Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures.
The computational identification of the optimal three-dimensional fold of even a small peptide chain from its sequence, without reference to other known structures, is a complex problem. There have been several attempts at solving this by sampling the potential energy surface of the molecule in a systematic manner. Here we present a new method to carry out the sampling, and to identify low energy conformers of the molecule. The method uses mutually orthogonal Latin squares to select (of the order of) n(2) points from the multidimensional conformation space of size m(n), where n is the number of dimensions (i.e., the number of conformational variables), and m specifies the fineness of the search grid. The sampling is accomplished by first calculating the value of the potential energy function at each one of the selected points. This is followed by analysis of these values of the potential energy to obtain the optimal value for each of the n-variables separately. We show that the set of the n-optimal values obtained in this manner specifies a low energy conformation of the molecule. Repeated application of the method identifies other low energy structures. The computational complexity of this algorithm scales as the fourth power of the size of the molecule. We applied this method to several small peptides, such as the neuropeptide enkephalin, and could identify a set of low energy conformations for each. Many of the structures identified by this method have also been previously identified and characterized by experiment and theory. We also compared the best structures obtained for the tripeptide (Ala)(3) by the present method, with those obtained by an exhaustive grid search, and showed that the algorithm is successful in identifying all the low energy conformers of this molecule.
Vengadesan
K
K
Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India.
Gautham
N
N
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004745:Enkephalins / Q000737:chemistry; D018499:Linear Energy Transfer; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011786:Quality Control; D018401:Sample Size
D004745:Enkephalins; D009842:Oligopeptides; D010455:Peptides; C039944:alanyl-alanyl-alanine