An energy-based mapping method for identifying the in-plane orientations of polypeptides and other macromolecules at crystalline interfaces

We present an energy-based algorithm, POINTER, which can determine the perm issible alignments of a polypeptide (or other macromolecule) with respect t o the lattice vectors of an interfacial surface (this alignment is defined by the angle theta). The algorithm represents both the interface and the ma cromolecule in three dimensions. For each value of theta, incremental moves of the macromolecule occur in the x, y, z direction along the theta orient ation, as well as rotation (omega, gamma, zeta) of either the macromolecula r chain or the interfacial slab. We utilized a simple forcefield that consi sts of a dipole-dipole, dipole-charge, or charge-charge electrostatic inter action term and a Lennard-Jones attraction-repulsion term to describe the n onbonding interactions between macromolecular atoms and interfacial atoms. We benchmarked our method by modeling ice- and mineral-interaction polypept ides on various Miller planes of hexagonal ice and inorganic solids, respec tively. In addition, we searched phase space for a simpler, nonpolypeptide system: The ice-nucleating C31 alcohol monolayer (comprised of 61 C31 molec ules) in contact with the {001} plane of hexagonal ice. Our results indicat e that the POINTER simulation method can reproduce the macromolecule orient ation observed for each benchmark system. In addition, our simulations poin t to a number of factors-polypeptide binding site structure, the positionin g of hydrophobic residues near the interface, and interface topology-which can influence the adsorption orientation of polypeptides on hexagonal ice a nd inorganic solids. (C) 2000 American Institute of Physics. [S0021-9606(00 )70211-X].