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Engineering and design 2001: A Design Odyssey Editorial overview
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Engineering and design 2001: A Design Odyssey Editorial overview Lynne Regan Addresses Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; e-mail: [email protected] Current Opinion in Structural Biology 2001, 11:449 0959-440X/01/$ — see front matter © 2001 Elsevier Science Ltd. All rights reserved.
“The most exciting phrase to hear in science, the one that heralds the most discoveries, is not ‘Eureka’ but ‘That’s funny…’” Isaac Asimov “Nothing is a waste of time if we use the experience wisely” Auguste Rodin The past decade has been a time of enormous excitement and achievement in the area of protein engineering and design — previously unimaginable successes have been realized. It has proven possible to create protein scaffolds of de novo design and to modify the activities of proteins in a rational fashion. During this period of intense activity, not all designs have turned out exactly as planned, but much has been learnt by the thorough characterization of these ‘experiences’. The review by Oakley and Hollenbeck (pp 450–457) discusses the design considerations associated with an apparently simple motif: self-associating helices. Two-, three- and four-stranded coiled coils play a variety of roles in nature, from mediating protein–protein interactions to RNA recognition. A key issue is the ability to specify the details of helix association: two or three stranded; parallel or antiparallel? Although considerable progress has been made, the design of associating helices illustrates that, although secondary structure is relatively easy to achieve, defining unique tertiary interactions is a greater challenge. Oakley and Hollenbeck discuss the problems associated with specifying a unique association state. Although there are examples in which a single oligomeric state or conformation forms crystals, these molecules often exist as an equilibrium population in solution. In a related review, Issac, Ham and Chmielewski (pp 458–463) discuss how the lessons learnt from the design of associating helices can be applied, in this case to self-replicating peptides. In nature, both DNA and RNA can replicate to generate any number of exact copies of the original molecule; extant proteins do not possess this ability. After synthesis, proteins are active, but rely upon their nucleic acid blueprint to generate additional copies.
Was this always the case? Chmielewski and colleagues speculate upon possible evolutionary implications of the self-replicating designs, in addition to detailing their interesting chemical properties. Woolfson (pp 464–471) discusses the design of the hydrophobic core of proteins in a more general context. He illustrates the review with a number of redesigns in which the entire hydrophobic core of a protein has been ‘repacked’ by design. In some examples, optimizing the packing and hydrophobicity of the core residues results in proteins that are substantially more stable than the parent or natural fold. In others, the designed proteins are more ‘molten-globule’ like in character. Through these studies, we are beginning to better understand the requirements for the design of proteins with native-like thermodynamic properties. Woolfson also raises a generally important issue, the power of combining design and selection to achieve desired goals. The synergy achieved by these two approaches in a variety of systems is remarkable. The theme of combining selection with design is extended in two other reviews. Michnick (pp 472–477) discusses elegantly designed systems in which genetic selections or screens are employed to investigate protein–protein interactions. Cheng, Calabro and Frankel (pp 478–484) discuss the design and selection of proteins with novel nucleic acid binding activities, from zinc-fingerbased DNA recognition to RRE-based RNA binding. The design of function is elaborated upon in the final two reviews. Kennedy and Gibney (pp 485–490) discuss the design of simple scaffolds that bind metal ions and heme. Such studies provide information that is complementary to that obtained from mutagenesis of natural metalloproteins or model compound studies. A remarkably wide range of redox potentials can be achieved in these simple designed systems. Gilardi, Fantizzi and Sadeghi (pp 491–499) discuss the usefulness of designed metalloproteins for electrochemical studies. The design of both the protein and electrode components of such systems is discussed in detail and a number of fascinating examples are described. The topics in this section were chosen to span the range from the de novo design of simple structural motifs to the incorporation of designed activities onto a number of protein frameworks. The authors discuss both expected and unexpected results of these efforts, and provide an exhilarating snapshot of the ever-maturing field of protein engineering and design.
Engineering and design 2001: A Design Odyssey Editorial overview Lynne Regan Addresses Department of Molecular Biophysics and Biochemistry, Department of Chemistry, Yale University, 266 Whitney Avenue, New Haven, CT 06511, USA; e-mail: [email protected] Current Opinion in Structural Biology 2001, 11:449 0959-440X/01/$ — see front matter © 2001 Elsevier Science Ltd. All rights reserved.
“The most exciting phrase to hear in science, the one that heralds the most discoveries, is not ‘Eureka’ but ‘That’s funny…’” Isaac Asimov “Nothing is a waste of time if we use the experience wisely” Auguste Rodin The past decade has been a time of enormous excitement and achievement in the area of protein engineering and design — previously unimaginable successes have been realized. It has proven possible to create protein scaffolds of de novo design and to modify the activities of proteins in a rational fashion. During this period of intense activity, not all designs have turned out exactly as planned, but much has been learnt by the thorough characterization of these ‘experiences’. The review by Oakley and Hollenbeck (pp 450–457) discusses the design considerations associated with an apparently simple motif: self-associating helices. Two-, three- and four-stranded coiled coils play a variety of roles in nature, from mediating protein–protein interactions to RNA recognition. A key issue is the ability to specify the details of helix association: two or three stranded; parallel or antiparallel? Although considerable progress has been made, the design of associating helices illustrates that, although secondary structure is relatively easy to achieve, defining unique tertiary interactions is a greater challenge. Oakley and Hollenbeck discuss the problems associated with specifying a unique association state. Although there are examples in which a single oligomeric state or conformation forms crystals, these molecules often exist as an equilibrium population in solution. In a related review, Issac, Ham and Chmielewski (pp 458–463) discuss how the lessons learnt from the design of associating helices can be applied, in this case to self-replicating peptides. In nature, both DNA and RNA can replicate to generate any number of exact copies of the original molecule; extant proteins do not possess this ability. After synthesis, proteins are active, but rely upon their nucleic acid blueprint to generate additional copies.
Was this always the case? Chmielewski and colleagues speculate upon possible evolutionary implications of the self-replicating designs, in addition to detailing their interesting chemical properties. Woolfson (pp 464–471) discusses the design of the hydrophobic core of proteins in a more general context. He illustrates the review with a number of redesigns in which the entire hydrophobic core of a protein has been ‘repacked’ by design. In some examples, optimizing the packing and hydrophobicity of the core residues results in proteins that are substantially more stable than the parent or natural fold. In others, the designed proteins are more ‘molten-globule’ like in character. Through these studies, we are beginning to better understand the requirements for the design of proteins with native-like thermodynamic properties. Woolfson also raises a generally important issue, the power of combining design and selection to achieve desired goals. The synergy achieved by these two approaches in a variety of systems is remarkable. The theme of combining selection with design is extended in two other reviews. Michnick (pp 472–477) discusses elegantly designed systems in which genetic selections or screens are employed to investigate protein–protein interactions. Cheng, Calabro and Frankel (pp 478–484) discuss the design and selection of proteins with novel nucleic acid binding activities, from zinc-fingerbased DNA recognition to RRE-based RNA binding. The design of function is elaborated upon in the final two reviews. Kennedy and Gibney (pp 485–490) discuss the design of simple scaffolds that bind metal ions and heme. Such studies provide information that is complementary to that obtained from mutagenesis of natural metalloproteins or model compound studies. A remarkably wide range of redox potentials can be achieved in these simple designed systems. Gilardi, Fantizzi and Sadeghi (pp 491–499) discuss the usefulness of designed metalloproteins for electrochemical studies. The design of both the protein and electrode components of such systems is discussed in detail and a number of fascinating examples are described. The topics in this section were chosen to span the range from the de novo design of simple structural motifs to the incorporation of designed activities onto a number of protein frameworks. The authors discuss both expected and unexpected results of these efforts, and provide an exhilarating snapshot of the ever-maturing field of protein engineering and design.