Generation of human TRIM5alpha mutants with high HIV-1 restriction activity.

Rhesus macaque tripartite motif (TRIM)5alpha potently inhibits early stages of human immunodeficiency virus (HIV)-1 replication, while the human orthologue has little effect on this virus. We used PCR-based random mutagenesis to construct a large library of human TRIM5alpha variants containing mutations in the PRYSPRY domain. We then applied a functional screen to isolate human cells made resistant to HIV-1 infection by the expression of a mutated TRIM5alpha. This protocol led to the characterization of a human TRIM5alpha variant containing a mutation at arginine 335 as conferring resistance to HIV-1 infection. The level of protection stemming from expression of this mutant was comparable to that of previously described mutations at position 332. R332/R335 double mutants decreased permissiveness to HIV-1 and to other lentiviruses by 20- to 50-fold in TE671 fibroblasts and in the T-cell line SUP-T1, and prevented HIV-1 spreading infection as efficiently as the rhesus macaque TRIM5alpha orthologue did. The finding that only two substitutions in human TRIM5alpha can confer resistance to HIV-1 at levels as high as one of the most potent natural orthologues of TRIM5alpha removes a roadblock toward the use of this restriction factor in human gene therapy applications.

Three-dimensional structure of the adenovirus major coat protein hexon.

The three-dimensional crystal structure of the adenovirus major coat protein is presented. Adenovirus type 2 hexon, at 967 residues, is now the longest polypeptide whose structure has been determined crystallographically. Taken with our model for hexon packing, which positions the 240 trimeric hexons in the capsid, the structure defines 60% of the protein within the 150 X 10(6) dalton virion. The assembly provides the first details of a DNA-containing animal virus that is 20 times larger than the spherical RNA viruses previously described. Unexpectedly, the hexon subunit contains two similar beta-barrels whose topology is identical to those of the spherical RNA viruses, but whose architectural role in adenovirus is very different. The hexon structure reveals several distinctive features related to its function as a stable protective coat, and shows that the type-specific immunological determinants are restricted to the virion surface.

Caspases: key players in programmed cell death.

Research in apoptosis has established a central role for caspases. The recent determination of structures of caspase-1, caspase-3 and caspase-8, together with biochemical studies, has greatly enhanced our understanding of the structure, function and specificity of these enzymes. This provides a basis for the further elucidation of the biological role of caspases and a guide to the design of selective inhibitors to treat caspase-mediated diseases.

Proteinase inhibitors: another new fold.

The three-dimensional descriptions of two serine proteinase inhibitors from the parasitic worm Ascaris--one in solution and the other in a complex with its substrate--reveal a new structural motif.

Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex with CGP 53820, a novel pseudosymmetric inhibitor.

BACKGROUND: The human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS). Two subtypes of the virus, HIV-1 and HIV-2, have been characterized. The protease enzymes from these two subtypes, which are aspartic acid proteases and have been found to be essential for maturation of the infectious particle, share about 50% sequence identity. Differences in substrate and inhibitor binding between these enzymes have been previously reported. RESULTS: We report the X-ray crystal structures of both HIV-1 and HIV-2 proteases each in complex with the pseudosymmetric inhibitor, CGP 53820, to 2.2 A and 2.3 A, respectively. In both structures, the entire enzyme and inhibitor could be located. The structures confirmed earlier modeling studies. Differences between the CGP 53820 inhibitory binding constants for the two enzymes could be correlated with structural differences. CONCLUSIONS: Minor sequence changes in subsites at the active site can explain some of the observed differences in substrate and inhibitor binding between the two enzymes. The information gained from this investigation may help in the design of equipotent HIV-1/HIV-2 protease inhibitors.

A new structural class of serine protease inhibitors revealed by the structure of the hirustasin-kallikrein complex.

BACKGROUND: Hirustasin belongs to a class of serine protease inhibitors characterized by a well conserved pattern of cysteine residues. Unlike the closely related inhibitors, antistasin/ghilanten and guamerin, which are selective for coagulation factor Xa or neutrophil elastase, hirustasin binds specifically to tissue kallikrein. The conservation of the pattern of cysteine residues and the significant sequence homology suggest that these related inhibitors possess a similar three-dimensional structure to hirustasin. RESULTS: The crystal structure of the complex between tissue kallikrein and hirustasin was analyzed at 2.4 resolution. Hirustasin folds into a brick-like structure that is dominated by five disulfide bridges and is sparse in secondary structural elements. The cysteine residues are connected in an abab cdecde pattern that causes the polypeptide chain to fold into two similar motifs. As a hydrophobic core is absent from hirustasin the disulfide bridges maintain the tertiary structure and present the primary binding loop to the active site of the protease. The general structural topography and disulfide connectivity of hirustasin has not previously been described. CONCLUSIONS: The crystal structure of the kallikrein-hirustasin complex reveals that hirustasin differs from other serine protease inhibitors in its conformation and its disulfide bond connectivity, making it the prototype for a new class of inhibitor. The disulfide pattern shows that the structure consists of two domains, but only the C-terminal domain interacts with the protease. The disulfide pattern of the N-terminal domain is related to the pattern found in other proteins. Kallikrein recognizes hirustasin by the formation of an antiparallel beta sheet between the protease and the inhibitor. The P1 arginine binds in a deep negatively charged pocket of the enzyme. An additional pocket at the periphery of the active site accommodates the sidechain of the P4 valine.

The 1.2 A crystal structure of hirustasin reveals the intrinsic flexibility of a family of highly disulphide-bridged inhibitors.

BACKGROUND: Leech-derived inhibitors have a prominent role in the development of new antithrombotic drugs, because some of them are able to block the blood coagulation cascade. Hirustasin, a serine protease inhibitor from the leech Hirudo medicinalis, binds specifically to tissue kallikrein and possesses structural similarity with antistasin, a potent factor Xa inhibitor from Haementeria officinalis. Although the 2.4 A structure of the hirustasin-kallikrein complex is known, classical methods such as molecular replacement were not successful in solving the structure of free hirustasin. RESULTS: Ab initio real/reciprocal space iteration has been used to solve the structure of free hirustasin using either 1.4 A room temperature data or 1.2 A low temperature diffraction data. The structure was also solved independently from a single pseudo-symmetric gold derivative using maximum likelihood methods. A comparison of the free and complexed structures reveals that binding to kallikrein causes a hinge-bending motion between the two hirustasin subdomains. This movement is accompanied by the isomerisation of a cis proline to the trans conformation and a movement of the P3, P4 and P5 residues so that they can interact with the cognate protease. CONCLUSIONS: The inhibitors from this protein family are fairly flexible despite being highly cross-linked by disulphide bridges. This intrinsic flexibility is necessary to adopt a conformation that is recognised by the protease and to achieve an optimal fit, such observations illustrate the pitfalls of designing inhibitors based on static lock-and-key models. This work illustrates the potential of new methods of structure solution that require less or even no prior phase information.

The three-dimensional structure of caspase-8: an initiator enzyme in apoptosis.

BACKGROUND: In the initial stages of Fas-mediated apoptosis the cysteine protease caspase-8 is recruited to the cell receptor as a zymogen (procaspase-8) and is incorporated into the death-signalling complex. Procaspase-8 is subsequently activated leading to a cascade of proteolytic events, one of them being the activation of caspase-3, and ultimately resulting in cell destruction. Variations in the substrate specificity of different caspases have been reported. RESULTS: We report here the crystal structure of a complex of the activated human caspase-8 (proteolytic domain) with the irreversible peptidic inhibitor Z-Glu-Val-Asp-dichloromethylketone at 2.8 A resolution. This is the first structure of a representative of the long prodomain initiator caspases and of the group III substrate specificity class. The overall protein architecture resembles the caspase-1 and caspase-3 folds, but shows distinct structural differences in regions forming the active site. In particular, differences observed in subsites S(3), S(4) and the loops involved in inhibitor interactions explain the preference of caspase-8 for substrates with the sequence (Leu/Val)-Glu-X-Asp. CONCLUSIONS: The structural differences could be correlated with the observed substrate specificities of caspase-1, caspase-3 and caspase-8, as determined from kinetic experiments. This information will help us to understand the role of the various caspases in the propagation of the apoptotic signal. The information gained from this investigation should be useful for the design of specific inhibitors.

Direct antiproliferative effects of recombinant human interferon-alpha B/D hybrids on human tumor cell lines.

The purpose of these studies was to examine the antiproliferative properties of 16 recombinant human IFN-alpha B/D hybrids against various human tumor lines of different histological origin and to determine whether any of the hybrid molecules possessed immunomodulating activity that could active antitumor properties in peripheral blood monocytes of normal donors. Hybrids with the B domain at the NH2 terminal end exhibited higher activity for antiviral activity and a higher level of direct antitumor antiproliferative activities as compared with hybrids with the D domain at the NH2 terminal end. The positive hybrids were directly cytostatic to melanoma, glioblastoma, renal carcinoma, colon carcinoma, and prostatic carcinoma cells. Tumor cell sensitivity to IFN-alpha hybrids was independent of sensitivity to IFN-gamma or to Adriamycin. The growth of a normal cell line (human embryo fibroblast) was unaffected by IFN-alpha hybrids but was completely arrested by Adriamycin. Some of the IFN-alpha hybrids were also cytostatic to mouse melanoma, lung carcinoma, and fibrosarcoma cell lines, albeit at lower levels than they were to human cells. The incubation of monocytes with IFN-alpha hybrids with the B domain at the NH2 terminal end was also associated with marked antitumor cytotoxicity. Kinetic studies, however, indicated that this activity was attributable to IFN-alpha carried on monocytes and acting directly on tumor cells. We conclude that recombinant human IFN-alpha B/D hybrids possess potent direct antiproliferative activity against a large variety of human tumor lines.

Structural genomics: opportunities and challenges.

Following the complete genome sequencing of an increasing number of organisms, structural biology is engaging in a systematic approach of high-throughput structure determination called structural genomics to create a complete inventory of protein folds/structures that will help predict functions for all proteins. First results show that structural genomics will be highly effective in finding functional annotations for proteins of unknown function.

Refined crystal structure of human transforming growth factor beta 2 at 1.95 A resolution.

Transforming growth factor beta 2 (TGF-beta 2), a homodimeric protein, is a member of a family of structurally related polypeptides that regulate various growth and differentiation processes in many cell types. The crystal structure of recombinant human TGF-beta 2 has been determined using a single heavy-atom derivative, anomalous scattering and by applying solvent flattening. The molecular model has been refined by a combination of simulated annealing and restrained least-squares refinement to a crystallographic R-factor of 0.194 including all data from 1.95 A to 8.0 A resolution. In the final structure, the root-mean-square deviation for bond lengths is 0.007 A and for bond angles 1.97 degrees. The final model includes 890 protein atoms (all 112 amino acid residues) as well as 84 water molecules. The new monomer fold consists of a separate alpha-helix and two pairs of antiparallel beta-sheet segments, which can be subdivided into nine individual beta-strands. The extended monomer lacks the typical hydrophobic core. A cluster of disulfide bridges, including the TGF-beta knot, connects the beta-strands with each other as well as the alpha-helix. Two monomers are covalently linked by a single disulfide bridge. In the dimer the alpha-helix of one subunit interacts with the beta-sheet of the other subunit forming two symmetrically related hydrophobic cores. The center of the dimer interaction is stabilized by a network of hydrogen bonds including several well-defined water molecules, which surround the central intersubunit disulfide bridge. The refined structure reveals the details of hydrogen bonding, electrostatic and hydrophobic interactions between intra- and intersubunit residues and allows the identification of possible receptor binding segments.

Thermodynamic stability and point mutations of bacteriophage T4 lysozyme.

The thermodynamics of melting of bacteriophage T4 lysozyme and four of its mutants have been measured by van't Hoff methods. The effect of pH has been explored and utilized to obtain the dependence of the enthalpy on temperature as suggested by Privalov and co-workers. The enthalpy change is a steep linear function of temperature. delta Cp is large and constant within experimental error. Changes in delta Hu are as large as 30% for a single point mutation. Changes in enthalpy are largely compensated by changes in entropy. Changes in stability, as measured by the free energy of unfolding, are smaller than those of delta H, but are very large in a relative sense, since delta G is very much smaller than delta H. Origins of the destabilization caused by mutations are discussed.

Crystallization of human leukocyte elastase with its inhibitor Pro44-eglin c.

Human leukocyte elastase has been crystallized in complex with recombinant Pro44-eglin c in the orthorhombic space group P2(1)2(1)2(1). The cell constants are a = 126.1 A, b = 127.8 A, c = 69.4 A, alpha = beta = gamma = 90 degrees. The crystals diffract to at least 2.5 A resolution and are suitable for crystallographic structure analysis.

The structure of the adenovirus capsid. I. An envelope model of hexon at 6 A resolution.

The structure of hexon, the major coat protein of adenovirus, has been determined by X-ray crystallography. Electron density maps were obtained with phases based on five heavy-atom derivatives at 2.9 A resolution. The main experimental finding derives from a low resolution electron density map calculated at 6.0 A resolution, but based on phases determined by the multiple isomorphous replacement method at 2.9 A resolution. Hexon consists of three subunits together forming two major components of different morphological symmetry. A triangular top with three towers of density is superimposed on a more bulky pseudo-hexagonal base. The symmetry of the top is in accord with the trimeric nature of hexon, but that of the base derives from the molecular function, which is to provide a densely packed impenetrable protective outer layer for the virion. A close-packed array of hexons forms a planar facet of the icosahedral capsid, with the tops presenting a spiky appearance that is consistent with electron micrographs of the adenovirus capsid. Hexon is hollow, permitting it to occupy a larger volume than normal for the same quantity of protein. The polypeptide chain has been traced in the 2.9 A electron density map for several non-contiguous stretches, allowing C alpha co-ordinates to be measured for 820 out of the 967 amino acid residues. The overall folding pattern confirms the assignment of shape, but the lack of connectivity so far precludes its complete description. The modest amount of alpha-helix and beta-sheet present is in accord with spectroscopic results.

The refined structures of goose lysozyme and its complex with a bound trisaccharide show that the "goose-type" lysozymes lack a catalytic aspartate residue.

The structure of goose egg-white lysozyme (GEWL) has been refined to an R-value of 15.9% at 1.6 A resolution. Details of the structure determination, the refinement and the structure itself are presented. The structure of a complex of the enzyme with the trisaccharide of N-acetyl glucosamine has also been determined and refined at 1.6 A resolution. The trisaccharide occupies sites analogous to the B, C and D subsites of chicken (HEWL) and phage T4 (T4L) lysozymes. All three lysozymes (GEWL, HEWL and T4L) display the same characteristic set of bridging hydrogen bonds between backbone atoms of the protein and the 2-acetamido group of the saccharide in subsite C. Glu73 of GEWL is seen to correspond closely to Glu35 of HEWL (and to Glu11 of T4L) and supports the established view that this group is critically involved in the catalytic mechanism. There is, however, no obvious residue in goose lysozyme that is a counterpart of Asp52 of chicken lysozyme (or of Asp20 in T4L), suggesting that a second acidic residue is not essential for the catalytic activity of goose lysozyme, and may not be required for the activity of other lysozymes.

Structural studies of mutants of the lysozyme of bacteriophage T4. The temperature-sensitive mutant protein Thr157----Ile.

To understand the roles of individual amino acids in the folding and stability of globular proteins, a systematic structural analysis of mutants of the lysozyme of bacteriophage T4 has been undertaken. The isolation, characterization, crystallographic refinement and structural analysis of a temperature-sensitive lysozyme in which threonine 157 is replaced by isoleucine is reported here. This mutation reduces the temperature of the midpoint of the reversible thermal denaturation transition by 11 deg.C at pH 2.0. Electron density maps showing differences between the wild-type and mutant X-ray crystal structures have obvious features corresponding to the substitution of threonine 157 by isoleucine. There is little difference electron density in the remainder of the molecule, indicating that the structural changes are localized to the site of the mutation. High-resolution crystallographic refinement of the mutant lysozyme structure confirms that it is very similar to wild-type lysozyme. The largest conformational differences are in the gamma-carbon of residue 157 and in the side-chain of Asp159, which shift 1.0 A and 1.1 A, respectively. In the wild-type enzyme, the gamma-hydroxyl group of Thr157 participates in a network of hydrogen bonds. Substitution of Thr157 with an isoleucine disrupts this set of hydrogen bonds. A water molecule bound in the vicinity of Thr155 partially restores the hydrogen bond network in the mutant structure, but the buried main-chain amide of Asp159 is not near a hydrogen bond acceptor. This unsatisfied hydrogen-bonding potential is the most obvious reason for the reduction in stability of the temperature-sensitive mutant protein.

Refined crystal structures of subtilisin novo in complex with wild-type and two mutant eglins. Comparison with other serine proteinase inhibitor complexes.

The crystal structures of the complexes formed between subtilisin Novo and three inhibitors, eglin c, Arg45-eglin c and Lys53-eglin c have been determined using molecular replacement and difference Fourier techniques and refined at 2.4 A, 2.1 A, and 2.4 A resolution, respectively. The mutants Arg45-eglin c and Lys53-eglin c were constructed by site-directed mutagenesis in order to investigate the inhibitory specificity and stability of eglin c. Arg45-eglin became a potent trypsin inhibitor, in contrast to native eglin, which is an elastase inhibitor. This specificity change was rationalized by comparing the structures of Arg45-eglin and basic pancreatic trypsin inhibitor and their interactions with trypsin. The residue Arg53, which participates in a complex network of hydrogen bonds formed between the core and the binding loop of eglin c, was replaced with the shorter basic amino acid lysine in the mutant Lys53-eglin. Two hydrogen bonds with Thr44, located in the binding loop, can no longer be formed but are partially restored by a water molecule bound in the vicinity of Lys53. Eglin c in complexes with both subtilisin Novo and subtilisin Carlsberg was crystallized in two different space groups. Comparison of the complexes showed a rigid body rotation for the eglin c core of 11.5 degrees with respect to the enzyme, probably caused by different intermolecular contacts in both crystal forms.

Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.

Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loci can cope with a larger number of pathogens. Here, we present the crystal structures of the murine MHC molecule H-2D(b) in complex with the peptides gp276 and np396 from the lymphocytic choriomeningitis virus (LCMV), solved at 2.18 A and 2.20 A resolution, respectively. The most prominent feature of H-2D(b) is a hydrophobic ridge that cuts across its antigen-binding site, which is conserved in the L(d)-like family of class I MHC molecules. The comparison with previously solved crystal structures of peptide/H-2D(b) complexes shows that the hydrophobic ridge focuses the conformational variability of the bound peptides in a "hot-spot", which could allow optimal TCR interaction and discrimination. This finding suggests a functional reason for the conservation of this structural element.

Viral escape at the molecular level explained by quantitative T-cell receptor/peptide/MHC interactions and the crystal structure of a peptide/MHC complex.

Viral escape, first characterized for the lymphocytic choriomeningitis virus (LCMV) in a mouse transgenic for the P14 T cell-receptor (TCR), can be due to mutations in T-cell epitopes. We have measured the affinity between the H-2D(b) containing the wild-type and two of its "viral escape" epitopes, as well as other altered peptide ligands (APL), by using BIACORE analysis, and solved the crystal structure of H-2D(b) in complex with the wild-type peptide at 2.75 A resolution. We show that viral escape is due to a 50 to 100-fold reduction in the level of affinity between the P14 TCR and the binary complexes of the MHC molecule with the different peptides. Structurally, one of the mutations alters a TCR contact residue, while the effect of the other on the binding of the TCR must be indirect through structural rearrangements. The former is a null ligand, while the latter still leads to some central tolerance. This work defines the structural and energetic threshold for viral escape.

Caspase-8 specificity probed at subsite S(4): crystal structure of the caspase-8-Z-DEVD-cho complex.

Caspase-8 is an initiator enzyme in the Fas-mediated pathway of which the downstream executioner caspase-3 is a physiological target. Caspases are cysteine proteases that are specific for substrates with an aspartic acid residue at the P(1) position and have an optimal recognition motif that incorporates four amino acid residues N-terminal to the cleavage site. Caspase-8 has been classified as a group III caspase member because it shows a preference for a small hydrophobic residue at the P(4) substrate position. We report the X-ray crystallographic structure of caspase-8 in complex with benzyloxycarbonyl-Asp-Glu-Val-Asp-aldehyde (Z-DEVD), a specific group II caspase inhibitor. The structure shows that the inhibitor interacts favourably with the enzyme in subsite S(4). Kinetic data reveal that Z-DEVD (K(i) 2 nM) is an almost equally potent inhibitor of caspase-8 as the specific group III inhibitor Boc-IETD-aldehyde (K(i) 1 nM). In view of this finding, the original classification of caspases into three specificity groups needs to be modified, at least for caspase-8, which tolerates small hydrophobic residues as well as the acidic residue Asp in subsite S(4). We propose that the subsite S(3) must be considered as an important specificity-determining factor.