Computational design of receptor and sensor proteins with novel functions

Abstract

The formation of complexes between proteins and ligands is fundamental to biological processes at the molecular level. Manipulation of molecular recognition between ligands and proteins is therefore important for basic biological studies and has many biotechnological applications, including the construction of enzymes, biosensors, genetic circuits, signal transduction pathways and chiral separations. The systematic manipulation of binding sites remains a major challenge. Computational design offers enormous generality for engineering protein structure and function. Here we present a structure-based computational method that can drastically redesign protein ligand-binding specificities. This method was used to construct soluble receptors that bind trinitrotoluene, l-lactate or serotonin with high selectivity and affinity. These engineered receptors can function as biosensors for their new ligands; we also incorporated them into synthetic bacterial signal transduction pathways, regulating gene expression in response to extracellular trinitrotoluene or l-lactate. The use of various ligands and proteins shows that a high degree of control over biomolecular recognition has been established computationally. The biological and biosensing activities of the designed receptors illustrate potential applications of computational design.

Computational design of antibody-affinity improvement beyond in vivo maturation

“…Previous work has addressed many problems related to the design of improved protein-protein binding affinity, such as the design of stable protein folds 2-4 , binding pockets for peptides and small molecules [5][6][7] , altered protein-protein specificity [8][9][10][11][12] , and altered enzymatic activity [13][14][15] . The design of improved antigen-binding affinity has met with limited success, however [16][17][18][19] .…”

Using multi-objective computational design to extend protein promiscuity

“…Their applications are enormous, and enzyme design holds the promise to provide important impact in society areas like medicine (i.e. treatment of neurodegenerative diseases [2], design of therapeutically antibodies to bind tumor-associated antigenic determinants while maintaining a small immunogenicity, development of peptide-based vaccines), biotechnology (biosensors [3,4], biocatalysts with activity in non-natural environments) and bioremediation (design of enzymes that would reduce waste by-products and toxicity [5]). …”

Editorial: Protein Design

“…[5] In parallel, numerous genome-sequencing projects and structural genomics initiatives provided huge data bases for the correlation of the amino acid sequence of a protein with its structure and function. The clever use of these data for the development of new algorithms resulted in the creation of artificial highaffinity receptors for non-natural ligands [6] and culminated recently in the design from scratch of a small protein with a novel folding topology. This completely artificial protein had all the hallmarks of a natural protein, while its crystal structure revealed that the three-dimensional structure was essentially as planned in the design.…”