Models of protein behavior: Action within and between unsolvated peptides

The behavior and conformations adopted by unsolvated peptides were examined utilizing mass spectrometry and ion mobility measurements, in conjunction with molecular dynamics (MD) simulations.; The disruption of unsolvated polyalanine peptides was followed as a function of increasing number of glycine residues inserted at midpoint. The influence of the glycine residues is to provide a global disruption of the helical structure, rather than a local disturbance. More than three glycines (out of 15 residues) are required to disrupt helix formation.; Aggregations of polyalanine-based peptides in vacuo were probed to determine their conformations. Mixtures of helix-forming monomers (Ac-A₁₄KH & Ac-A₁₅KH and Ac-(GA)₇KH & Ac-A(GA)₇KH) formed unusual “pinwheel” trimers and “V” shaped dimers, both achieving greatest stability through an exchanged lysine motif. The analogs with lysines at the N-terminus form antiparallel helical dimers and globular aggregates. The antiparallel helical dimer is the dominant conformation for the peptides without glycines and a minor constituent for the glycine containing peptides.; The dissociation of the polyalanine-based peptide aggregates was then examined over the temperature range of 273–423 K. Arrhenius activation energies and preexponential factors were determined for the dissociation of aggregates from a Ac-(GA)₇KH & Ac-A(GA)₇KH mixture. Aggregates from the mixture of globule-forming peptides dissociated at significantly higher temperatures.; The study of the structure and folding behavior of the designed helix-coil-helix, or α-helical hairpin, peptides Ac-A₁₄KG₃A ₁₄K and Ac-A₁₄KSar₃A₁₄K (Sar = sarcosine, N-methylglycine) showed that the G₃ variant adopts three distinct geometries: an extended helical conformation, which is only stable at low temperatures (<230 K), a relatively high energy but metastable structure with exchanged lysines, and a coiled coil (the dominant configuration). ΔH o and ΔSo were determined for the couplingcoupling transition of the coiled coil. The Sar₃ variant did not exhibit the metastable conformation.; Unsolvated peptides were designed to form parallel coiled coils (Ac-A ₁₄KC-CKA₁₄-Ac, AcA₂₁KC-CKA₂₁-Ac, and Ac(DA₂DA₃)₂KC-CK(DA₃DA₂) ₂-Ac), but only the aspartic acid dimer exhibited a coiled coil geometry (as a minor component). The two polyalanine dimers adopted extended configurations. The A₁₄ variant was observed to exhibit a roughly tetrahedral, exchanged lysines, dimer-of-dimers. Under gentle electrospray conditions, numerous noncovalent aggregations occur.