Helices folding dynamics

See also a-Helix, / -Sheet, Factors Determining Secondary and Tertiary Structure, Thermodynamics of Protein Folding, Dynamics of Protein Folding, Covalent Modifications to Regulate Enzyme Activity (from Chapter 11). 

Elber et al. [48] applied this method to explore the dynamics of the C-peptide in water with impressive results. More than 30 trajectories of C-peptide were generated, and the process of helix fonnation in water was examined. Remarkably, a time step of 500 ps was used, which allowed for the study of peptide folding on extended time scales. 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

The NMR data (James et al., 1997 Liu et al., 1999) show a slight reverse turn in the HI domain, similar to that proposed from X-ray diffraction (Inouye and Kirschner, 1998) however, NMR indicates that the turn is close to Alai 17. A molecular dynamics study of the helix-coil transition of PrP106—126 (Levy et al., 2001) indicates that the turn is near Alai 15, such that Hislll would interact with Vall22 rather than with Alall7. The HI domain, initially modeled as an z-helix. also adopts a /Miairpin fold as shown by molecular dynamics simulation (Daidone et al., 2005). 

Dyer, R.B. Probing the folding and unfolding dynamics of secondary and tertiary structures in a three-helix bundle protein. Biochemistry 2004, 43, 3582-3589. 

Melittin, which is an amphipathic peptide from honeybee venom, consists of 26 amino acid residues and adopts different conformations from a random coil, to an a-helix, and to a self-assembled tetramer under certain aqueous environments see Fig. 9. We have carried out our systematic studies of the hydration dynamics in these three conformations using a single intrinsic tryptophan ( W19) as a molecular probe. The folded a-helix melittin was formed with lipid interactions to mimic physiological membrane-bound conditions. The self-assembled tetramer was prepared under high-salt concentration (NaCl = 2 M). The tryptophan emission of three structures under three different aqueous environments is 348.5 nm, 341 nm, and 333.5 nm, which represents different exposures of aqueous solution from complete in random-coil, to locating at the lipid surface of a nanochannel (50 A in diameter) in a-helix and to partially buried in tetramer. Figure 10 shows... 

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