Structural region

Fig. 2.1 (A) Structure of the HCV genome, with 5 - and 3 -untranslated regions and individual proteins of the polyprotein indicated Regions of the genome (approximately 3,000 bases) are drawn to scale. Structural protein regions are in light gray, nonstructural proteins in white, and untranslated regions in dark gray. (B) Structure of a typical replicon sequence, with the antibiotic resistance gene (Neo ) in place of the structural region and the second IRES (EMCV) inserted. The NS2 sequence is often rwt present in the replicon.

Likewise, amide protons protected from exchange are a useful indication of structured regions in partly folded proteins and molten globules (Hughson etal., 1990). 

Both methods are also limited in accuracy of secondary structure determinations because spectral peaks must be deconvolved estimates are made of the overlapping contributions of different structural regions. These estimates may introduce error based on the reference spectra used and because deconvolution methods equate crystallographic secondary structure with the secondary structure of the protein in solution (Pelton and McLean, 2000). As amyloid fibrils are neither crystalline nor soluble, there may be even greater error in estimates of secondary structure. To compound the problem, estimates of /f-sheet content are less reliable than those of a-helix, because of the flexibility and variable twist of / -structure (Pelton and McLean, 2000). In addition, / -sheet and turn bands overlap in FTIR spectroscopy (Jackson and Mantsch, 1995 Pelton and McLean, 2000). Side chains also contribute to spectral peaks in both methods, and they can skew estimates of secondary structure if not properly accounted for. In FTIR spectra, up to 10-15% of the amide I band may arise from side chain contributions (Jackson and Mantsch, 1995). 

The chemical picture of this modified collagen is not yet complete, but its mixed structural regions already hint at similar new synthetic materials. For the NIH, which has supported this biotechnological research, the hope is that this unique material, with its variable elasticity, will lead to more comfortable and pliable artificial skin. Ultimately, it could also improve the quality of such goods as footwear and radial tires, where softness and toughness are equally desirable. 

Figure 1 Schematic representation of tomato ACS poiypeptide with marked a-heiicai and /3-strand secondary structure regions (according to PDB with entry code 1 iAX), residues criticai for cataiysis, and fragments of the poiypeptide representing the iarge and the smaii domain in the spatiai structure of enzyme. Open biocks denote a-heiicai regions and fiiied biocks, /3-strand regions. For detaiis see Sections 5.04.2.2.4 and 5.04.2.2.5.

Figure 4 The biosynthesis of nisin A as a representative example of the posttranslational maturation process of lantibiotics. Following ribosomal synthesis, NisB dehydrates serine and threonine residues in the structural region of the prepeptide NisA. NisC subsequently catalyzes intramolecular addition of cysteine residues onto the dehydro amino acids in a stereo- and regioselective manner. Subsequent transport of the final product across the cell membrane by NisT and proteolytic cleavage of the leader sequence by NisP produces the mature lantibiotic. For the sequence of the leader peptide, see Figure 6. Adapted with permission from J. M. Willey W. A. van der Donk, Annu. Rev. Microbiol. 2007, 61, 477-501.

Figure 5 The structural region of the NisA prepeptide is modified by a putative muitienzyme compiex consisting of the dehydratase NisB, the cyclase NisC, and the transporter NisT. After export, the leader peptide is removed by NisP, which is anchored to the cell wall. Mature nisin activates the two-component response regulatory system NisRK, and phosphorylated NisR serves as a positive regulator of nisA and the biosynthetic and immunity operons expressing NisABTC and NisFEG,...

The current hypothesis for the role of the leader peptide in dehydratase activity and processivity is shown in Figure 8 and is based on the results from several studies. LctM is proposed to recognize a certain secondary structure, possibly helical (see Section 5.08.3.2), adopted by the C-terminal segment of the leader peptide. Leader peptide binding is then postulated to bring the structural region of the substrate in close proximity to... 

Although the histone fold was first described from the structure of the histone octamer core of the nucleosome [17], the high a-helical content was predicted much earlier [43]. The core histones possess three functional domains (1) the histone fold domain, (2) an N-terminal tail domain, and (3) various accessory helices and less structured regions. The N-terminal tail domains of the core histones are currently the focus of intense research. Covalent modifications of residues in these unstructured domains appear to modify local chromatin structure, either directly or... 

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