Peptide folding

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. 

A Caflisch, M Karplus. Molecular dynamics studies of protein and peptide folding and unfolding. In K Merz Jr, S Le Grand, eds. The Protein Eoldmg Problem and Tertiary Structure Prediction. Boston Birkhauser, 1994, pp 193-230. 

Ozbas B, Kretsinger J, Rajagopal K et al (2004) Salt-triggered peptide folding and consequent self-assembly into hydrogels with tunable modulus. Macromolecules 37 7331-7337... 

Rajagopal K, Lamm MS, Haines-Butterick LA et al (2009) Tuning the ph responsiveness of beta-hairpin peptide folding, self-assembly, and hydrogel material formation. Biomacromolecules 10 2619-2625... 

Esler WP, Stimson ER, Ghilardi JR, Lu YA, Felix AM, Vinters HV, Mantyh PW, Lee JP, Maggio JE. Point substitution in the central hydrophobic cluster of a human beta-amyloid congener disrupts peptide folding and abolishes plaque competence. Biochemistry 1996 35 13914-13921. 

Khandogin J, Chen J, Brooks CL III (2006) Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci USA 103 18546-18550. 

The unfolded states of eight different peptides, sampled in a corresponding number of molecular dynamics simulations of reversible peptide folding in solution under equilibrium conditions, are analyzed in this section (see Table I). 

Daura, X., Gademann, K., Jaun, B., Seebach, D., van Gunsteren, W. F., and Mark, A. E. (1999a). Peptide folding When simulation meets experiment. Angew. Chem. Int. Ed. 38, 236-240. 

Chen, C., Xiao, Y., Zhang, L., A directed essential dynamics simulation of peptide folding, Biophys. J. 2005, 88, 3276-3285... 

All-atom Simulations of Protein Unfolding and Short Peptide Folding... 

Controlling Peptide Folding by Metal to Ligand Coordination. .. 70... 

A folded native protein exists in a local minimum energy conformation. Typically 5 to 15kcal/mol free energy is sufficient to allow rapid interconversion (millisecond to second time scale) between folded and partially unfolded states. In general, proteins and peptides fold in a manner that minimizes the exposure of hydrophobic side chains of the peptide to water. 

The Mittag-Leffler function, or combinations thereof, has been obtained from fractional rheological models, and it convincingly describes the behavior of a number of rubbery and nonrubbery polymeric substances [79, 85]. The numerical behavior of the Mittag-Leffler function is equivalent to asymptotic power-law patterns that are often used to fit experimental data, see the comparative discussion of data from early events in peptide folding in Ref. 86, where the asymptotic power-law was confronted with the stretched exponential fit function. 

Zimmermann, G.R., Legault, P, Selsted, M.E. and Pardi, A. (1995) Solution structure of bovine neutrophil beta-defensin-12 the peptide fold of the beta-defensins is identical to that of the classical defensins. Biochemistry 34,13663-13671. 

Dieckmann et al. in 2003 described an amphiphilic a-helical peptide specifically designed to coat and solubilize CNTs and to control the assembly of the peptide-coated nanotubes into macromolecular structures through peptide-peptide interactions between adjacent peptide-wrapped nanotubes [227]. They claimed that the peptide folds into an amphiphilic a-helix in the presence of carbon nanotubes and disperses them in aqueous solution by noncovalent interactions with the nanotube surface. EM and polarized Raman studies revealed that the peptide-coated nanotubes assemble into fibers with the nanotubes aligned along the fiber axis. The size and morphology of the fibers could be controlled by manipulating the solution conditions that affect peptide-peptide interactions [227]. 

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