connectivity of the proteins in these nanotubes is provided by weak bonds, like hydrogen bonds. These structures benefit from the relative flexibility of the protein backbone, which does not exist in nanotubes of covalently bonded inorganic compounds. 

Finally, it is important to explain the strategy that we have used to construct model compounds on which to carry out ab initio calculations from which we can gain insight into the two classes of electron transfer discussed above. For the kind of polypeptides shown in Figures 1 and 4 and for most species used in ETD or ECD experiments, the positively charged sites reside primarily on side chains that possess great motional flexibility. This means that, as the peptide undergoes... 

The conformation of membrane-bound enzymes is undoubtedly restricted by the membrane. However, the mechanism of action of these enzymes appears to be similar to that of soluble enzymes, so that the presence of clefts and conformational flexibility is to be expected. The mitochondrial coupling factor apparently contains both the ATP synthesizing enzyme and a proton channel conformational changes undoubtedly play a role in the function of this system. A large movement of polypeptide chains has been proposed in the functioning of this system (and for other membrane-bound enzymes), but no convincing experimental evidence is available to support such a hypothesis. 

There is another source of flexibility in polypeptide helices. It is the thermal fluctuations of bond rotation angles about their preferred a-helix values. This effect occurs without destroying the overall helical structure of the molecule and will become more important at higher temperature. 

The separateness of two domains within a subunit varies all the way from independent globular domains joined only by a flexible length of polypeptide chain, to domains with tight and extensive contact and a smooth globular surface for the outside of the entire subunit, as in the proteolytic enzyme elastase (fig. 4.20). An intermediate level of domain separateness, characterized by a definite neck or cleft between the domains, is found in phosphoglycerate kinase (fig. 4.21). 

Interestingly, one can use a Cys-Gly-Gly linker at the N- or C-terminal of the polypeptide chain in the design of disulfide-bridged coiled coils. The advantage of this approach is that the Cys-Gly-Gly linker allows complete flexibility of the polypeptide chains to adopt their most stable conformation, which includes different oligomerization states, while maintaining the polypeptide chains in a parallel manner. 49 In addition, the Cys-Gly-Gly linker eliminates the monomer-dimer equilibrium and the peptide concentration effect on stability, which is observed in two-stranded coiled-coil formation of noncovalent linked polypeptides. 49 861... 

The functional behavior of a food protein depends on a number of molecular properties including the chemical characteristics of the surface such as the distribution of the charge and polar and nonpolar residues, and the flexibility of the structure (Huang et al., 1996). These characteristics are modified by limited hydrolysis (see Section UFA.). Size and structure of a polypeptide are important for good functionality. Consequently, DH must be carefully controlled (Huang et al., 1996). Such a control is best achieved by using immobilized enzymes, which in turn avoids the necessity of a downstream enzyme inactivation step that may destroy the structure of the polypeptide, prevents enzyme autolysis, and avoids contamination of the product... 

Figure 2.7. Polypeptide chain structure containing proline. Chains containing proline lack the flexibility of other peptides because the proline ring has only one available angle for backbone rotation. Rotation occurs around the angles ( ), /, and co.

Conformational maps show values of phi and psi that fall into two regions the first region contains points that are always allowable and the second region contains points that are sometimes allowed. As shown in Figure 2.11, all points within the inner lines are always allowed and those within the outer solid lines are sometimes allowed. Hence the entropy (or rotational freedom of a peptide) is obtained from the area surrounded by the solid lines on a conformational map (Figure 2.11) and is proportional to the number of allowable conformations of a dipeptide unit. Please note a flexible chain with a lot of rotational freedom is easier to stretch than a rigid chain. We define the flexibility of a polypeptide as the natural logarithm of the number of allowable conformations,, times Boltzmann s constant (Equation (2.1)). 

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