Photosynthetic reaction centers: interfacing molecular genetics and optical spectroscopy

Topological study of PSI-A and PSI-B, the large subunits of the photosystem-I reaction center

The core of the photosystem-I reaction center is formed by polypeptides PSI-A and PSI-B, the products of the homologous psaA and psaB genes. Based on hydropathy analyses, models have been proposed for the folding of these polypeptide chains in the membrane [Fish, L. E., Kück, U. & Bogorad, L. (1985), in Molecular biology of the photosynthetic apparatus, pp. 111-120, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY]. To test these models, we have tried to identify regions of PSI-A that are exposed to the surrounding medium, on the stromal or lumenal surface of the membrane. Immunogold labeling of thylakoid vesicles, with antibodies to synthetic peptides, shows that residues 413-421 of PSI-A are exposed on the stromal surface of the membrane, and that the accessibility of this region is enhanced by NaSCN treatment, which removes extrinsic polypeptides. This treatment also enhances a trypsin-cleavage site which may lie just after residues 413-421. Immunogold labeling also indicates that residues 371-379 and 497-505 are exposed on the lumenal surface. These results establish the conformation of the central portion of the polypeptide. Assuming that the transmembrane regions are correctly predicted by the 11-helix model, the N-terminal domain, as well as the conserved region proposed to bind the iron-sulfur center FX, would be expected to be on the stromal surface.

An algorithm for protein engineering: simulations of recursive ensemble mutagenesis

An algorithm for protein engineering, termed recursive ensemble mutagenesis, has been developed to produce diverse populations of phenotypically related mutants whose members differ in amino acid sequence. This method uses a feedback mechanism to control successive rounds of combinatorial cassette mutagenesis. Starting from partially randomized "wild-type" DNA sequences, a highly parallel search of sequence space for peptides fitting an experimenter's criteria is performed. Each iteration uses information gained from the previous rounds to search the space more efficiently. Simulations of the technique indicate that, under a variety of conditions, the algorithm can rapidly produce a diverse population of proteins fitting specific criteria. In the experimental analog, genetic selection or screening applied during recursive ensemble mutagenesis should force the evolution of an ensemble of mutants to a targeted cluster of related phenotypes.

Optimizing Nucleotide Mixtures to Encode Specific Subsets of Amino Acids for Semi-Random Mutagenesis

In random mutagenesis, synthesis of an NNN triplet (i.e. equiprobable A, C, G, and T at each of the three positions in the codon) could be considered an optimal nucleotide mixture because all 20 amino acids are encoded. NN(G,C) might be considered a slightly more intelligent "dope" because the entire set of amino acids is still encoded using only half as many codons. Using a general algorithm described herein, it is possible to formulate more complex doping schemes which encode specific subsets of the twenty amino acids, excluding others from the mix. Maximizing the equiprobability of amino acid residues contributing to such a subset is suggested as an optimal basis for performing semi-random mutagenesis. This is important for reducing the nucleotide complexity of combinatorial cassettes so that "sequence space" can be searched more efficiently. Computer programs have been developed to provide tables of optimized dopes compatible with automated DNA synthesizers.