Leu-Gly-Gly

The hydromedusa Polyorchis penicillatus is a good model system to study neurotransmission in coelenterates. Using a radioimmunoassay for the peptide sequence Arg-Phe-NH2 (RFamide), two peptides have now been purified from acetic acid extracts of this medusa. The structure of one of these peptides was established as pyroGlu-Leu-Leu-Gly-Gly-Arg-Phe-NH2, and was named Pol-RFamide. This peptide belongs to the same peptide family as a recently isolated neuropeptide from sea anemones (pyroGlu-Gly-Arg-Phe-NH2). Using antisera to Pol-RFamide, the peptide was found to be exclusively localized in neurones of Polyorchis, among them neurones associated with smooth-muscle fibres. This suggests that Pol-RFamide might be a transmitter or modulator at neuromuscular junctions.

Molecular Dynamics Simulations (MD) at Constant-Temperature or Constant-total Energy for the conformational Global-Minimum (GM) of elastin tetrapeptide Boc-Gly-Leu-Gly-Gly-NMe have been performed. The thermalization problem concerning the initial state of Constant-Temperature MD has been solved developing two effective strategies. In the first one, the run starts from the room-temperature state reached by Molecular Dynamics Simulated Annealing (SA). In the second one, one starts from the annealed-state at low-temperature and performs a long constant-low-temperature run until the initial conformer is perfectly equilibrated. Then, the low-temperature equilibrated-state is used as initial state for MD at room-temperature. heuristic criteria on order to define the onset of steady-state have been established monitoring the hystories of collective parameters (e.g., the total energy, temperature, end-to-end distance, etc.) and their amplitude fluctuations. Moreover, the equilibrium between the system and the heat bath is verified analyzing the total linear momentum conservation by the time evolution of center mass velocity. The slow drift of total energy during Constant-total Energy MD has been corrected using a loose coupling between the system and the heat bath. Moreover, we have verified that the roto-translational motions do not affect significantly the properties of molecular vibrations. The librations of peptide unit inside the type II beta-turn [Gly1]C = 0 ... HN[Gly4], previously detected, were confirmed. Large -Gly-Gly- chain motions were identified and modeled as fluctuations occurring between the tetratepeptide GM and the saddle-point corresponding to the transition state of the conversion toward the extended-chain conformation. All these peptide motions could contribute to the elasticity mechanism of elastin.

Experimental data from ion mobility measurements and electron transfer dissociation were combined with extensive computational analysis of ion structures and dissociation energetics for Gly-Leu-Gly-Gly-Lys cations and cation radicals. Experimental and computational collision cross sections of (GLGGK + 2H)(2+) ions pointed to a dominant folding motif that is represented in all low free-energy structures. The local folding motifs were preserved in several fragment ions produced by electron transfer dissociation. Gradient optimizations of (GLGGK + 2H)(+·) cation-radicals revealed local energy minima corresponding to distonic zwitterionic structures as well as aminoketyl radicals. Both of these structural types can isomerize to low-energy tautomers that are protonated at the radical-containing amide group forming a new type of intermediates, -C(·)O(-)NH2(+)- and -C(·)(OH)NH2(+)-, respectively. Extensive mapping with B3LYP, M06-2X, and MP2(frozen core) calculations of the potential energy surface of the ground doublet electronic state of (GLGGK + 2H)(+·) provided transition-state and dissociation energies for backbone cleavages of the N-Cα and amide C-N bonds leading to ion-molecule complexes. The complexes can undergo facile prototropic migrations that are catalyzed by the Lys ammonium group and isomerize enolimine c-type fragments to the more stable amide tautomers. In contrast, interfragment hydrogen atom migrations in the complexes were found to have relatively high transition energies and did not compete with fragment separation. The extensive analysis of the intermediate and transition-state energies led to the conclusion that the observed dissociations cannot proceed competitively on the same potential energy surface. The reactive intermediates for the dissociations originate from distinct electronic states that are accessed by electron transfer.