Franz-Xaver Gomis-Rüth

Insights into MMP-TIMP interactions.

ABSTRACT: The proteolytic activity of the matrix metalloproteinases (MMPs) involved in extracellular matrix degradation must be precisely regulated by their endogenous protein inhibitors, the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance can result in serious diseases such as arthritis and tumor growth and metastasis. Knowledge of the tertiary structures of the proteins involved in such processes is crucial for understanding their functional properties and to interfere with associated dysfunctions. Within the last few years, several three‐dimensional structures have been determined showing the domain organization, the polypeptide fold, and the main specificity determinants of the MMPs. Complexes of the catalytic MMP domains with various synthetic inhibitors enabled the structure‐based design and improvement of high‐affinity ligands, which might be elaborated into drugs. Very recently, structural information also became available for some TIMP structures and MMP‐TIMP complexes, and these new data elucidated important structural features that govern the enzyme‐inhibitor interaction.

The C-terminal (haemopexin-like) domain structure of human gelatinase A (MMP2): structural implications for its function.

In common with most other matrix metalloproteinases, gelatinase A has a non‐catalytic C‐terminal domain that displays sequence homology to haemopexin. Crystals of this domain were used by molecular replacement to solve its molecular structure at 2.6 Å resolution, which was refined to an R value of 17.9%. This structure has a disc‐like shape, with the chain folded into a β‐propeller structure that has pseudo four‐fold symmetry. Although the topology and the side‐chain arrangement are very similar to the equivalent domain of fibroblast collagenase, significant differences in surface charge and contouring are observable on 1 side of the gelatinase A disc. This difference might be a factor in allowing the gelatinase A C‐terminal domain to bind to natural inhibitor TIMP‐2.

Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family

The proline iminopeptidase from Xanthomonas campestris pv. citri is a serine peptidase that catalyses the removal of N‐terminal proline residues from peptides with high specificity. We have solved its three‐dimensional structure by multiple isomorphous replacement and refined it to a crystallographic R‐factor of 19.2% using X‐ray data to 2.7 Å resolution. The protein is folded into two contiguous domains. The larger domain shows the general topology of the α/β hydrolase fold, with a central eight‐stranded β‐sheet flanked by two helices and the 11 N‐terminal residues on one side, and by four helices on the other side. The smaller domain is placed on top of the larger domain and essentially consists of six helices. The active site, located at the end of a deep pocket at the interface between both domains, includes a catalytic triad of Ser110, Asp266 and His294. Cys269, located at the bottom of the active site very close to the catalytic triad, presumably accounts for the inhibition by thiol‐specific reagents. The overall topology of this iminopeptidase is very similar to that of yeast serine carboxypeptidase. The striking secondary structure similarity to human lymphocytic prolyl oligopeptidase and dipeptidyl peptidase IV makes this proline iminopeptidase structure a suitable model for the three‐dimensional structure of other peptidases of this family.

The metzincin-superfamily of zinc-peptidases.

Over the past three years, the three-dimensional structures of a number of zinc proteinases that share the zinc-binding motif HEXXHXXGXXH have been elucidated. These proteinases comprise astacin, a digestive enzyme from crayfish [1,2,3], adamalysin II [4,5] and atrolysin C [6] from snake venom, the Pseudomonas aeruginosa alkaline proteinase [7] and serralysin from Serratia marcescens proteinase [8], the collagenases from human neutrophils [9,10,11]) and fibroblasts [12,13,14,15], human stromelysin 1 [16; K. Appelt, personal communication] and matrilysin [M. Browner, Keystone Symposia, March 5–12, 1994]. These enzymes represent four different families of zinc peptidases: the astacins [3,17], the bacterial serralysins [18], the adamalysins/reprolysins [19,20], and the matrixins (matrix metalloproteinases, MMPs) [21,22].

THE THREE-DIMENSIONAL STRUCTURE OF THE NATIVE TERNARY COMPLEX OF BOVINE PANCREATIC PROCARBOXYPEPTIDASE A WITH PROPROTEINASE E AND CHYMOTRYPSINOGEN C

The metalloexozymogen procarboxypeptidase A is mainly secreted in ruminants as a ternary complex with zymogens of two serine endoproteinases, chymotrypsinogen C and proproteinase E. The bovine complex has been crystallized, and its molecular structure analysed and refined at 2.6 A resolution to an R factor of 0.198. In this heterotrimer, the activation segment of procarboxypeptidase A essentially clamps the other two subunits, which shield the activation sites of the former from tryptic attack. In contrast, the propeptides of both serine proproteinases are freely accessible to trypsin. This arrangement explains the sequential and delayed activation of the constituent zymogens. Procarboxypeptidase A is virtually identical to the homologous monomeric porcine form. Chymotrypsinogen C displays structural features characteristic for chymotrypsins as well as elastases, except for its activation domain; similar to bovine chymotrypsinogen A, its binding site is not properly formed, while its surface located activation segment is disordered. The proproteinase E structure is fully ordered and strikingly similar to active porcine elastase; its specificity pocket is occluded, while the activation segment is fixed to the molecular surface. This first structure of a native zymogen from the proteinase E/elastase family does not fundamentally differ from the serine proproteinases known so far.

Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite

Roundworms of the genus Ascaris are common parasites of the human gastrointestinal tract. A battery of selective inhibitors protects them from host enzymes and the immune system. Here, a metallocarboxypeptidase (MCP) inhibitor, ACI, was identified in protein extracts from Ascaris by intensity-fading MALDI-TOF mass spectrometry. The 67-residue amino acid sequence of ACI showed no significant homology with any known protein. Heterologous overexpression and purification of ACI rendered a functional molecule with nanomolar equilibrium dissociation constants against MCPs, which denoted a preference for digestive and mast cell A/B-type MCPs. Western blotting and immunohistochemistry located ACI in the body wall, intestine, female reproductive tract, and fertilized eggs of Ascaris, in accordance with its target specificity. The crystal structure of the complex of ACI with human carboxypeptidase A1, one of its potential targets in vivo, revealed a protein with a fold consisting of two tandem homologous domains, each containing a β-ribbon and two disulfide bonds. These domains are connected by an α-helical segment and a fifth disulfide bond. Binding and inhibition are exerted by the C-terminal tail, which enters the funnel-like active-site cavity of the enzyme and approaches the catalytic zinc ion. The findings reported provide a basis for the biological function of ACI, which may be essential for parasitic survival during infection.

The α-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis

The α‐amylase from Tenebrio molitor larvae (TMA) was purified from a crude larval extract. After removal of the N‐terminal pyroglutamate residue and identification of the following 17 residues by Edman sequencing, the cDNA of mature TMA was cloned from larval mRNA. The encoded enzyme consists of 471 amino acid residues and has 57–79% sequence identity to other insect α‐amylases and also shows high homology to the mammalian enzymes. TMA was crystallized in form of well‐ordered orthorhombic crystals of space group P212121 diffracting beyond 1.6 Å resolution with unit cell dimensions of a=51.24 Å, b=93.46 Å, c=96.95 Å. TMA may serve as model system for the future analysis of interactions between insect α‐amylase and proteinaceous plant inhibitors on the molecular level.

Crystal structure analysis, refinement and enzymatic reaction mechanism of N-carbamoylsarcosine amidohydrolase from Arthrobacter sp. at 2·0Åresolution

N-carbamoylsarcosine amidohydrolase from Arthrobacter sp., a tetramer of polypeptides with 264 amino acid residues each, has been crystallized and its structure solved and refined at 2.0 A resolution, to a crystallographic R-factor of 18.6%. The crystals employed in the analysis contain one tetramer of 116,000 M(r) in the asymmetric unit. The structure determination proceeded by multiple isomorphous replacement, followed by solvent-flattening and density averaging about the local diads within the tetramer. In the final refined model, the root-mean-square deviation from ideality is 0.01 A for bond distances and 2.7 degrees for bond angles. The asymmetric unit consists of 7853 protein atoms, 431 water molecules and four sulfate ions bound into the putative active site clefts in each subunit. One subunit contains a central six-stranded parallel beta-pleated sheet packed by helices on both sides. On one side, two helices face the solvent, while two of the helices on the other side are buried in the tight intersubunit contacts. The catalytic center of the enzyme, tentatively identified by inhibitor binding, is located at the interface between two subunits and involves residues from both. It is suggested that the nucleophilic group involved in hydrolysis of the substrate is the thiol group of Cys117 and a nucleophilic addition-elimination mechanism is proposed.

EXPRESSION, PURIFICATION, CHARACTERIZATION, AND X-RAY ANALYSIS OF SELENOMETHIONINE 215 VARIANT OF LEUKOCYTE COLLAGENASE

Matrix metalloproteinases belong to the superfamily of metzincins containing, besides a similar topology and a strictly conserved zinc environment, a 1,4-tight turn with a strictly conserved methionine residue at position three (the so called Met-turn [Bode et al. (1993) FEBS331, 134–140; Stöcker et al. (1995) Protein Sci.4, 823–840]. The distal S–CH3 moiety of this methionine residue forms the hydrophobic basement of the three His residues liganding the catalytic zinc ion. To assess the importance of this methionine, we have expressed the catalytic domain of neutrophil collagenase (rHNC, residues Met80–Gly242) in the methionine auxotrophic Escherichia coli strain B834[DE3](hsd metB), with the two methionine residues replaced by Selenomethionine. Complete replacement was confirmed by amino acid analysis and electrospray mass spectrometry. The folded and purified enzyme retained its catalytic activity, but showed modifications which are reflected in changed kinetic parameters. The Met215SeMet substitution caused a decrease in conformational stability upon urea denaturation. The X-ray crystal structure of this Selenomethionine rHNC was virtually identical to that of the wild-type catalytic domain except for a very faint local disturbance around the sulfur-seleno substitution site.

Protein-Crystal Density by Volume Measurement and Amino-Acid Analysis

The densities of protein crystals have been determined by crystal-volume measurement and amino-acid analysis. For this purpose, protein crystals were freely mounted under humidity control by means of airstream-crystal-regulated humidity. With a video system (charge-coupled-device camera) the two-dimensional shadow projections of crystals are recorded and by the method of back projection the crystal shape is reconstructed and the volume determined. It is shown that the method is independent of the crystal morphology by the consistency of the results from a number of different crystals and materials.