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Engineering and design
Engineering and design Editorial overview Bjiirn Nilsson and William F DeGrado Pharmacia
AB, Stockholm,
Sweden and The Du Pont Merck Pharmaceutical
Current
Opinion
in Structural
Protein engineering and design are exciting disciplines in which theoretical hypotheses derived from the analysis of three-dimensional structures are tested experimentally. The motivation for a given experiment could be to corroborate a model or, very often it seems, simply to tinker in an attempt to learn something new. In the early days of protein engineering much of the research was methodological in focus, leading to a technology basis that now allows numerous new practical applications. Today, protein engineering is ubiquitously used to elucidate structure/fimction relationships and to manipulate the properties of therapeutically important proteins and industrial enzymes. Similarly, the field of de nova protein design has matured from generating molten-globular structures into understanding the basic rules underlying packing of secondary elements into native and ordered structures.
This year’s section on engineering and design contains six selected topics that describe nicely these recent trends. Three of these topics (phage display, antibody engineering, and the design of a-helical peptides and proteins) have been extensively reviewed, and therefore these three papers highlight only the most recent progress in these intensive fields. The three remaining papers describe areas that have not been reviewed recently (folding of p-sheet proteins, superantigen engineering, and engineering of IgG-binding proteins), and these papers should give the reader an insight into recent progress in these interesting areas.
The paper by O’Neil and Hoess (pp 443-449) describes recent progress of phage-display technologies. The basic idea of displaying peptides on the surface of fllamentous phages is more than 10 years old, but most of the developments and applications of this technology have emerged only during the past few years. Phage display is, without doubt, a breakthrough in the field of protein engineering. In recent years, the versatility of the technology has expanded rapidly into novel areas, including DNA-binding proteins, protein folding, and protein-protein interactions. In addition, the platform of technologies is constantly improving. 0 Current
Biology
Biology
1995,
Co, Wilmington,
USA
5:441-442
Antibodies are among the most frequently engineered class of proteins, and the paper by Nilsson (pp 450-456) reviews recent trends in this field. Novel applications of antibody engineering and the generation of large libraries constitute the most recent advances in the field. The use of the antibody fold is questioned in the paper, and alternative scaffolds could prove more favorable for many future applications, as also independently pointed out by O’Neil and Hoess. Betz, Bryson and DeGrado (pp 457-463) deal with the rapidly maturing area of designing a-helical bundles. They describe how de novo design has advanced our understanding of how a molten globule may be packed into a native-like structure. The rules governing the topology of coiled coils, three-helix bundles and fourhelical bundles are also discussed. An emerging theme is that proteins achieve unique conformations through the destabilization of alternative conformations - a feature which seems to be as important as stabilization of the preferred topology. The paper by AbrahmsCn (pp 464-470) describes the engineering of bacterial superantigens, an area that has not been reviewed previously in this journal. Superantigens are extremely potent activators of the immune system, and protein engineering has been used extensively in recent years to study their mode of action. These studies have revealed very interesting differences among the mechanisms of the structurally related bacterial superantigens. In combination with recent structural work, the protein engineering data have generated models of how these superantigens act at the molecular level by interacting with the T-cell receptor and MHC class II molecules in an antigen-independent manner. Bacterial IgG-binding receptors comprise an interesting class of proteins, and have been the target of extensive protein engineering and structural work in recent years, as described by Tashiro and Montelione (pp 471-481). Staphylococcal protein A and streptococcal protein G exhibit very similar modes of biological action (strong Fc binding and weak Fab binding) and the binding domains are of almost identical size (60 amino acids). Yet, Ltd ISSN 0959-440X
441
442
Engineering and design most interestingly, the folds are completely different and their binding sites for Fc are structurally distinct. In the final article in this section, Carlsson and Jonsson (pp 482-487) describe the use of protein engineering, H/D exchange, and mass spectrometry to study the folding of p-sheet proteins. These studies have revealed many interesting differences between B-sheet and the more fiequently studied a-helical folds. In the field of protein engineering, the introduction of cysteine residues and the mutagenesis of tryptophan residues have revealed interesting details in the folding mechanism of all b sheet
proteins, such as carbonic anhydrase II. These results can be evaluated against studies of different p-sheet proteins studied previously using other techniques (IL-l p and the SH3 domain) _
B Nilsson, Department of Structural Biochemistry, Pharmacia AB, Biopharmaceuticals, S-l 12 87 Stockholm, Sweden. WF DeGrado, The Du Pont Merck Pharmaceutical Co, Research and Development, Experimental Station, PO Box 80328, Wilmington, DE 19880-0328, USA.
AB, Stockholm,
Sweden and The Du Pont Merck Pharmaceutical
Current
Opinion
in Structural
Protein engineering and design are exciting disciplines in which theoretical hypotheses derived from the analysis of three-dimensional structures are tested experimentally. The motivation for a given experiment could be to corroborate a model or, very often it seems, simply to tinker in an attempt to learn something new. In the early days of protein engineering much of the research was methodological in focus, leading to a technology basis that now allows numerous new practical applications. Today, protein engineering is ubiquitously used to elucidate structure/fimction relationships and to manipulate the properties of therapeutically important proteins and industrial enzymes. Similarly, the field of de nova protein design has matured from generating molten-globular structures into understanding the basic rules underlying packing of secondary elements into native and ordered structures.
This year’s section on engineering and design contains six selected topics that describe nicely these recent trends. Three of these topics (phage display, antibody engineering, and the design of a-helical peptides and proteins) have been extensively reviewed, and therefore these three papers highlight only the most recent progress in these intensive fields. The three remaining papers describe areas that have not been reviewed recently (folding of p-sheet proteins, superantigen engineering, and engineering of IgG-binding proteins), and these papers should give the reader an insight into recent progress in these interesting areas.
The paper by O’Neil and Hoess (pp 443-449) describes recent progress of phage-display technologies. The basic idea of displaying peptides on the surface of fllamentous phages is more than 10 years old, but most of the developments and applications of this technology have emerged only during the past few years. Phage display is, without doubt, a breakthrough in the field of protein engineering. In recent years, the versatility of the technology has expanded rapidly into novel areas, including DNA-binding proteins, protein folding, and protein-protein interactions. In addition, the platform of technologies is constantly improving. 0 Current
Biology
Biology
1995,
Co, Wilmington,
USA
5:441-442
Antibodies are among the most frequently engineered class of proteins, and the paper by Nilsson (pp 450-456) reviews recent trends in this field. Novel applications of antibody engineering and the generation of large libraries constitute the most recent advances in the field. The use of the antibody fold is questioned in the paper, and alternative scaffolds could prove more favorable for many future applications, as also independently pointed out by O’Neil and Hoess. Betz, Bryson and DeGrado (pp 457-463) deal with the rapidly maturing area of designing a-helical bundles. They describe how de novo design has advanced our understanding of how a molten globule may be packed into a native-like structure. The rules governing the topology of coiled coils, three-helix bundles and fourhelical bundles are also discussed. An emerging theme is that proteins achieve unique conformations through the destabilization of alternative conformations - a feature which seems to be as important as stabilization of the preferred topology. The paper by AbrahmsCn (pp 464-470) describes the engineering of bacterial superantigens, an area that has not been reviewed previously in this journal. Superantigens are extremely potent activators of the immune system, and protein engineering has been used extensively in recent years to study their mode of action. These studies have revealed very interesting differences among the mechanisms of the structurally related bacterial superantigens. In combination with recent structural work, the protein engineering data have generated models of how these superantigens act at the molecular level by interacting with the T-cell receptor and MHC class II molecules in an antigen-independent manner. Bacterial IgG-binding receptors comprise an interesting class of proteins, and have been the target of extensive protein engineering and structural work in recent years, as described by Tashiro and Montelione (pp 471-481). Staphylococcal protein A and streptococcal protein G exhibit very similar modes of biological action (strong Fc binding and weak Fab binding) and the binding domains are of almost identical size (60 amino acids). Yet, Ltd ISSN 0959-440X
441
442
Engineering and design most interestingly, the folds are completely different and their binding sites for Fc are structurally distinct. In the final article in this section, Carlsson and Jonsson (pp 482-487) describe the use of protein engineering, H/D exchange, and mass spectrometry to study the folding of p-sheet proteins. These studies have revealed many interesting differences between B-sheet and the more fiequently studied a-helical folds. In the field of protein engineering, the introduction of cysteine residues and the mutagenesis of tryptophan residues have revealed interesting details in the folding mechanism of all b sheet
proteins, such as carbonic anhydrase II. These results can be evaluated against studies of different p-sheet proteins studied previously using other techniques (IL-l p and the SH3 domain) _
B Nilsson, Department of Structural Biochemistry, Pharmacia AB, Biopharmaceuticals, S-l 12 87 Stockholm, Sweden. WF DeGrado, The Du Pont Merck Pharmaceutical Co, Research and Development, Experimental Station, PO Box 80328, Wilmington, DE 19880-0328, USA.