The Alacoil is an antiparallel (rather than the usual parallel) coiled-coil of a-helices with Ala or another small residue in every seventh position, allowing a very close spacing of the helices (7.5-8.5 A between local helix axes), often over four or five helical turns. It occurs in two distinct types that differ by which position of the heptad repeat is occupied by Ala and by whether the closest points on the backbone of the two helices are aligned or are offset by half a turn. The aligned, or ROP, type has Ala in position "d" of the heptad repeat, which occupies the "tip-to-tip" side of the helix contact where the Ca-Cp bonds point toward each other. The more common offset, or ferritin, type of Alacoil has Ala in position "a" of the heptad repeat (where the Ca-Cp bonds lie back-to-back, on the "knuckle-touch" side of the helix contact), and the backbones of the two helices are offset vertically by half a turn. In both forms, successive layers of contact have the Ala first on one and then on the other helix.The Alacoil structure has much in common with the coiled-coils of fibrous proteins or leucine zippers: both are a-helical coiled-coils, with a critical amino acid repeated every seven residues (the Leu or the Ala) and a secondary contact position in between. However, Leu zippers are between aligned, parallel helices (often identical, in dimers), whereas Alacoils are between antiparallel helices, usually offset, and much closer together. The Alacoil, then, could be considered as an "Ala anti-zipper.'' Leu zippers have a classic "knobs-into-holes" packing of the Leu side chain into a diamond of four residues on the opposite helix; for Alacoils, the helices are so close together that the Ala methyl group must choose one side of the diamond and pack inside a triangle of residues on the other helix.We have used the ferritin-type Alacoil a; the basis for the de novo design of a 66-residue, coiled helix hairpin called "Alacoilin." Its sequence is: cmSPDQWDKE AAQYDAHAQE FEKKSHRNng TPEADQYRHM ASQY QAMAQK LKAIANQLKK Gsetcr (with "a" heptad positions underlined and nonhelical parts in lowercase), which we will produce and test for both stability and uniqueness of structure.Keywords: Alacoil; coiled-coil; helix contacts; protein design; side-chain packing; zipper The work reported here has two distinct origins: one in the generalized study of helix-packing interactions, and the other in the current challenges of de novo protein design. Both sets of background considerations are briefly summarized here.The formation of contacts between a-helices is an impwtant part of the assembly of protein tertiary structure. Several general descriptions have been given of how side chains on the surface of helices can fit together to achieve particular geometries

We describe a new paradigm for modeling proteins in interactive computer graphics systems-continual maintenance of a physically valid representation, combined with direct user control and visualization. This is achieved by a fast algorithm for energy minimization, capable of real-time performance on all atoms of a small protein, plus graphically specified user tugs. The modeling system, called Sculpt, rigidly constrains bond lengths, bond angles, and planar groups (similar to existing interactive modeling programs), while it applies elastic restraints to minimize the potential energy due to torsions, hydrogen bonds, and van der Waals and electrostatic4 interactions (similar to existing batch minimization programs), and user-specified springs. The graphical interface can show bad and/or favorable contacts, and individual energy terms can be turned on or off to determine their effects and interactions.Sculpt finds a local minimum of the total energy that satisfies all the constraints using an augmented Lagrangemultiplier method; calculation time increases only linearly with the number of atoms because the matrix of constraint gradients is sparse and banded. On a 100-MHz MIPS R4000 processor (Silicon Graphics Indigo), Sculpt achieves 11 updates per second on a 20-residue fragment and 2 updates per second on an 80-residue protein, using all atoms except non-H-bonding hydrogens, and without electrostatic interactions. Applications of Sculpt are described: to reverse the direction of bundle packing in a designed 4-helix bundle protein, to fold up a 2-stranded @-ribbon into an approximate @-barrel, and to design the sequence and conformation of a 30-residue peptide that mimics one partner of a protein subunit interaction. Computer models that are both interactive and physically realistic (within the limitations of a given force field) have 2 significant advantages: (1) they make feasible the modeling of very large changes (such as needed for de novo design), and ( 2 ) they help the user understand how different energy terms interact to stabilize a given conformation. The Sculpt paradigm combines many of the best features of interactive graphical modeling, energy minimization, and actual physical models, and we propose it as an especially productive way to use current and future increases in computer speed. Keywords: energy minimization; interactive computer graphics; molecular modeling; protein structure.We describe a new paradigm for modeling proteins in interactive computer graphics systems -continual maintenance of a physically valid representation, combined with direct user control and visualization. A modeling system, called Sculpt, maintains valid bond lengths, bond angles, and van der Waals separations in a model as a user changes its structure by interactively moving atoms, peptides, and side chains. Like a phys- ical model, Sculpt prevents certain movements due to bond rigidity, propagates changes throughout a model due to coupling in secondary structure or packing, and changes local conformation when ...

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