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Proteins
701
Proteins Editorial overview Johann Deisenhofer* and Janet L Smith† Addresses *Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA; e-mail: [email protected] † Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; e-mail: [email protected] Current Opinion in Structural Biology 2001, 11:701–702 0959-440X/01/$ — see front matter © 2001 Elsevier Science Ltd. All rights reserved.
Proteins continue to surprise and amaze us in the myriad of ways in which they achieve biological function. The Proteins section in this issue of Current Opinion in Structural Biology highlights several proteins in which large conformational changes and evolutionary divergence in structure and function, play essential roles in their adaptation to a variety of biological functions. In addition, fundamental advances have been made in research, spurred on by industrial interest in the use of proteins as drug targets or as catalysts. All of the reviews in this section document the fact that multiple crystal structures of a protein in different functional states, and of different members of protein families, are necessary for the composition of a complete structural picture. The nuclear core complex is one of the macromolecular machines that remains a formidable challenge to structural biologists. The import and export of proteins through the nuclear core complex are fascinating processes, the first details of which have come to light only recently. In the first article, Chook and Blobel (pp 703–715) review structures of the karyopherins (importins and exportins), their complexes with substrates, with the regulator RanGTPase and with fragments from the nuclear core complex itself. These structures provide glimpses of some of the many protein–protein interactions that must take place during the transport process. The reductionist approach taken by the structural biologists has clearly been enforced by the sheer size and complexity of the problem, but nevertheless, has already led to important insights. Still, the article leaves no doubt that it will take time until we fully understand transport through the nuclear membrane. Conformational changes, caused by binding, hydrolysis and release of nucleotides are the essence of the mechanism of molecular motors. Sablin and Fletterick (pp 716–724) present an overview of the current state of knowledge which has led to a convergent view of kinesin and myosin; two types of motors that not long ago were considered unrelated. They also emphasize the relationship between the conformational transitions in motors and those that occur in G proteins upon the binding and hydrolysis of ATP and GTP, respectively. This utilization
of nucleotide–triphosphates is one of the grand unifying themes in biology. Leucine-rich repeats (LRRs) caused some astonishment when the crystal structure of the ribonuclease inhibitor was first reported. Our perception of ‘globular’ proteins was unprepared for the horseshoe shape of this molecule. Kobe and Kajava (pp 725–732) bring us up to date on the new structures of LRR proteins. These include proteins with LRRs of various lengths, ranging from 20–41 amino acid residues; often, the LRRs are embedded into the sequences of much larger proteins. The available structures provide insight into the structural plasticity of the LRR motif. Its suitability for taking part in protein–protein interactions appears to be the main functional characteristic. The protein family named PRT — after the phosphoribosyltransferase enzymes — is a diverse protein group whose unifying motif is structural, but whose members have different functions. Sinha and Smith (pp 733–739) review some of the 40 crystal structures of the 16 different PRT proteins known to date. This family is a striking example of the inventiveness of protein evolution. Some structural elements, especially a ‘flexible loop’, are employed for a variety of purposes, whereas others remain largely unchanged. Conformational change and a stable folding intermediate are exploited by the serpins to regulate the activity of a wide variety of proteolytic enzymes. Ye and Goldsmith (pp 740–745) review the latest important discoveries about this fascinating group of proteins. The process of serpin inhibition has been difficult to elucidate and the field is somewhat controversial because the structural biochemistry of serpins is unprecedented and the reaction pathway is not 100% robust. The newest player in the game, the p35 caspase inhibitor, is not strictly a serpin, but uses the same strategy as the serpins to control proteolysis; large-scale conformational change and the addition of strands to a β-sheet. Undoubtedly, more varied examples are yet to come. Two papers concern proteins that are important drug targets. Istvan (pp 746–751) reviews the fascinating story of HMG-CoA reductase, an essential enzyme in cholesterol biosynthesis and the target of the statin class of cholesterollowering drugs. Recently elucidated structures of substrate and inhibitor complexes of the human and eubacterial enzymes have advanced the understanding of catalysis and specificity of HMG-CoA. Its complicated active site reveals a remarkable combination of divergence and conservation among the three sub-sites for HMG, CoA and NAD(P) binding. The binding sites for HMG and for the nicotinamide end of NAD(P) are different; in the mammalian and
702
Proteins
eubacterial enzymes, different lysine side chains are catalytic and hydride transfer takes place from opposite sides of the nicotinamide ring. Istvan also points out that the HMG binding sites are sufficiently different that antibacterial compounds may be designed to specifically target the bacterial enzyme. Kurumbail, Kiefer and Marnett (pp 752–760) tell a rather different catalytic story. The cyclooxygenases are targets of anti-inflammatory drugs and act on variants of arachidonic acid. In contrast to HMG-CoA reductase, the two human COX isozymes have virtually identical catalytic centers. However, their substrate and inhibitor specificities differ. An unusual feature of the COX enzymes is the combination of specificity and promiscuity at their active sites. The oxygenation reactions are highly stereospecific, but the isoprenoid substrates can be bound in a variety of conformations. New structures and new kinetic and biophysical
studies are beginning to help us to unravel the mechanism of this interesting enzyme. Research that has been driven by the development of anti-inflammatory drugs targeted to COX-2 has also revealed new substrates of biological relevance. Another topic of industrial interest is that of protein life in organic solvents. Mattos and Ringe (pp 761–764) review recent work on the catalysis and basic structural properties of proteins in hydrophobic solvent systems. In this inside-out environment, native conformations are thought to be maintained by favorable interactions of polar groups inside the proteins. Ordered solvent molecules appear to associate more frequently with binding sites than with other areas of the protein surface. The ability to transfer proteins into nonpolar solvents is being used to develop industrial protein catalysts, to study protein folding and to elucidate the ligand binding or active sites in proteins of unknown function.
Proteins Editorial overview Johann Deisenhofer* and Janet L Smith† Addresses *Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75235-9050, USA; e-mail: [email protected] † Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; e-mail: [email protected] Current Opinion in Structural Biology 2001, 11:701–702 0959-440X/01/$ — see front matter © 2001 Elsevier Science Ltd. All rights reserved.
Proteins continue to surprise and amaze us in the myriad of ways in which they achieve biological function. The Proteins section in this issue of Current Opinion in Structural Biology highlights several proteins in which large conformational changes and evolutionary divergence in structure and function, play essential roles in their adaptation to a variety of biological functions. In addition, fundamental advances have been made in research, spurred on by industrial interest in the use of proteins as drug targets or as catalysts. All of the reviews in this section document the fact that multiple crystal structures of a protein in different functional states, and of different members of protein families, are necessary for the composition of a complete structural picture. The nuclear core complex is one of the macromolecular machines that remains a formidable challenge to structural biologists. The import and export of proteins through the nuclear core complex are fascinating processes, the first details of which have come to light only recently. In the first article, Chook and Blobel (pp 703–715) review structures of the karyopherins (importins and exportins), their complexes with substrates, with the regulator RanGTPase and with fragments from the nuclear core complex itself. These structures provide glimpses of some of the many protein–protein interactions that must take place during the transport process. The reductionist approach taken by the structural biologists has clearly been enforced by the sheer size and complexity of the problem, but nevertheless, has already led to important insights. Still, the article leaves no doubt that it will take time until we fully understand transport through the nuclear membrane. Conformational changes, caused by binding, hydrolysis and release of nucleotides are the essence of the mechanism of molecular motors. Sablin and Fletterick (pp 716–724) present an overview of the current state of knowledge which has led to a convergent view of kinesin and myosin; two types of motors that not long ago were considered unrelated. They also emphasize the relationship between the conformational transitions in motors and those that occur in G proteins upon the binding and hydrolysis of ATP and GTP, respectively. This utilization
of nucleotide–triphosphates is one of the grand unifying themes in biology. Leucine-rich repeats (LRRs) caused some astonishment when the crystal structure of the ribonuclease inhibitor was first reported. Our perception of ‘globular’ proteins was unprepared for the horseshoe shape of this molecule. Kobe and Kajava (pp 725–732) bring us up to date on the new structures of LRR proteins. These include proteins with LRRs of various lengths, ranging from 20–41 amino acid residues; often, the LRRs are embedded into the sequences of much larger proteins. The available structures provide insight into the structural plasticity of the LRR motif. Its suitability for taking part in protein–protein interactions appears to be the main functional characteristic. The protein family named PRT — after the phosphoribosyltransferase enzymes — is a diverse protein group whose unifying motif is structural, but whose members have different functions. Sinha and Smith (pp 733–739) review some of the 40 crystal structures of the 16 different PRT proteins known to date. This family is a striking example of the inventiveness of protein evolution. Some structural elements, especially a ‘flexible loop’, are employed for a variety of purposes, whereas others remain largely unchanged. Conformational change and a stable folding intermediate are exploited by the serpins to regulate the activity of a wide variety of proteolytic enzymes. Ye and Goldsmith (pp 740–745) review the latest important discoveries about this fascinating group of proteins. The process of serpin inhibition has been difficult to elucidate and the field is somewhat controversial because the structural biochemistry of serpins is unprecedented and the reaction pathway is not 100% robust. The newest player in the game, the p35 caspase inhibitor, is not strictly a serpin, but uses the same strategy as the serpins to control proteolysis; large-scale conformational change and the addition of strands to a β-sheet. Undoubtedly, more varied examples are yet to come. Two papers concern proteins that are important drug targets. Istvan (pp 746–751) reviews the fascinating story of HMG-CoA reductase, an essential enzyme in cholesterol biosynthesis and the target of the statin class of cholesterollowering drugs. Recently elucidated structures of substrate and inhibitor complexes of the human and eubacterial enzymes have advanced the understanding of catalysis and specificity of HMG-CoA. Its complicated active site reveals a remarkable combination of divergence and conservation among the three sub-sites for HMG, CoA and NAD(P) binding. The binding sites for HMG and for the nicotinamide end of NAD(P) are different; in the mammalian and
702
Proteins
eubacterial enzymes, different lysine side chains are catalytic and hydride transfer takes place from opposite sides of the nicotinamide ring. Istvan also points out that the HMG binding sites are sufficiently different that antibacterial compounds may be designed to specifically target the bacterial enzyme. Kurumbail, Kiefer and Marnett (pp 752–760) tell a rather different catalytic story. The cyclooxygenases are targets of anti-inflammatory drugs and act on variants of arachidonic acid. In contrast to HMG-CoA reductase, the two human COX isozymes have virtually identical catalytic centers. However, their substrate and inhibitor specificities differ. An unusual feature of the COX enzymes is the combination of specificity and promiscuity at their active sites. The oxygenation reactions are highly stereospecific, but the isoprenoid substrates can be bound in a variety of conformations. New structures and new kinetic and biophysical
studies are beginning to help us to unravel the mechanism of this interesting enzyme. Research that has been driven by the development of anti-inflammatory drugs targeted to COX-2 has also revealed new substrates of biological relevance. Another topic of industrial interest is that of protein life in organic solvents. Mattos and Ringe (pp 761–764) review recent work on the catalysis and basic structural properties of proteins in hydrophobic solvent systems. In this inside-out environment, native conformations are thought to be maintained by favorable interactions of polar groups inside the proteins. Ordered solvent molecules appear to associate more frequently with binding sites than with other areas of the protein surface. The ability to transfer proteins into nonpolar solvents is being used to develop industrial protein catalysts, to study protein folding and to elucidate the ligand binding or active sites in proteins of unknown function.