Protein Chemistry - Part 1 - General Protein Chemistry - Ashmarin, I. P. 1968

Spatial Organization of the Protein Molecule
Methods for Studying the Secondary Structure of Proteins and Polypeptides

Analysis of A number of Globular Proteins has revealed that in solution they adopt highly compact shapes, the dimensions of which are incomparable with those expected for rod-like α-helices of similar molecular weight. Hydrodynamic and light-scattering data also indicate that the spatial configuration of proteins in this Class is more compact than that of random coils. To account for this apparent discrepancy, one must assume that globular protein molecules are "super-coils" consisting of short helical segments separated by non-helical regions. The latter provide The polypeptide chains with sufficient flexibility to fold into a compact globule stabilized by various types of secondary bonds. Consequently, a protein molecule contains both helical and amorphous regions. As for synthetic Polypeptides, here, as already mentioned, the conformation of the polypeptide chain depends on The Nature of the solvent: in some cases, the Introduction/11.html">Secondary Structure of these compounds is helical, while in others it is a random coil. How can one distinguish between these Two Types of secondary structure?

Undoubtedly, the most sophisticated technique for determining primary chain conformation is X-Ray Diffraction. However, aside from its technical difficulty, this method is applicable only to crystalline proteins or oriented polypeptide films. Meanwhile, the configuration of proteins in solution and in the solid state is not always identical. Therefore, additional criteria are needed to evaluate the Secondary Structure of Polypeptides and proteins. Since the optical and hydrodynamic Properties of the helical and coil forms differ sharply, Methods such as optical activity measurements, ultraviolet absorption, Infrared Spectroscopy, intrinsic viscosity determination, and others can be used to obtain such criteria. It should be noted, however, that all these methods can only estimate—and even then with approximate precision—either the overall fraction of the chain that exists in a helical configuration or the type of secondary structure. They are unable to pinpoint the specific helical regions within the protein or distinguish a single long helix from several short ones. Nevertheless, many of the methods described below are the only ones available for estimating the degree of protein helicity in solution. Their relative simplicity and applicability to non-crystalline proteins often make them the sole source of information for the majority of proteins.