One of the major goals of molecular biology is to understand how protein chains fold into a unique 3-dimensional structure. Given this knowledge, perhaps the most exciting prospect will be the possibility of designing new proteins to perform designated tasks, an application that could prove to be of great importance in medicine and biotechnology. It is possible that effective protein design may be achieved without the requirement for a full understanding of the protein folding process. In this paper a simple method is described for designing an amino acid sequence to fit a given 3-dimensional structure. The compatibility of a designed sequence with a given fold is assessed by means of a set of statistically determined potentials (including interresidue pairwise and solvation terms), which have been previously applied to the problem of protein fold recognition. In order to generate sequences that best fit the fold, a genetic algorithm is used, whereby the sequence is optimized by a stochastic search in the style of natural selection.

De novo protein design using pairwise potentials and a genetic algorithm

New approaches in molecular structure prediction.

Aspects of protein energetics and dynamics

Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry.

In the context of simplified models of globular proteins, the requirements for the unique folding to a four-helix bundle have been addressed through a new Monte Carlo procedure. In particular, the relative im- portance of secondary versus tertiary interac- tions in determining the nature of the folded structure is examined. Various cases spanning the extremes where tertiary interactions com- pletely dominate to that where tertiary interac- tions are negligible have been explored. Not surprisingly, the folding to unique four-helix bundles is found to depend on an adequate bal- ance of the secondary and tertiary interactions. Moreover, because the simplified model is com- posed of spheres representing a-carbons and side chains, the geometry of the latter being based on small real amino acids, the role played by the side chains, and the problems associated with packing and hard-core repulsions, are considered. Also, possible folding intermedi- ates and their relationship with the experimen- tally observed molten globule state are ex- plored. From these studies, a general set of rules is extracted which should aid in the fur- ther design of more detailed protein models ad- equate to more fully investigate the protein folding problem. Finally, the relationship be- tween our conclusions and experimental work with specifically designed sequences is briefly discussed.

Computer Modeling and Folding of Four-Helix Bundles

What is the current state of the art in protein design? This question was approached in a recent two-week protein design workshop sponsored by EMBO and held at the EMBL in Heidelberg. The goals were to test available design tools and to explore new design strategies. Five novel proteins were designed: Shpilka, a sandwich of two four-stranded beta-sheets, a scaffold on which to explore variations in loop topology; Grendel, a four-helical membrane anchor, ready for fusion to water-soluble functional domains; Finger-clasp, a dimer of interdigitating beta-beta-alpha units, the simplest variant of the "handshake" structural class; Aida, an antibody binding surface intended to be specific for flavodoxin; Leather--a minimal NAD binding domain, extracted from a larger protein. Each design is available as a set of three-dimensional coordinates, the corresponding amino acid sequence and a set of analytical results. The designs are placed in the public domain for scrutiny, improvement, and possible experimental verification.

Stephen C. Emery

Papers

Protein design on computers. Five new proteins: Shpilka, grendel, fingerclasp, leather, and aida