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Interactions of the protein main chain are probed for their role in folding and self-assembly. The interactions are assessed with serine nonapeptide Ac-(Ser-Ala)-Ser-NH in poly-L and alternating-L,D structure variations. Being a neutral molecule, Serine nonapeptide has been found to display not only folding-unfolding equilibrium, but also association-dissociation equilibrium as a function of solvent and concentration. Thus scrutiny of intra- and inter-molecular interactions have been undertaken in water, methanol, and DMSO solvents. In water, poly-L peptide displays a PPII-helix conformation which unfolds to extended β-conformation with increase of temperature, apparently in a two-state equilibrium. Poly-L peptide at high concentration and on transfer to the low polarity solvent, methanol, displays ordering as a β-hairpin. This implies folding of the peptide by self assembly. Self assembly and ordering possibly as double-stranded β-helix is also evidence for alternating-L,D peptide. Both isomers were observed to be unfolded in high polarity solvent DMSO. Dynamic light scattering suggests that assembly in both isomers may involve large size aggregates. The results have established that folding and self-assembly can be coupled equilibria dependent upon solute structure, concentration, and solvent. The interactions of the protein main chain involved in folding and self assembly of unfolded structure are illuminated and have been discussed.


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