Comparative study of global minimum energy conformations of hydrated peptides

Abstract

A global optimization method is described for identifying the global minimum energy conformation, as well as lower and upper bounds on the global minimum conformer of solvated peptides. In considering the effects of hydration, two independent continuum‐based solvation models are employed. The first method is based on the calculation of solvent‐accessible surface areas, whereas the second method uses information on the solvent‐accessible volume of hydration shells. The hydration effects predicted by the area‐ and volume‐based models, using a variety of atomic solvation parameter (ASP) sets, are tested and compared by identifying global minimum energy structures of terminally blocked peptides and oligopeptides. Significant differences are observed, indicating that appropriate model selection is essential for accurately predicting hydrated peptide structures. Using this information, the applicability of these hydration models and ASP sets is discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 636–654, 1999

Global optimization in the 21st century: Advances and challenges

“…Androulakis et al (1998) studied the parallel computation issues that arise using the ␣BB global optimization approach. Klepeis, Androulakis, Ierapetritou, and Floudas (1998)and Klepeis and Floudas (1999a) proposed new global optimization approaches for the structure prediction of solvated peptides using area and volume accessible to the solvent models. A review of the global optimization activities in the areas of protein folding and peptide docking can be found in Floudas, Klepeis, and Pardalos (1999b).…”

Deterministic Global Optimization

“…Therefore, the surface-accessible solvation energies are only included at local minimum conformations. A detailed comparative study of several solvation models coupled with rigorous global optimization searches can be found in Klepeis and Floudas (1999a).…”

“…The values of the 24 dihedral angles are given in Table 16.10. Klepeis and Floudas (1999a), as part of their study and implementation of the aBB for solvated peptides, tested the unsolvated Leu-enkephalin with a equal to 5.0 and obtained a slightly lower energy of -9.349kcal/mole. This new unsolvated global minimum structure also possesses a type II' ,B-bend, although the bend is shifted to the N-C' peptidic bond of Gly2-Gly3.…”

“…The first approach is for separable continuous and integer domains while the second approach addresses general mixed-integer nonlinear problems. Klepeis and Floudas (1999a) presented a detailed comparative study of the putative global minimum structures of solvated oligopeptides where the solvation models employed were based on the area and volume accessible to the sol vent. proposed a novel deterministic global optimization approach for free energy calculations of peptides and presented extensive computational studies on solvated and unsolvated pentapeptides.…”

Predicting peptide structures using NMR data and deterministic global optimization

“…10 ᎐ 14 In more recent work, the algorithm has been shown to be successful for isolated peptide systems using the realistic ECEPPr3 potential energy model, 23,24 and including several solvation effects. 25,26 The ␣BB global optimization algorithm effectively brackets the global minimum solution by developing converging sequences of lower and upper bounds. These bounds are refined by iteratively partitioning the initial domain.…”