Regulated proteolysis by the two-component NS2B/ NS3 protease of dengue virus is essential for virus replication and the maturation of infectious virions. The functional similarity between the NS2B/NS3 proteases from the four genetically and antigenically distinct serotypes was addressed by characterizing the differences in their substrate specificity using tetrapeptide and octapeptide libraries in a positional scanning format, each containing 130,321 substrates. The proteases from different serotypes were shown to be functionally homologous based on the similarity of their substrate cleavage preferences. A strong preference for basic amino acid residues (Arg/Lys) at the P1 positions was observed, whereas the preferences for the P2-4 sites were in the order of Arg > Thr > Gln/Asn/Lys for P2, Lys > Arg > Asn for P3, and Nle > Leu > Lys > Xaa for P4. The prime site substrate specificity was for small and polar amino acids in P1 and P3. In contrast, the P2 and P4 substrate positions showed minimal activity. The influence of the P2 and P3 amino acids on ground state binding and the P4 position for transition state stabilization was identified through single substrate kinetics with optimal and suboptimal substrate sequences. The specificities observed for dengue NS2B/NS3 have features in common with the physiological cleavage sites in the dengue polyprotein; however, all sites reveal previously unrecognized suboptimal sequences.Dengue virus is the etiologic agent of dengue fever, dengue hemorrhagic fever, and dengue shock syndrome and is the most prevalent arthropod-transmitted infectious disease in humans. Dengue consists of four closely related but antigenically distinct viral serotypes (DEN1-4), 1 of the genus Flavivirus (1, 2).Following primary infection, lifelong immunity develops that prevents repeated assault by the same serotype but does not provide protection from a virus of a different serotype (3). Dengue diseases are endemic in the tropics and subtropics, and the viruses are maintained in a cycle that involves humans and the Aedes aegypti mosquito. Infection with dengue viruses produces a spectrum of clinical illness ranging from a nonspecific viral syndrome to severe and fatal hemorrhagic disease (1, 2). Currently there is no antiviral drug or vaccine available against dengue viruses, and the pathogenesis of the disease is poorly understood.As with other members of the Flaviviridae family, the genomes of the dengue viruses consist of a positive singlestranded RNA of ϳ10,700 bases in length (4). Co-translational processing and post-translational processing of the polyprotein give rise to three structural proteins and at least seven nonstructural proteins (4). The correct processing of these proteins is essential for virus replication and requires host proteases such as signalase and furin (5) and a two-component viral protease, NS2B/NS3 (4). Previous studies have shown that the N-terminal part of NS3 contains trypsin-like protease domain (6) and that the activity of NS3 was dependent on at least 40 amino ...

Thrombin is a serine protease that plays a central role in blood coagulation. It is inhibited by hirudin, a polypeptide of 65 amino acids, through the formation of a tight, noncovalent complex. Tetragonal crystals of the complex formed between human alpha‐thrombin and recombinant hirudin (variant 1) have been grown and the crystal structure of this complex has been determined to a resolution of 2.95 A. This structure shows that hirudin inhibits thrombin by a previously unobserved mechanism. In contrast to other inhibitors of serine proteases, the specificity of hirudin is not due to interaction with the primary specificity pocket of thrombin, but rather through binding at sites both close to and distant from the active site. The carboxyl tail of hirudin (residues 48‐65) wraps around thrombin along the putative fibrinogen secondary binding site. This long groove extends from the active site cleft and is flanked by the thrombin loops 35‐39 and 70‐80. Hirudin makes a number of ionic and hydrophobic interactions with thrombin in this area. Furthermore hirudin binds with its N‐terminal three residues Val, Val, Tyr to the thrombin active site cleft. Val1 occupies the position P2 and Tyr3 approximately the position P3 of the synthetic inhibitor D‐Phe‐Pro‐ArgCH2Cl. Thus the hirudin polypeptide chain runs in a direction opposite to that expected for fibrinogen and that observed for the substrate‐like inhibitor D‐Phe‐Pro‐ArgCH2Cl.

The cysteine protease CPP32 has been expressed in a soluble form in Escherichia coli and purified to >95% purity. The three-dimensional structure of human CPP32 in complex with the irreversible tetrapeptide inhibitor acetyl-Asp-Val-Ala-Asp fluoromethyl ketone was determined by x-ray crystallography at a resolution of 2.3 Å. The asymmetric unit contains a (p17/p12) 2 tetramer, in agreement with the tetrameric structure of the protein in solution as determined by dynamic light scattering and size exclusion chromatography. The overall topology of CPP32 is very similar to that of interleukin-1␤-converting enzyme (ICE); however, differences exist at the N terminus of the p17 subunit, where the first helix found in ICE is missing in CPP32. A deletion/insertion pattern is responsible for the striking differences observed in the loops around the active site. In addition, the P1 carbonyl of the ketone inhibitor is pointing into the oxyanion hole and forms a hydrogen bond with the peptidic nitrogen of Gly-122, resulting in a different state compared with the tetrahedral intermediate observed in the structure of ICE and CPP32 in complex with an aldehyde inhibitor. The topology of the interface formed by the two p17/p12 heterodimers of CPP32 is different from that of ICE. This results in different orientations of CPP32 heterodimers compared with ICE heterodimers, which could affect substrate recognition. This structural information will be invaluable for the design of small synthetic inhibitors of CPP32 as well as for the design of CPP32 mutants.Genetic and biochemical studies have established the importance of the CED3/ICE 1 proteases in programmed cell death or apoptosis (1-4). Of the known mammalian CED3/ICE proteases, CPP32 is the most similar in sequence homology and substrate specificity to the CED3 protease (2, 5), whose function is required for programmed cell death in the developing Caenorhabditis elegans hermaphrodite (6). CED3/ICE proteases are synthesized as single chain proenzymes that are cleaved proteolytically to produce catalytically active cysteine proteases with specificity for cleavage at Asp-X peptide bonds (7-9). In several apoptotic model systems, CPP32 is rapidly processed from its p32 proenzyme form to a p17/p12 catalytically active form (10 -12). Cleavage and activation of CPP32 are thought to be mediated by CED3/ICE proteases (12, 13), possibly including active CPP32 itself, MCH2, and/or MCH4 (14, 15). Several proteins that regulate cellular homeostasis and function, including poly(ADP-ribose) polymerase, the 70-kDa subunit of the U1 small ribonucleoprotein, the catalytic subunit of DNA-dependent protein kinase, and the Huntington's disease gene product (huntingtin), are thought to be target substrates for activated CPP32 (8, 16 -18). Thus, activation of CED3/ICE proteases, including CPP32, within pre-apoptotic cells is thought to lead to the proteolytic inactivation of proteins that are necessary for cell viability. In support of this hypothesis, CED3/ICE protease inhibitors have been shown to bl...

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Transforming growth factors /? belong to a group of cytokines that control cellular proliferation and differentiation. Five isoforms are known that share approximately 75% sequence identity, but exert different biological activities. The structure of TGF-/?3 was solved by X-ray crystallography and refined to a final R-factor of 17.5% at 2.0 A resolution. Comp~ison with the structure of TGF-02 (Schlunegger MP, Grutter MG, 1992, Nature 358430-434; Daopin S, Piez KA, Ogawa Y, Davies DR, 1992, Science 252369-373) reveals a virtually identical central core. Differences exist in the conformations of the N-terminal a-helix and in the P-sheet loops. In TGF-03, the N-terminal cu-helix has moved = 1 A away from the central core. This movement can be correlated with the mutation of Leu 17 to Val and Ala 47. to Pro in TGF-63. The /?-sheet loops rotate as a rigid body 9" around an axis that runs approximately parallel to the dimer axis. If these differences are recognized by the TGF-0 receptors, they might account for the individual cellular responses. A molecule of the precipitating agent dioxane is bound in a crystal contact, forming a hydrogen bond with Trp 32. This dioxane may occupy a carbohydrate-binding site, because dioxane possesses some structural similarity with a carbohydrate. The dioxane is in contact with two tryptophans, which are often involved in carbohydrate recognition.