Helix bending

When instead assemblies of helices are taken into account, it is well known that for many aspects DNA duplexes in solution can be treated as a charged anisotropic particle [2]. Accordingly, steric, electrostatic, and Van der Waals interactions, together with the mechanical properties of the helix (bending and torsional rigidity), play a major role in the formation of DNA mesophases. In addition, all these different kinds of interactions combine in a subtle and still poorly understood way to generate other forces relevant for the case of DNA. A notable example is the helix-specific, chiral interaction, whose importance for DNA assemblies will be discussed below. 

Tan, Z. J., and Chen, S. J. (2008a). Electrostatic free energy landscapes for DNA helix bending. Biophys.J. 94, 3137-3149. 

X-Ray crystallographic analysis of two crystalline forms of tetrameric melittin showed that the conformation of the peptide is essentially the same in each form. " Melittin was found to adopt a helical conformation in the crystalline state. The presence of Pro-14 also caused the helix to bend with an angle of about 120° between residues 1-10 and 16-26. The large helix bend allows for the optimal packing of hydrophobic side-chains vnthin the tetramer. Melittin provides a rare example of a membrane-bound peptide whose structure has been determined in low dielectric solvents, micelles and in the crystalline state and found to be quite similar. The similarities of these structures lends confidence to the idea that they represent good models for the membrane-bound conformation. ... 

Young, M.A., Ravishanker, G., Beveridge, D.L., and Berman, H.M. (1995) Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys.J., 68, 2454-2468. 

In the even tighter 7 turn, bonding is to residue i + 2 (Figure 6.19). Proline often plays a role in turns, as in Figure 6.19, and also as a breaker of ot helices, because this residue cannot be accommodated in the helix. Bends and turns most often occur at the surface of proteins. 

The second major structural class studied is the O-helical class. Interestingly, such structures tend to be rather disorganized in aqueous solution, but they become a-helical structured upon entering a membrane environment or exposure to nonpolar solvents (89,90). The predominant structures observed upon interaction with membranes are helix-bend-helix with a 9-16 amino acid amphipathic a-helix, a 2-4 residue bend, and a 11-14 amino acid amphipathic but more hydrophobic a-helix, as demonstrated by two-dimensional NMR of cecropins A and B, melittin, the magainins, and a synthetic cecropin-melittin hybrid (89,91-93). A small variation is provided by mammalian cecropin Pi, which comprises an uninterrupted amphiphilic helix for 24 amino acids, bounded by 2-4 residues at the N- and C-termini. 

To check stability of helix itself, we have calculated RMS fluctuations of C atoms (Fig. 8.5). In general, the highest fluctuations took place at the polar part of the membrane (both ends) and in its central, hydrophobic core. The ends are in hydrophilic regions with many small movable water molecules, while the central part is in region of membrane of lower density. The major fluctuations occur when peptide linear helix bends or breaks (for example I24/LC simulation). Beside of this, the I24 is generally of lowest stability and the L24 peptide is in contrast the most stable. The V24 and (LA)j2 fluctuate more than L24, but less than I,. The P, fluctuates... 

M. A. Young, G. Ravishanker, D. L. Beveridge, and H. M. Berman, Biophys. J., 68, 2452 (1995). Analysis of Local Helix Bending in Crystal Structures of DNA Oligonucleotides and DNA-Protein Complexes. 

Figure 22 shows a single snapshot of the coordinates for the ice/AFP/water after 200 ps of total simulation time. In Figure 22 notice that the a-helix is more well-defined than it was at the beginning of the simulation (See Figure 21). The helicity was determined using the DSSP algorithm in RasMol 2.6[32]. The THR residues are in a line and remain spaced approximately 16.7 A apart. Finally it appears that the helix bends to follow the contour of the ice/water interface. This bending of the winter flounder AFP was observed in the molecular dynamics simulations of McDonald et al. [33] and Jorgensen et al. [34]. Merz et al. [35, 36] have published two papers, one on the dynamics of a Type I antifreeze protein in water using an NPT dynamics method and a second paper where they place a shell of liquid water over the antifreeze protein bound to ice. Unfortunately at this time we have not been able to fully characterize the ice/water interface in this simulation or perform any other necessary analysis. It is clear that additional simulations at the ice/water interface are necessary and that the results of these simulations will provide a clear molecular explanation of AFP binding at the ice/water interlace.

Recently, it has been demonstrated that helix bending can be induced by partial phosphate neutralization. In line with the early suggestions of Mirzabekov and Rich, Strauss and Maher have shown that neutralizing the phosphate groups on one face of the DNA helix leads to unbalanced electrostatic repulsions between the remaining anionic phosphates... 

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