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We have computed the low energy minima for the two endomorphin peptides, N-acetyl-Tyr-Pro-Trp-Phe-NHCH 3 (endomorphin 1) and Tyr-Pro-Phe-Phe-NHCH 3 (endomorphin 2) in aqueous solution. These peptides block pain without inducing the harmful side effects of the opiates that bind to the same mu opiate receptor but have short half lives. From over 1000 starting conformations for each peptide, we find less than 200 low energy structures whose conformational energies were ≤ 5 kcal/mole of the energy of the global minimum. The most probable conformations calculated using the Boltzmann distribution for both peptides were similar to one another. Using the letter representation for backbone conformational states, these most probable structures were D A E E for endomorphin 1 and E A E E for endomorphin 2. Both of these structures form reverse turns at Pro 2-Trp (Phe) 3 resulting in the juxtaposition of the aromatic rings of Tyr 1 and Phe 4. The Trp residue of endomorphin 1 points to the back of the reverse turn. These features may be useful in the design of non-peptide analogues that will have longer half-lives than the peptides.

We have computed the low energy conformations of the negative regulatory domain of p53, residues 374-388 using Empirical Conformational Energies of Peptides Program including solvation and computed the statistical weights of distinct conformational states. We find that there are two high probability conformations, one an α-helix from Lys 374-Lys 381, followed by another helical structure involving Lys 382-Glu 388 (statistical weight of 0.48) and an all-α-helix for the entire sequence (statistical weight of 0.23). Both structure are superimposable on the NMR structure of this sequence bound to the S100 protein. The global minimum structure (statistical weight of 0.014) is a beta structure from Gly 374-Arg 379 followed by an α-helix from His 380-Glu 388. Based on these results, we propose a possible strategy for enhancement of p53 anti-tumor activity in cancer cells. Since the structure of this sequence bound to the sirtuin protein, Sir2, is a β-sheet, we further propose that the global minimum may be an intermediate on the α-β structure transition.

Using the chain-build-up method based on Empirical Conformational Energies of Peptides Program including solvation, we have computed, the low energy conformations of gonadotrpin-releasing hormone, GnRH, whose sequence is Pyro-Glu(PG)-His-Trp-Ser-Tyr-Gly-Leu-Arg-Pro-Gly-NH2. We have found 5,077 solvated conformations with conformational energies that were within 5 kcal/mole of that of the global minimum. These minima were found to occur in 802 distinct conformational classes of which 25 represented 70 % of the Boltzmann energy-weighted structures. Virtually all of these structures adopted bend conformations from Tyr 5-Leu 8, and 3,861 structures adopted bend conformations at residues 4-7. However, these structures differed significantly from one another, indicating that GnRH does not adopt a well-defined structure in aqueous solution consistent with the absence of a well-defined NMR structure of GnRH in water. A total of 300 of these structures were found to be superimposable on possible NMR structures for GnRH in DMSO with a combined statistical weight of 1.6 %. We found that Gly 6 adopts low energy "starred" states, e.g., C* and D*, that are energetically forbidden to L-amino acids but are low energy for D-amino acids, with a statistical weight of 43 %. This can explain why substitutions of L-amino acids for Gly 6 are known to inactivate GnRH while D-amino acid substitutions enhance its activity. Using these findings, in the accompanying manuscript, we compute the low energy conformations for the substituted GnRHs that enable inference of possible receptor-bound conformations.

In the preceding paper, using ECEPP, including the effects of water, and the chain build-up procedure, we computed the low energy structures for GnRH and found that there were no distinct low energy structures or structures with high statistical weights. To attempt to deduce possible structures of GnRH that may bind to the GnRH receptor, we computed the low energy structures for GnRH peptides that have L- and D-amino acids substituting for Gly 6. The L-amino acid-substituted peptides (L-Ala and L-Val) have very low or no affinity for the receptor and on activity (release of FSH and LH) while the D-Ala-, D-Leu-, D-Trp- and D-Phe-substituted peptides have significantly higher relative affinities and activities than those for native GnRH; the D-Val-substituted peptide has about one-third of the affinity and activity as native GnRH. Unlike native GnRH, our computations suggest that both sets of peptides form well-defined structures in water: the L-amino acid-substituted peptides are predominantly α-helical while the D-amino acid-substituted peptides adopted E*A A A E D*(C*) A E C A(C*) and minor variants of these structures. By eliminating structures that lay in common to the D-Ala and L-Val peptides and further eliminating structures that differed between the D-Ala and D-Leu peptides, we reduced the number of possible distinct binding conformations to 254. Searching for structures among these 254 conformations that had relative statistical weights that paralleled their relative affinities, we found two candidate structures: D*E A A E C*A E C A and D*G A A E D*A E C G*, both of which have conformations for residues 3-9 that are similar to the computed most probable structures for the D-amino acid-substituted GnRH peptides in water.

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp)(2). We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-NHCH(3) as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH(3)CO-Pro-Pro-Pro-Pro-Asn-Pro-Asn-Asp-Pro-Pro-Pro-NHCH(3). We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.