Peptides a-helix

FIGURE 22.29 (a) Side view of a peptide a-heiix. (b) Top down view of a peptide a-helix. 

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... 

The primary structure of a peptide is its ammo acid sequence We also speak of the secondary structure of a peptide that is the conformational relationship of nearest neighbor ammo acids with respect to each other On the basis of X ray crystallographic studies and careful examination of molecular models Linus Pauling and Robert B Corey of the California Institute of Technology showed that certain peptide conformations were more stable than others Two arrangements the a helix and the (5 sheet, stand out as... 

Secondary structure (Section 27 19) The conformation with respect to nearest neighbor ammo acids m a peptide or pro tern The a helix and the pleated 3 sheet are examples of protein secondary structures... 

Fig. 8. De novo designed a-hehcal proteins. Dimers of the amphiphilic helix-forming peptide a B, GELEELLKKLKELLKG (see Table 1), in which the nature of the linker connecting the individual heflces plays a critical role in the stmcture of the final protein, (a) Using a Pro residue as the linker, ie, a B-Pro-a B, three molecules aggregated to form a trimeric coded-cod. (b) Using Pro-Arg-Arg as the linker, ie, a B-Pro-Aig-Arg-a, resulted in the...

The major stmctural feature of the HAz chain (blue in Figure 5.20) is a hairpin loop of two a helices packed together. The second a helix is 50 amino acids long and reaches back 76 A toward the membrane. At the bottom of the stem there is a i sheet of five antiparallel strands. The central i strand is from HAi, and this is flanked on both sides by hairpin loops from HAz. About 20 residues at the amino terminal end of HAz are associated with the activity by which the vims penetrates the host cell membrane to initiate infection. This region, which is quite hydrophobic, is called the fusion peptide. 

Figure 6.21 Schematic diagram of the conformational changes of calmodulin upon peptide binding, (a) In the free form the calmodulin molecule is dumhhell-shaped comprising two domains (red and green), each having two EF hands with bound calcium (yellow), (b) In the form with bound peptides (blue) the a helix linker has been broken, the two ends of the molecule are close together and they form a compact globular complex. The internal structure of each domain is essentially unchanged. The hound peptide binds as an a helix.

Figure 17.15 Schematic diagrams of the main-chain conformations of the second zinc finger domain of Zif 268 (red) and the designed peptide FSD-1 (blue). The zinc finger domain is stabilized by a zinc atom whereas FSD-1 is stabilized by hydrophobic interactions between the p strands and the a helix. (Adapted from B.I. Dahiyat and S.L. Mayo, Science 278 82-87, 1997.)...

Proline is the only amino acid in Table 27.1 that is a secondary amine, and its presence in a peptide chain introduces an amide nitrogen that has no hydrogen available for hydrogen bonding. This disrupts the network of hydrogen bonds and divides the peptide into two separate regions of a helix. The presence of proline is often associated with a bend in the peptide chain. 

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