Protein helix

The a-helix is perhaps the most important structural unit in the folding of proteins. However, it is not very stable as an isolated unit in aqueous solution due to the competition for hydrogen bonding with water. Thus, in globular proteins helices often pack together or with other structural elements, such as sheets, and form solvent-excluded (hydrophobic) regions. 

Protein helices generally adopt variations of the usual helix geometries depending on the environment. 1 The methods described in Sections 12.3.1 and 12.3.2 will refer only to the synthesis of peptides incorporating inducers and mimetics for the a- and 310-helices. 

Helix propensities have been measured by different groups for all 20 proteinogenic amino acids using statistical surveys of protein helices/8,91 host-guest analysis/101 small model peptides and protein fragments/11-141 site-directed mutagenesis/151 and calculation studies/16171 The results from each method are different, although some correlations can be made. 

The existence of electrostatic interactions between oppositely charged residues and hydrogen bonding between side chains agrees with the observations in protein helices that (1) helix probability correlates with the frequency of occurrence of oppositely charged residues spaced i, i + 4 apart in proteins 88 and (2) there is a strong tendency for nearby, oppositely charged, side chains to point toward each other. 89 In the case of C-peptide, the side-chain interactions were also evident in the crystal structure of RNase A. 

Figure 42 The structure of apoferritin. N = N-terminus protein helices E form hydrophobic channels (reproduced with permission from Adv. Inorg. Biochem., 1984, 5, 39, Elsevier, Amsterdam)...

The three-dimensional structure of the reaction center of photosynthetic bacteria has been known for well over a decade now [see Chapter 3], but structural information on the photosystem-1 reaction center is still preliminary, although some tentative but important information regarding the distances and orientation between the various electron-transport cofactors and the placement of the protein helices is now available. 

Color Plate 5. The octameric LH-II complex from Rs. molischianum. (A) shows both protein helices and pigment molecules (B) shows the BChls and carotenoids. (Courtesy of Dr. K. Schulten). [See Chapter 3, Fig. 7.]... 

Figure 5.1. Modelled structure of a 42-residue peptide folded into a helix-loop-helix motif and dimerized to form a four-helix bundle protein. Helices are amphiphilic with a hydrophobic and a polar face. Due to the robustness and ease of synthesis this has become a popular motif in de novo protein design.

Cholesterol, which is largely insoluble in aqueous m a, travels through the blood circulation in the form of Upoprotein complexes. The plasma lipoproteins are a family of globular particles that share common structural features. A core of hydrophobic lipid, principally triacylglycerols (triglycerides) and cholesterol esters, is surrounded by a hydrophilic monolayer of phospholipid and protein (the apolipoproteins) [1-3]. Lipid-apolipoprotein interactions, facihtated byi amphi-pathic protein helices that segregate polar from nonpolar surfaces [2,3], provide the mechanism by which cholesterol can circulate in a soluble form. In addition, the apolipoproteins modulate the activities of certain enzymes involved in Upoprotein metabolism and interact with specific cell surface receptors which take up Upopro-teins by receptor-mediated endocytosis. Differences in the Upid and apoUpoprotein compositions of plasma Upoproteins determine their target sites and classification based on buoyant density. 

Analysis of the linear strain in crystalline amino acids, in particular - the analysis of the compressibility of selected structural elements - molecular chains, layers, intermolecular hydrogen bonds, voids - is important for an understanding of the compressibilities of structural fragments of peptides and proteins - helices, sheets, turns, non-structured fragments and cavities. For example, in proteins loops are often more compressible than helices, which are in turn more compressible than / -sheets [9, 88, 107, 108, 110, 192, 193]. The compressibility of main chains is comparable with the strain in crystalline amino acids. This comparison should... 

In this section, we treat a simple but important model—the rigid rod (Pecora, 1964, 1968). This model illustrates the conditions under which rotational motions of rigid, nonspherical molecules affect the isotropic spectral distributions. It is also of great practical importance, since it is applicable to a wide variety of real macromolecules such as fibrous proteins, helical polypeptides, and some viruses (e.g., tobacco mosaic virus). 

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