The crystal structure of human procathepsin K.

Cathepsin K is a cysteine protease present in human osteoclasts that plays an important role in bone resorption. Cathepsin K is synthesized as an inactive proenzyme and activated under conditions of low pH. Autoproteolytic processing of the N-terminal 99 amino acid propeptide produces the active, mature form of cathepsin K. It is presumed that the activation of procathepsin K in vivo occurs in the bone resorption pit, which has a low-pH environment. We have determined the structure of human procathepsin K at 2.8 A resolution. The structure of the mature enzyme domain within procathepsin K is virtually identical to that of mature cathepsin K. The fold of the propeptide of procathepsin K is similar to that observed in procathepsins B and L despite differences in length and sequence. A portion of the propeptide occupies the active site cleft of cathepsin K. Hydrophobic interactions, salt bridges, and hydrogen-bonding interactions are observed in the structure of the propeptide and between the propeptide and the mature enzyme of procathepsin K. These interactions suggest an explanation for the stability of the proenzyme. The structure of procathepsin K contributes to an understanding of the molecular basis of inhibition by the propeptide portion of the molecule and activation of this important member of the cysteine protease family.

Use of papain as a model for the structure-based design of cathepsin K inhibitors: crystal structures of two papain-inhibitor complexes demonstrate binding to S'-subsites.

Papain has been used as a surrogate enzyme in a drug design effort to obtain potent and selective inhibitors of cathepsin K, a new member of the papain superfamily of cysteine proteases that is selectively and highly expressed in osteoclasts and is implicated in bone resorption. Here we report the crystal structures of two papain-inhibitor complexes and the rational design of novel cathepsin K inhibitors. Unlike previously known crystal structures of papain-inhibitor complexes, our papain structures show ligand binding extending deep within the S'-subsites. The two inhibitor complexes, carbobenzyloxyleucinyl-leucinyl-leucinal and carbobenzyloxy-L-leucinyl-L-leucinyl methoxymethyl ketone, were refined to 2.2- and 2.5-A resolution with R-factors of 0.190 and 0. 217, respectively. The S'-subsite interactions with the inhibitors are dominated by an aromatic-aromatic stacking and an oxygen-aromatic ring edge interaction. The knowledge of S'-subsite interactions led to a design strategy for an inhibitor spanning both subsites and yielded a novel, symmetric inhibitor selective for cathepsin K. Simultaneous exploitation of both S- and S'-sites provides a general strategy for the design of cysteine protease inhibitors having high specificity to their target enzymes.

The up-and-down beta-barrel proteins.

The up-and-down beta-barrel is a common folding motif found frequently in proteins that bind and transport hydrophobic ligands. It is formed by an array of beta-strands arranged in an antiparallel manner with each strand hydrogen-bonded to neighboring strands nearly always adjacent in the amino acid sequence. The arrangement is completed by forming hydrogen bonds between the first and last strands. The barrel motif so formed produces interior and exterior components. Proteins belonging to this class of up-and-down beta-barrels are found typically to be lipid-binding proteins in which the interior surface forms a cavity or pit that serves as the ligand binding region. Two evolutionarily distinct but structurally related families of such carriers have been identified by comparing known crystal structures. One group found intracellularly uses a 10-stranded beta-structure and a second family of proteins typically found extracellularly utilizes an 8-stranded motif. The 10-stranded beta-barrels have a large, hydrophilic water-filled interior cavity that serves as the ligand-binding domain. Hydrophobic lipids such as fatty acids and retinoids bind within the cavity, totally sequestered from the external milieu. The 8-stranded beta-barrel proteins have a hydrophobic pit, which serves as the ligand-binding domain for compounds such as bilins and retinoids. The up-and-down beta-barrel motif appears to be one of nature's primary choices for hydrophobic ligand transport proteins.

Adipocyte lipid-binding protein complexed with arachidonic acid. Titration calorimetry and X-ray crystallographic studies.

The association of the adipocyte lipid-binding protein (ALBP) with arachidonic acid (all cis, 20:4 delta 5,8,11,14) and oleic acid (cis, 18:1 delta 9) has been examined by titration calorimentry. In addition, the crystal structure of ALBP with bound arachidonic acid has also been obtained. Crystallographic analysis of the arachidonic acid.ALBP complex along with the previously reported oleic acid-ALBP structure (Xu, Z., Bernlohr, D. A., and Banaszak, L. J. (1993) J. Biol. Chem. 268, 7874-7884) provides a framework for the molecular examination of protein-lipid association. Isothermal titration calorimetry revealed high affinity association of both unsaturated fatty acids with the protein. The calorimetric data yielded the following thermodynamic parameters for arachidonic acid: Kd = 4.4 microM, n = 0.8, delta G = -7370 cal/mol, delta H = -6770 cal/mol, and T delta S = +600 cal/mol. For oleic acid, the thermodynamic parameters were Kd = 2.4 microM, n = 0.9, delta G = -7770 cal/mol, delta H = -6050 cal/mol, and T delta S = +1720 cal/mol. The identification of thermodynamically dominating enthalpic factors for both fatty acids are consistent with the crystallographic studies demonstrating the interaction of the fatty acid carboxylate with a combination of Arg106, Arg126, and Tyr128. The crystallographic refinement of the protein-arachidonate complex was carried out to 1.6 A with the resultant R factor of 0.19. Within the cavity of the crystalline binding protein, the arachidonate was found in a hairpin conformation. The conformation of the bound ligand is consistent with acceptable torsional angles and the four cis double bonds in arachidonate. These results demonstrate that arachidonate is a ligand for ALBP. They provide thermodynamic and structural data concerning the physical basis for protein-lipid interaction and suggest that intracellular lipid-binding proteins may mediate the biological effects of polyunsaturated fatty acids in vivo.

X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites.

Adipocyte lipid-binding protein is a 14.6-kDa polypeptide that is responsible for the intracellular trafficking of fatty acids. Its structure previously has been solved in the apo and holo forms complexed with stearate and oleate. To examine the binding of lipids other than those with a carboxylate headgroup, we have determined the structure of ALBP in complex with a sulfonic acid, hexadecanesulfonic acid, and compared its structure with the natural fatty acid analog, palmitate. Crystallographic refinement led to similar models, both with R-factors of about 20% and a resolution of 1.6 A. results can be compared with earlier studies on C18 fatty acids, both saturated and unsaturated. The previously refined complexes with stearate and oleate in combination with the complexes of palmitate and hexadecanesulfonic acid demonstrate specific positions for water molecules bound in the internal cavity. Many of the water-binding sites are present in both the apo form and the holo forms of the protein. With ligand present, a network of 10 internalized water molecules appear to form a hydrophobic hydration region. In spite of the sp3 geometry of the sulfonic acid derivative, the headgroup occupies the same site as that of the planar carboxylate in natural fatty acids. These results demonstrate that intracellular lipid-binding proteins are capable of binding a wider variety of lipids than previously considered and reveal the importance of interior ordered water molecules in the binding cavity.

Carrageenan-induced intestinal injury: possible role of oxygen free radicals.

There is a growing body of evidence that implicates oxygen free radicals in a wide variety of inflammatory conditions in various body systems including the gastrointestinal tract. The purpose of this study was to ascertain whether or not oxy-radicals play a role in carrageenan-mediated intestinal injury. Allopurinol, superoxide dismutase-polyethylene glycol, and dimethyl sulfoxide, respectively, were administered to the carrageenan rat model for 30 to 32 days. Collectively, all three drugs attenuated the carrageenan-mediated injury as shown by four indices of intestinal damage: ulceration (p = 0.0007); abnormal villous pattern (p = 0.0002); degree of inflammation (p = 0.0001); and extent of inflammation (p = 0.0025). Dimethyl sulfoxide appeared to be the least efficacious of the three drugs. The results suggest that oxygen free radicals play a role in carrageenan-mediated intestinal injury, and that one of the sources of these oxy-radicals may be the intestinal macrophage.

A comparison of the atomic composition of siderosomes (haemosiderin) in cryosections of unfixed frozen tissues and Epon-embedded tissues.

Siderosomes (i.e. single membrane-bound lysosomal bodies containing haemosiderin) were produced in the liver and muscle of rats by injections of iron dextran. Electron-probe X-ray analysis was executed on siderosomes in cryosections of quick-frozen fresh unfixed tissues (liver and muscle) and sections of Epon-embedded tissues. There were no statistically significant differences between the ratios of iron:phosphorus and iron:sulphur in these two types of preparations. Hence it is concluded that there is no significant loss or gain of phosphorus or sulphur during preparation of tissues for Epon embedding. The results confirm past belief that so little phosphorus or sulphur is present in siderosomes that haemosiderin is best regarded as ferric hydroxide oxide. A new finding in the present study was the demonstration of small amounts of potassium in siderosomes in cryosections. It seems that potassium is lost (leaches out) from siderosomes during preparation of tissues for Epon-embedding.

Carrageenan-induced intestinal injury in the rat--a model for inflammatory bowel disease.

The cause of inflammatory bowel disease (IBD) remains unknown. In this report, an attempt is made to produce a suitable animal model for studying the pathobiology of IBD, especially its pathogenesis. Sprague-Dawley rats were divided into four groups of six (A, B, C, D). The experimental design involved prior parenteral sensitization of groups A and B by a 1.5 percent solution of lambda degraded carrageenan followed by oral administration of the same solution for 30 days to groups A and C. The animals were then sacrificed, and the small intestine was evaluated for injury. Oral carrageenan caused significant intestinal injury as evidenced by ulceration, abnormal villous pattern, degree and extent of inflammation [p = 0.0001 for groups (A + C) versus (B + D)]. Prior sensitization aggravated the effects of oral carrageenan. Overall, the inflammation produced was reminiscent of human IBD in that there was pin-point ulceration, focality of lesions and lymphoid hyperplasia with microgranulomas. It was concluded that this carrageenan model may prove to be particularly useful for studying the pathobiology of human IBD.

A comparative ultrastructural study of cutaneous blue naevi of humans and hamsters.

A comparative study of 12 human blue naevi and 15 carcinogen-induced hamster blue naevi showed no significant ultrastructural difference between these two groups of tumours. Both groups of tumours showed melanotic and hypomelanotic variants, and both were composed almost entirely of cells acceptable as melanocytes and melanophages. However, a few cells in some human and hamster tumours were partially or completely surrounded by a slender or quite thick external lamina. This may indicate a tendency towards a schwannocytic type of differentiation, but no other feature of schwannocytic differentiation such as the formation of mesaxons or pseudomesaxons was detected. Several cutaneous nerves were embedded in some of these tumours but they were clearly uninvolved in the neoplastic process and there was no evidence whatsoever that the tumours had developed from neural elements. We conclude that both human and hamster blue naevi are essentially melanocytomas which develop from dermal melanocytes which failed to reach the epidermis during development. We regard the occasional occurrence of an external lamina as an aberration of the neoplastic state which reflects the close kinship of melanocytes and Schwann cells i.e. their common origin from the neural crest.

Ultrastructure of an intraocular lacrimal gland choristoma.

An intraocular lacrimal gland choristoma which was at first mistaken for a medulloepithelioma (diktyoma) was studied with the electron microscope. The tumour did not contain cells with neuronal and glial differentiation as expected in a medulloepithelioma but it did contain acini, ducts and dilated ducts or cysts. The tumour, in fact, bore much resemblance to the lacrimal gland, in that it contained electron-dense serous granules, and at times, a myoepithelial cell was detected at the base of an acinus. The ductal and cystic elements were lined by a single layer of cells or by stratified or pseudostratified epithelium. An interesting, unexpected feature was the occurrence of a myoid band (composed of thin filaments with focal densities along their course) under the cell membrane of the epithelial cells adjacent to the lumen of the ducts and cysts.

Experimental methods of repairing injured menisci.

A longitudinal incision resembling a bucket-handle tear was made in the menisci of 8 rabbits, 6 dogs, 11 pigs and 12 sheep. In some of the animals of each species the cut was repaired by suturing, and in others it was not. Gross inspection, as well as examination by light and electron microscopy, showed that no healing had occurred after six months in the sutured or the unsutured wounds and that the meniscus was incapable of significant intrinsic repair. In a second experiment longitudinal, transverse and T-shaped cuts were made in the menisci of 12 sheep, and a flap of synovium was sutured into the wound. Three months later there was clear evidence of healing by the formation of cartilaginous tissue. Examination by light and electron microscopy showed that the newly formed repair tissue, possibly derived by metaplasia from the synovium, had a morphology intermediate between hyaline cartilage and fibrocartilage. Synovial implantation may therefore be considered as an alternative to meniscectomy in the management of the torn meniscus.

Diagnosis of pulmonary talcosis by electron-probe x-ray analysis.

A miner with a long history of drug abuse developed pulmonary fibrosis. It was not clear whether his disease was due to drug abuse or exposure to mine dust. Electron-probe x-ray analysis of mineral deposits in the lung showed that his disease was due to drug abuse and not occupational exposure to mine dust.

Dynorphin-(1-13). I. Structure-function relationships of Ala-containing analogs.

Dynorphin-(1-13) (Dyn-(1-13] and its analogs substituted by single introduction of Ala in positions 1-11 were synthesized by the solid-phase method and purified by high pressure liquid chromatography. Relative potencies of the synthetic compounds were determined by their ability to inhibit electrically-evoked contractions of the guinea pig ileum (GPI) and of the mouse vas deferens (MVD) and to compete with [3H]-etorphine for opiate receptors in rat brain homogenates. Introduction of Ala in positions 1 and 4 of Dyn-(1-13) provoked most important decreases in the activity of the molecule in the three assays (relative potency of 0.2% or less). Substitution of Ala in positions 2 or 5, but not 3, also severely decreased the potency of the peptide in the smooth muscle preparations (0.6-5.0% activity). However, the opiate receptor binding assay was less sensitive to the replacement of residue in position 2 (20% activity) than that in positions 3 or 5 (12% and 6% relative potencies, respectively). In the GPI assay and the opiate binding test, the other substitutions which greatly lowered the potency of the molecule were seen in positions 6, 7, 9 and 11, four basic residues. Among these, Arg6 and Arg7 were demonstrated to be the most important in the three biological tests. Finally, the replacement of Ile8 by Ala increased the relative potency of Dyn-(1-13) up to 191% and 900% in the MVD and the opiate binding tests, respectively.

Myofibroblastoma: a tumour of myofibroblasts.

A myofibroblastoma occurring in the abdominal cavity of a 15 year old boy is described. This tumour was diagnosed as a low grade sarcoma by light microscopy but electron microscopy showed that the tumour was composed almost entirely of myofibroblasts and a few macrophages. Intermediate forms between myofibroblasts and macrophages were not seen nor were any fibroblasts seen in the main tumour mass. Total excision was impossible because the tumour had trapped loops of bowel and was adherent to the abdominal organs. The patient died of cachexia and haemorrhage but there were no distant metastases nor was there any marked infiltration of the abdominal organs. This case and a review of the literature shows that myofibroblastomas are locally aggressive tumours which do not metastasize and that if total excision is possible an uneventful recovery can be expected.

Ultrastructure of normal and torn menisci of the human knee joint.

Normal human menisci obtained at autopsy (seven cases) and the injured and uninjured portions of torn menisci obtained at surgery (nine cases) were studied with the electron microscope. The surface of menisci is composed of collagen fibrils surmounted by an electron-dense surface coat. Most of the cells in menisci are chondrocytes but a few fibroblasts and cells of an intermediate form difficult to classify as either fibroblasts or chondrocytes also occur. Mast cells are found at the vascularised periphery of the meniscus. Myofibroblasts were found in the injured portions of menisci in three out of the nine cases studied. A territorial matrix containing fibrils and proteoglycan particles with associated filaments is seen around or adjacent to chondrocytes, but sometimes this matrix is sparse or absent. The interterritorial or general matrix comprises collagen fibrils of widely varying diameters (25-180 nm) set in a sparse interfibrillary matrix containing proteoglycan particles. A few mature elastic fibres and several small or immature elastic fibres and collections of electron-dense filaments are seen in the general matrix. Also seen in this region are calcified bodies and matrical lipidic debris derived by the shedding of cell processes and in situ necrosis of cells. Other features seen in the matrix of the injured portion of the meniscus include: (1) membrane-bound cystic structures; (2) parting and fraying of collagen fibrils; and (3) pools of proteoglycan particles.

A transmission electron microscopic comparison of the articular surface of cartilage processed attached to bone and detached from bone.

The purpose of this study was to ascertain whether the surface asperities detected with the transmission electron microscope in shavings of young adult articular cartilage detached from bone reflect an in vivo condition or are artefacts. With this in view shavings of rabbit articular cartilage processed in the conventional manner were compared with pieces of cartilage attached to bone processed by a new method which we have evolved. An undulating surface and asperities up to about 0.3 micrometer deep were found in cartilage shavings processed in the conventional manner, but such asperities were not seen on cartilage processed attached to bone. We have therefore concluded that such asperities are artefactual and that they are engendered by cartilage curling. Cartilage processed attached to bone has an amazingly smooth surface; any so-called 'asperities' are less than 0.03 micrometer in depth and are confined to the surface coat which seems to be of a transient nature. On rare occasions, however, focal areas of roughening were found, where the asperities reached a depth of about 0.15 micrometer. Several past studies (reviewed in this paper) have shown that virtually all the asperities seen with the scanning electron microscope on the articular surface are artefacts of tissue processing. We have now shown that even most of the much smaller asperities seen with the transmission electron microscope are also artefacts. Therefore one has to conclude that the articular surface of young adults is remarkably smooth and that the surface asperities must be attributed to artefacts, ageing or pathological changes.

The effect of uranyl acetate on human lymphoblastoid cells (RPMI 6410) and HeLa cells.

RPMI 6410 cells and HeLa cells were exposed to uranyl acetate. In RPMI 6410 cell cultures this produced single-membrane-bound presumably lysosomal bodies (called "uraniosomes") containing electron-dense crystals in the cultured cells and crystalline deposits in extracellular locations. Neither uraniosomes nor extracellular uranium deposits were found in HeLa cell cultures. All uraniosomes and extracellular uranium deposits analysed by electron-probed X-ray analysis were found to contain uranium, potassium and phosphorus. Traces of sulphur were detected in some but not all uraniosomes and extracellular uranium deposits. Traces of calcium were found in all extracellular uranium deposits and in some uraniosomes also.

Uraniosomes produced in the synovial membrane by uranyl acetate.

Uranyl acetate was injected into the rabbit knee joint. This produced single-membrane-bound presumably lysosmal bodies (called 'uraniosomes') containing electron-dense crystals in Type A and Type B synovial intimal cells, subsynovial macrophages and lipocytes. Uranium deposits were also seen in the extracellular matrix. All uraniosomes and extracellular deposits analysed by electron-probe X-ray analysis were found to contain uranium, potassium and phosphorus. Traces of calcium and sulphur were also found in some of the uraniosomes and extracellular uranium deposits.

Ultrastructure and electron-probe x-ray analysis of the pigment in melanosis duodeni.

A patient with peptic ulceration developed melanosis duodeni, which was studied by light microscopy, histochemistry, electron microscopy and electron-probe x-ray analysis. Our studies show that the pigment in melanosis duodeni resides in the lysosomes of macrophages in the lamina propria. The pigment is not melanin or a melanin-like compound as has been claimed by previous workers. On the basis of electron-probe x-ray analytical findings we have concluded that the pigment is essentially FeS. On the basis of the history of this patient and cases reported in the literature we think that the Fe in this pigment is derived from haemorrhage in the gastrointestinal tract. We also found small amounts of Ca, K, Al, Mg, Si, and Ag. It would appear that Al, Mg and Si were probably derived from the biological milieu and/or other drugs and/or food and/or specimen contamination.

The morphology and atomic composition of aurosomes produced by sodium aurothiomalate in human monocytes.

Aurosomes were found in monocytes (from the peripheral blood of man) incubated with sodium aurothiomalate. In electron micrographs the aurosome presents as a single-membrane-bound lysosomal body with an electron-lucent or medium density matrix in which lie electron-dense filamentous (straight or curled), rod-like and lamellar profiles studded with particles and granules. Similar deposits did not develop in monocytes incubated with sodium thiomalate but myelinoid membranes and rod-like structures presumably derived from them were seen in the lysosomes of these cells. The aurosomes (and their characteristic electron-dense contents) produced in the monocytes in vitro were morphologically indistinguishable from those known to occur in various tissues of man and experimental animals treated with soluble goldsalts. The atomic composition of the aurosomes produced in vitro appears to be similar to that produced in vivo for in both instances Au, P and S can be demonstrated in the aurosome. It is concluded that the aurosomes produced in our experimental model is an accurate copy of that found in in vivo situations.