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L Ditzel

Publications and source records attributed to L Ditzel.

13 recordsLinked to original sources

Review: nucleotide binding to the thermoplasma thermosome: implications for the functional cycle of group II chaperonins.

Structural information on group II chaperonins became available during recent years from electron microscopy and X-ray crystallography. Three conformational states have been identified for both archaeal and eukaryotic group II chaperonins: an open state, a spherical closed conformation, and an intermediate asymmetric bullet-shaped form. However, the functional cycle of group II chaperonins appears less well understood, although major principles are conserved when compared to group I chaperonins: binding of the substrate polypeptide to the apical domains of the open state and MgATP-driven conformational changes that result in encapsulation of the substrate where folding can proceed presumably in the closed ring of the bullet-shaped form. Binding of the transition state analogue MgADP-AlF3-H2O in the crystal structure of the Thermoplasma acidophilum thermosome suggests that the closed geometry is the enzymatically active conformation that performs ATP hydrolysis. Domain movements observed by electron microscopy suggest a coupling of ATP hydrolysis and domain movement similar to that in the GroE system. The hydrophilic interior of the closed thermosome corresponds to the cis-ring of the asymmetric GroEL-GroES complex implicated in protein folding.

Adenosine Triphosphate↗

Bifunctional inhibitors of the trypsin-like activity of eukaryotic proteasomes.

BACKGROUND: The 20S proteasome is a multicatalytic protease complex that exhibits trypsin-like, chymotrypsin-like and post-glutamyl-peptide hydrolytic activities associated with the active sites of the beta2, beta5 and beta1 subunits, respectively. Modulation of these activities using inhibitors is essential for a better understanding of the proteasome's mechanism of action. Although there are highly selective inhibitors of the proteasome's chymotryptic activity, inhibitors of similar specificity have not yet been identified for the other activities. RESULTS: The X-ray structure of the yeast proteasome reveals that the sidechain of Cys118 of the beta3 subunit protrudes into the S3 subsite of the beta2 active site. The location of this residue was exploited for the rational design of bidentated inhibitors containing a maleinimide moiety at the P3 position for covalent linkage to the thiol group and a carboxy-terminal aldehyde group for hemiacetal formation with the Thr1 hydroxyl group of the active site. Structure-based modelling was used to determine the optimal spacing of the maleinimide group from the P2-P1 dipeptide aldehydes and the specificity of the S1 subsite was exploited to limit the inhibitory activity to the beta2 active site. X-ray crystallographic analysis of a yeast proteasome-inhibitor adduct confirmed the expected irreversible binding of the inhibitor to the P3 subsite. CONCLUSIONS: Maleoyl-beta-alanyl-valyl-arginal is a new type of inhibitor that is highly selective for the trypsin-like activity of eukaryotic proteasomes. Despite the reactivity of the maleinimide group towards thiols, and therefore the limited use of this inhibitor for in vitro studies, it might represent an interesting new biochemical tool.

Binding Sites↗

The proteasome.

Proteasomes are large multisubunit proteases that are found in the cytosol, both free and attached to the endoplasmic reticulum, and in the nucleus of eukaryotic cells. Their ubiquitous presence and high abundance in these compartments reflects their central role in cellular protein turnover. Proteasomes recognize, unfold, and digest protein substrates that have been marked for degradation by the attachment of a ubiquitin moiety. Individual subcomplexes of the complete 26S proteasome are involved in these different tasks: The ATP-dependent 19S caps are believed to unfold substrates and feed them to the actual protease, the 20S proteasome. This core particle appears to be more ancient than the ubiquitin system. Both prokaryotic and archaebacterial ancestors have been identified. Crystal structures are now available for the E. coli proteasome homologue and the T. acidophilum and S. cerevisiae 20S proteasomes. All three enzymes are cylindrical particles that have their active sites on the inner walls of a large central cavity. They share the fold and a novel catalytic mechanism with an N-terminal nucleophilic threonine, which places them in the family of Ntn (N terminal nucleophile) hydrolases. Evolution has added complexity to the comparatively simple prokaryotic prototype. This minimal proteasome is a homododecamer made from two hexameric rings stacked head to head. Its heptameric version is the catalytic core of archaebacterial proteasomes, where it is sandwiched between two inactive antichambers that are made up from a different subunit. In eukaryotes, both subunits have diverged into seven different subunits each, which are present in the particle in unique locations such that a complex dimer is formed that has six active sites with three major specificities that can be attributed to individual subunits. Genetic, biochemical, and high-resolution electron microscopy data, but no crystal structures, are available for the 19S caps. A first step toward a mechanistic understanding of proteasome activation and regulation has been made with the elucidation of the X-ray structure of the alternative, mammalian proteasome activator PA28.

Adenosine Triphosphatases↗

Conformational constraints for protein self-cleavage in the proteasome.

The proteasome is the central enzyme of protein degradation in the cytosol and the nucleus. It is involved in the removal of abnormal, misfolded or incorrectly assembled proteins, in the processing or degradation of transcriptional regulators in stress response, in degradation of cyclins in cell-cycle control, in the destruction of transcription factors or metabolic enzymes in cell differentiation and metabolic response, and in MHC class I mediated cellular immune response. By the analysis of the crystal and molecular structures of the 20 S proteasomes from the archaeon Thermoplasma acidophilum and from yeast it was shown that the beta-type subunits in which the proteolytic activities reside are members of the N-terminal nucleophile (Ntn) protein family. They are synthesized as proproteins and become active by autoprocessing at a Gly-1-Thr1 bond. The Thr1Ala mutant of subunit beta1/Pre3 of the 20 S proteasome from yeast is unable to autolyse. Its crystal and molecular structure at 2.2 A resolution described here shows that the pro-segment adopts a well-defined gamma-turn conformation at Gly-1 and provides a first view at an autolysis site in Ntn hydrolases. The Gly-1 carbonyl oxygen displays two hydrogen bonds. The modelled Thr1 side-chain is located above the gamma-turn bulge such that addition of its nucleophilic hydroxyl group to the electrophilic Gly-1 carbonyl carbon atom may proceed by very small motions. The pro-segment binding site and the catalytic site provide a rigid structural framework and appropriate hydrogen bond donors for this reaction. The same structure also supports addition of the Thr1 hydroxyl group to the carbonyl carbon atom of Leu-2 as a model for the first step in substrate hydrolysis by the proteasome.

Archaeal Proteins↗

Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT.

We have determined to 2.6 A resolution the crystal structure of the thermosome, the archaeal group II chaperonin from T. acidophilum. The hexadecameric homolog of the eukaryotic chaperonin CCT/TRiC shows an (alphabeta)4(alphabeta)4 subunit assembly. Domain folds are homologous to GroEL but form a novel type of inter-ring contact. The domain arrangement resembles the GroEL-GroES cis-ring. Parts of the apical domains form a lid creating a closed conformation. The lid substitutes for a GroES-like cochaperonin that is absent in the CCT/TRiC system. The central cavity has a polar surface implicated in protein folding. Binding of the transition state analog Mg-ADP-AIF3 suggests that the closed conformation corresponds to the ATP form.

Adenosine Diphosphate↗

Crystal structure of heat shock locus V (HslV) from Escherichia coli.

Heat shock locus V (HslV; also called ClpQ) is the proteolytic core of the ATP-dependent protease HslVU in Escherichia coli. It has sequence similarity with the beta-type subunits of the eukaryotic and archaebacterial proteasomes. Unlike these particles, which display 72-point symmetry, it is a dimer of hexamers with 62-point symmetry. The crystal structure of HslV at 3.8-A resolution, determined by isomorphous replacement and symmetry averaging, shows that in spite of the different symmetry of the particle, the fold and the contacts between subunits are conserved. A tripeptide aldehyde inhibitor, acetyl-Leu-Leu-norleucinal, binds to the N-terminal threonine residue of HslV, probably as a hemiacetal, relating HslV also functionally to the proteasomes of archaea and eukaryotes.

ATP-Dependent Proteases↗

Structure of 20S proteasome from yeast at 2.4 A resolution.

The crystal structure of the 20S proteasome from the yeast Saccharomyces cerevisiae shows that its 28 protein subunits are arranged as an (alpha1...alpha7, beta1...beta7)2 complex in four stacked rings and occupy unique locations. The interior of the particle, which harbours the active sites, is only accessible by some very narrow side entrances. The beta-type subunits are synthesized as proproteins before being proteolytically processed for assembly into the particle. The proforms of three of the seven different beta-type subunits, beta1/PRE3, beta2/PUP1 and beta5/PRE2, are cleaved between the threonine at position 1 and the last glycine of the pro-sequence, with release of the active-site residue Thr 1. These three beta-type subunits have inhibitor-binding sites, indicating that PRE2 has a chymotrypsin-like and a trypsin-like activity and that PRE3 has peptidylglutamyl peptide hydrolytic specificity. Other beta-type subunits are processed to an intermediate form, indicating that an additional nonspecific endopeptidase activity may exist which is important for peptide hydrolysis and for the generation of ligands for class I molecules of the major histocompatibility complex.

Acetylcysteine↗

Hypomethylation of the Xmrk oncogene promoter in melanoma cells of Xiphophorus.

Melanoma formation in Xiphophorus is caused by the tissue-specific overexpression of the Xmrk oncogene. This gene arose by a non-homologous recombination event between the Xmrk proto-oncogene and an unrelated locus, D, during which the Xmrk transcribed regions were fused to new upstream sequences. Functional analyses of this newly acquired promoter revealed the presence of positive regulatory elements. Since these elements did not activate transcription in a melanoma-specific manner, the methylation state of the Xmrk oncogene promoter in different tissues was analyzed. Digestion with methylation sensitive restriction enzymes followed by PCR amplification demonstrated differential methylation in a melanoma cell line and non-melanoma tissue. The methylation state of single CpG-dinucleotides in genomic DNA from different cell types was investigated by bisulfite genomic sequencing. This analysis revealed a high degree of methylation of the Xmrk oncogene promoter in non-transformed tissues. In contrast, the DNA-region analyzed was completely unmethylated in the melanoma cell line PSM. This effect was oncogene-specific, since the Xmrk proto-oncogene showed CpG-methylation in these cells. Studies with melanoma tissue demonstrated that hypomethylation of the Xmrk oncogene promoter can also be found in DNA from these tumors. This correlation suggests that the methylation status of the promoter might play a role in the overexpression of the Xmrk oncogene in vivo.

Animals↗

Synthesis, kinetic characterization and X-ray analysis of peptide aldehydes as inhibitors of the 20S proteasomes from Thermoplasma acidophilum and Saccharomyces cerevisiae.

A comparative kinetic characterization of the peptide aldehydes Ac-Leu-Leu-X-H [X = Trp, Tyr and Tyr(tBu)] and Z-Gly-Pro-Gly-Gly-Leu-Leu-Nle-H as inhibitors of the chymotryptic activity of 20S proteasomes from the archaebacterium T. acidophilum and yeast S. cerevisiae revealed significantly differentiated inhibitory potencies that can be rationalized on the basis of X-ray crystallographic data.

Aldehydes↗

Structural investigation of proteasome inhibition.

The novel proteolytic mechanism of the 20S proteasome from T. acidophilum has been investigated by X-ray crystallography using small-molecule inhibitors and substrate analogues. The 20S proteasome degrades unfolded substrates into small peptides of a defined length. Calpain inhibitor II, chymostatin and lactacystin all bind in the previously identified active site pocket near Thr1 of all fourteen beta-subunits. The chromogenic substrate analogue Suc-LLVY-AMC binds in the same pocket of the proteolytically inactive T1A mutant of the beta-subunit, but with a significantly altered geometry. The heavy-atom cluster Ta6Br12(2+) used in X-ray structure determination occupies seven sites in the inner compartment of the proteasome and exhibits inhibition of the chymotrypsin-like activity. Other effectors of proteasome activity showed no significant difference in electron density.

Acetylcysteine↗

[Pilocytic astrocytoma in childhood: presentation of six cases].

OBJECTIVE: To present 6 cases of pilocytic astrocytomas whose clinic, epidemiological and histopathological aspects were studied. METHODS: Between 1990 and 1994 the records of the laboratories of pathology of the main hospitals in Curitiba were analysed and all cases of pilocytic astrocytomas were studied with special attention to age of onset, sex and site of the lesions. The biopsies, which were reviewed, have been processed according to conventional techniques and in a few cases electron microscopy and immunohistochemistry was further done. RESULTS: Five patients were females and 1 was male. Medium age was 4,5 years (range 1-8). The pilocytic astrocytomas affected optic chiasm (n=3), midline of cerebral hemisfere (n=2) and third ventricle (n=1). The symptoms reflected the location and extension of the tumour. The commonest signs and symptoms were those of intracranial hypertension, visual disturbances, hydrocephalus, among others. The patients were treated with surgical ressection and chemotherapy. Three patients died after a medium survival of 45 days, and three remain alive. CONCLUSIONS: The authors emphasize that pilocytic astrocytoma, mainly the juvenile variant, affect mostly the midline brain structures of infants through signs of visual disturbance. These lesions are low grade astrocytomas and should be treated predominantly by total surgical ressection.

English Abstract↗