Steven A. Benner
Structure, Function and Design of Macromolecules
One goal of contemporary biological chemistry is to gain manipulative control over proteins and nucleic acids, to understand their conformation and reactivity in terms of underlying chemical principles, to use them to meet biotechnological and pharmaceutical goals, and to join their chemical behavior directly to biological function in living systems. Over the past ten years, structural theory from chemistry and evolutionary theory from biology have been combined in S.A. Benner's research group to meet these goals. Research techniques are drawn from organic chemistry (synthesis of small molecules, polypeptides, nucleic acids, and nucleic acid analogs), enzymology (isolation, purification, kinetics, and physical measurements on enzymes), and molecular biology (cloning, heterologous expression, site-directed mutation).
In developing an understanding of protein conformation and reactivity, S.A. Benner's research group has used new computer data structures to organize the protein sequence database and match every subsequence in the database with every other subsequence. This has provided information necessary to model mutation, insertion, and deletion, the three fundamental processes in the divergent evolution of proteins. These models have supported methods for predicting the folded structure of proteins from sequence data alone. The methods have been proven by predicting the conformation of proteins before crystallographic data are available. In four cases now, subsequently determined crystal structures have shown the predictions to have been remarkably accurate. An understanding of conformation and reactivity in proteins has also permitted the rational de novo design of polypeptides that fold in solution and catalyze reactions.
Manipulation of proteins has been facilitated by techniques that permit site-specific alteration of the protein's sequence. These were the focus of the 1993 Nobel Prize in chemistry. S.A. Benner's research group has been using site directed mutation to study structure, catalysis, evolution and the physiological of ribonucleases. An understanding of the function of ribonucleases has supported efforts to design small molecules that reproduce the catalytic activity of the enzyme. Further, ribonucleases from extinct organisms that are intermediates in the evolution of the ribonuclease family have been prepared in the laboratory. These have provided a better view of how this family of proteins have arisen, allowed the development of immunosuppressive and cytostatic variants of ribonuclease, and led to unexpected discoveries of new physiological roles for ribonucleases. Mutation has also allowed the preparation of modified forms of ribonuclease and alcohol dehydrogenase with altered substrate specificity, stability, and stereospecificity, and a small research program in applied enzymology has explored the application of enzymes to small and intermediate scale synthesis of chiral organic compounds.
Work in S.A. Benner's research group in nucleic acid chemistry has focused on the redesign of nucleic acids, and the chemical, enzymatic and physiological properties of redesigned oligonucleotides. Nucleic acids bearing bases with non-standard hydrogen bonding patterns increases the number of base pairs in nucleic acids capable of independent recognition. These have allowed the incorporation of a non-standard amino acid into a polypeptide by ribosome-based translation of a non-standard mRNA. The enzymology of these new base pairs is being studied in detail. The phosphate diester linkages in the backbone of natural oligonucleotides has been replaced in analogs of oligonucleotides joined by sulfur. These have shown promise as anti-sense oligonucleotide analogs.