Globular proteins crystalline

The structures of the basic building blocks of the architecture of proteins were determined by Linus Pauling and R. B. Corey many years before the solution of the structures of globular proteins.13 They solved the structures of crystalline small peptides to find the dimensions and geometry of the peptide bond. Then, by constructing very precise models, they found structures that could fit the x-ray diffraction patterns of fibrous proteins. The diffraction patterns of fibers do not consist of the lattice of points found from crystals, but a series of lines corresponding to the repeat distances between constantly recurring elements of structure. 

Nuclease behaves like a typical globular protein in aqueous solution when examined by classic hydrodynamic methods (40) or by measurements of rotational relaxation times for the dimethylaminonaphth-alene sulfonyl derivative (48)- Its intrinsic viscosity, approximately 0.025 dl/g is also consistent with such a conformation. Measurements of its optical rotatory properties, either by estimation of the Moffitt parameter b , or the mean residue rotation at 233 nin, indicate that approximately 15-18% of the polypeptide backbone is in the -helical conformation (47, 48). A similar value is calculated from circular dichroism measurements (48). These estimations agree very closely with the amount of helix actually observed in the electron density map of nuclease, which is discussed in Chapter 7 by Cotton and Hazen, this volume, and Arnone et al. (49). One can state with some assurance, therefore, that the structure of the average molecule of nuclease in neutral, aqueous solution is at least grossly similar to that in the crystalline state. As will be discussed below, this similarity extends to the unique sensitivity to tryptic digestion of a region of the sequence in the presence of ligands (47, 48), which can easily be seen in the solid state as a rather anomalous protrusion from the body of the molecule (19, 49). 

Although the association between lipids and proteins is fundamental in understanding the physiological functions of membranes, information on such structures is very limited. Studies of a few systems of lipids and globular proteins indicate that the proteins tend to remain in their native form. The structures can be separated into two somewhat simplified types. Usually the lipid structure seems to dominate, and the protein molecules are incorporated into liquid crystalline structures of lipids. In other cases, the lipid molecules are distributed within the protein units,... 

In this context, some comments on protein crystallisation can be made. The process of crystallisation can be viewed as one of self-assembly of the quaternary structure, although the constituent units now have a well-defined arrangement in space, in contrast to their less rigid shape in liquid crystalline mesophases. Indeed, twisted structures are very commonly found in globular protein crystals, which are reminiscent of the hyperbolic forms of micro- and mesoporous zeolites, described in Chapter 2. 

It would seem reasonable to expect that the displacements of the chemical shifts could be used as an intrinsic probe of local environment of a given amino acid residue, if the transferability of the conformation-dependent shifts of polypeptides to more complicated protein systems is guaranteed. Fibrous proteins such as silk fibroin, collagen and collagen-like polypeptides can serve as ideal systems to justify this view, because several crystalline polymorphs are available depending on a variety of physical treatments and the spectral pattern is very simple as compared with those of globular proteins because of the limited numbers of amino acid residues involved. 

The analysis of the amide I band to obtain the estimation of protein secondary structure content in terms of percentage helix, j3 strand, and reverse turn that was developed by Williams has proved very successful and has now been used by numerous workers.In this method the amide I region is analyzed as a linear combination of the spectra of the reference proteins whose structures are known. As noted above the Raman spectra of globular proteins in the crystal and in solution are almost identical, reflecting the compact nature of the macromolecules. Thus one may use the fraction of each type of secondary structure determined in the crystalline state by the X-ray diffraction studies for proteins in solution. If there are n reference proteins with the Raman spectrum of each of them represented as normalized intensity measurements at p different wave numbers, then this information is related by the following matrix equation ... 

In contrast to rigid crystalline globular proteins, surface residues of such loops and N- or C-terminal residues of bR as a typical membrane protein turned out to be very flexible at ambient temperature, even if they are embedded in lipid bilayer to form naturally occurring 2D crystals (PM). This kind of flexibility is essential to exhibit its specific biological function. Nevertheless, it is cautioned that spectral resolution of such C-labeled proteins might be desperately deteriorated, if a directly bonded sequence is present in the dense spin networks under-... 

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