Helical regions

Class 1 and class II MHC molecules bind peptide antigens and present them at the cell surface for interaction with receptors on T cells. The extracellular portion of these molecules consists of a peptide-binding domain formed by two helical regions on top of an eight-stranded antiparallel p sheet, separated from the membrane by two lower domains with immunoglobulin folds. These domains are differently disposed between the two protein subunits in class I and class II molecules. 

From a map at low resolution (5 A or higher) one can obtain the shape of the molecule and sometimes identify a-helical regions as rods of electron density. At medium resolution (around 3 A) it is usually possible to trace the path of the polypeptide chain and to fit a known amino acid sequence into the map. At this resolution it should be possible to distinguish the density of an alanine side chain from that of a leucine, whereas at 4 A resolution there is little side chain detail. Gross features of functionally important aspects of a structure usually can be deduced at 3 A resolution, including the identification of active-site residues. At 2 A resolution details are sufficiently well resolved in the map to decide between a leucine and an isoleucine side chain, and at 1 A resolution one sees atoms as discrete balls of density. However, the structures of only a few small proteins have been determined to such high resolution. 

Figure 26.5 (a) The o-helical secondary structure of proteins is stabilized by hydrogen bonds between the N—H group of one residue and the C=0 group four residues away, (b) The structure of myoglobin, a globular protein with extensive helical regions that are shown as coiled ribbons in this representation. 

Figure 6-2. A model of myoglobin at low resolution. Only the a-carbon atoms are shown. The a-helical regions are named A through H. (Based on Dickerson RE in The Proteins, 2nd ed. Vol 2. Neurath H [editor]. Academic Press, 1964. Reproduced with permission.)...

Each protein has a unique three-dimensional shape called its tertiary structure. The tertiary structure is the result of the bends and folds that a polypeptide chain adopts to achieve the most stable structure for the protein. As an analogy, consider the cord in Figure 13-39 that connects a computer to its keyboard. The cord can be pulled out so that it is long and straight this corresponds to its primary structure. The cord has a helical region in its center this is its secondary structure. In addition, the helix may be twisted and folded on top of itself This three-dimensional character of the cord is its tertiary structure. 

Fig. 5. A speculative model for the arrangement of the helical regions of the sugar transporters in the membrane. The helices are numbered as shown in Fig. 4. The small circle labelled s represents a glucose molecule.

Fig. 3. Secondary chemical shifts for 13C , 13CO, H , and 13C as a function of residue number in apomyoglobin at pH 4.1. Bars at the top of the figure indicate the presence of NOEs the smaller bars indicate that the NOE was ambiguous due to resonance overlap. Black rectangles at the base of the top panel indicate the locations of helices in the native holomyoglobin structure (Kuriyan et al, 1986). Hashed rectangles indicate putative boundaries for helical regions in the pH 4 intermediate, based on the chemical shift and NOE data. Reproduced from Eliezer et al (2000). Biochemistry 39, 2894-2901, with permission from the American Chemical Society.

Figure 6.12 (a) The overall fold of the rubrerythrin subunit. Helical regions are in yellow, 6-sheet... 

A single molecule of RNA often contains segments of sequence that are complementary to each other. These complementary sequences can base-pair and form helical regions of secondary structure. Interactions between the secondary structures give RNA a significant folded, three-dimensional structure. 

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