Search

Polycomb repressive complex 1 (PRC1) catalyses monoubiquitination of histone H2A on Lys119, promoting gene silencing. Cells at different developmental stages and in different tissues express different PRC1 isoforms. The topology, subunit composition, structural architecture and molecular mechanism of most of these isoforms are still poorly characterized. Here, we have purified a PRC1 isoform comprising subunits RING1B, PCGF2, CBX2 and PHC2, two stable subcomplexes (RING1B-PCGF2 and RING1B-PHC2) and the catalytic subunit RING1B in isolation. By crosslinking mass spectrometry, we identified novel interactions between RING1B and the three non-catalytic subunits. Biochemical, biophysical, and enzymatic data suggest that CBX2 and PHC2 play a structural role, whereas PCGF2 also modulates catalysis. Our data offer insights into the molecular architecture of PRC1 and its histone ubiquitination activity.

Summary Synthesis and scission of phosphodiester bonds in DNA and RNA regulate vital processes within the cell. Enzymes that catalyze these reactions operate mostly via the recognized two-metal-ion mechanism. Our analysis reveals that basic amino acids and monovalent cations occupy structurally conserved positions nearby the active site of many two-metal-ion enzymes for which high-resolution (, Graphical Abstract, Highlights • Basic residues in the active site of two-metal-ion enzymes are structurally conserved • These residues are also conserved in evolution • Mutagenesis suggests these residues may exert an effect on DNA- and RNA processing • Our work offers insights into CRISPR/Cas9, spliceosome, and DNA/RNA polymerases, Genna et al. reveal structural conservation of basic amino acids and monovalent cations in the active site of two-metal-ion enzymes and ribozymes, which catalyze the vital biological reactions of DNA and RNA synthesis and scission. The work offers insights into fundamental two-metal-ion machineries such as CRISPR/Cas9, the spliceosome, and DNA/RNA polymerases.

TET aminopeptidases are dodecameric particles shared in the three life domains involved in various biological processes, from carbon source provider in archaea to eye-pressure regulation in humans. Each subunit contains a dinuclear metal site (M1 and M2) responsible for the enzyme catalytic activity. However, the role of each metal ion is still uncharacterized. Noteworthy, while mesophilic TETs are activated by Mn2+, hyperthermophilic TETs prefers Co2+. Here, by means of anomalous x-ray crystallography and enzyme kinetics measurements of the TET3 aminopeptidase from the hyperthermophilic organism Pyrococcus furiosus (PfTET3), we show that M2 hosts the catalytic activity of the enzyme, while M1 stabilizes the TET3 quaternary structure and controls the active site flexibility in a temperature dependent manner. A new third metal site (M3) was found in the substrate binding pocket, modulating the PfTET3 substrate preferences. These data show that TET activity is tuned by the molecular interplay among three metal sites.

β-2 microglobulin (β2m) is an amyloidogenic protein responsible for dialysis-related amyloidosis in man. In the early stages of amyloid fibril formation, β2m associates into dimers and higher oligomers, although the structural details of such aggregates are poorly understood. To characterize the protein-protein interactions supporting the formation of oligomers, three individual β2m cysteine mutants and their disulfide-linked homodimers (DIMC20, DIMC50 and DIMC60) were prepared. Amyloid propensity, oligomerization state in solution and crystallogenesis were tested for each β2m homodimer: DIMC20 and DIMC50 display a mixture of tetrameric and dimeric species in solution and also yield protein crystals and amyloid fibrils, whereas DIMC60 is dimeric in solution but does not form protein crystals nor amyloid fibrils. The X-ray structures of DIMC20 and DIMC50 show that the two engineered dimers form a tetrameric assembly; for both tetrameric species, the noncovalent association interface is based on the interaction of facing β2m D-strands and is conserved. Notably, DIMC20 and DIMC50 trigger amyloid formation in wild-type β2m in unseeded reactions. Thus, when the D-D-strand interface is impaired by an intermolecular disulfide bond (as in DIMC60), the formation of tetramers is hindered, and the protein is not amyloidogenic and does not promote amyloid aggregation of wild-type β2m. Implications for β2m oligomerization are discussed.

International audience; The TET peptidases are large polypeptide destruction machines present among prokaryotes. They form 12-subunits hollow tetrahedral particles, and belong to the family of M42 metallo-peptidases. Structural characterization of various archaeal and bacterial complexes has revealed a unique mechanism of internal compartmentalization and peptide trafficking that distinguishes them from the other oligomeric peptidases. Different versions of the TET complex often co-exist in the cytosol of microorganisms. In depth enzymatic studies have revealed that they are non-processive cobalt-activated aminopeptidases and display contrasting substrate specificities based on the properties of the catalytic chambers. Recent studies have shed light on the assembly mechanism of homo and hetero-dodecameric TET complexes and shown that the activity of TET aminopeptidase towards polypeptides is coupled with its assembly process. These findings suggested a functional regulation based on oligomerization control in vivo. This review describes a current knowledge on M42 TET peptidases biochemistry and discuss their possible physiological roles. This article is a part of the Special Issue entitled: «A potpourri of proteases and inhibitors: from molecular toolboxes to signalling scissors».

Proteins hosting main β-sheets adopt specific strategies to avoid intermolecular interactions leading to aggregation and amyloid deposition. Human beta-2 microglobulin (β2m) displays a typical immunoglobulin fold and is known to be amyloidogenic in vivo. Upon severe kidney deficiency, β2m accumulates in the bloodstream, triggering, over the years, pathological deposition of large amyloid aggregates in joints and bones. A β-bulge observed on the edge D β-strand of some β2m crystal structures has been suggested to be crucial in protecting the protein from amyloid aggregation. Conversely, a straight D-strand, observed in different crystal structures of monomeric β2m, could promote amyloid aggregation. More recently, the different conformations observed for the β2m D-strand have been interpreted as the result of intrinsic flexibility, rather than being assigned to a functional protective role against aggregation. To shed light on such contrasting picture, the mutation Asp53→Pro was engineered in β2m, aiming to impair the formation of a regular/straight D-strand. Such a mutant was characterized structurally and biophysically by CD, X-ray crystallography and MS, in addition to an assessment of its amyloid aggregation trends in vitro. The results reported in the present study highlight the conformational plasticity of the edge D-strand, and show that even perturbing the D-strand structure through a Pro residue has only marginal effects on protecting β2m from amyloid aggregation in vitro.

β2 microglobulin (β2m) is the light chain of class-I major histocompatibility complex (MHC-I). Its accumulation in the blood of patients affected by kidney failure leads to amyloid deposition around skeletal joints and bones, a severe condition known as Dialysis Related Amyloidosis (DRA). In an effort to dissect the structural determinants of β2m aggregation, several β2m mutants have been previously studied. Among these, three single-residue mutations in the loop connecting strands D and E (W60G, W60V, D59P) have been shown to affect β2m amyloidogenic properties, and are here considered. To investigate the biochemical and biophysical properties of wild-type (w.t.) β2m and the three mutants, we explored thermal unfolding by Trp fluorescence and circular dichroism (CD). The W60G mutant reveals a pronounced increase in conformational stability. Protein oligomerization and reduction kinetics were investigated by electrospray-ionization mass spectrometry (ESI-MS). All the mutations analyzed here reduce the protein propensity to form soluble oligomers, suggesting a role for the DE-loop in intermolecular interactions. A partially folded intermediate, which may be involved in protein aggregation induced by acids, accumulates for all the tested proteins at pH 2.5 under oxidizing conditions. Moreover, the kinetics of disulfide reduction reveals specific differences among the tested mutants. Thus, β2m DE-loop mutations display long-range effects, affecting stability and structural properties of the native protein and its low-pH intermediate. The evidence presented here hints to a crucial role played by the DE-loop in determining the overall properties of native and partially folded β2m.

High-throughput screening highlighted 9-oxo-9H-indeno[1,2-b]pyrazine-2,3-dicarbonitrile (1) as an active inhibitor of ubiquitin-specific proteases (USPs), a family of hydrolytic enzymes involved in the removal of ubiquitin from protein substrates. The chemical behavior of compound 1 was examined. Moreover, the synthesis and in vitro evaluation of new compounds, analogues of 1, led to the identification of potent and selective inhibitors of the deubiquitinating enzyme USP8.

In the last few years click chemistry reactions, and in particular copper-catalyzed cycloadditions, have been used intensively for the preparation of new bioconjugate molecules and materials applicable to biomedical and pharmaceutical areas. This review will be focused on conjugates of the tripeptide Arg-Gly-Asp formed by means of click chemistry reactions. This sequence is a well known binding motif for specific transmembrane proteins and is involved in cellular adhesion to the extracellular matrix, allowing the selective recognition of the biomolecule or polymer in which it is incorporated.

A small library of cyclic RGD pentapeptide mimics, including benzyl-substituted azabicycloalkane amino acids, was synthesized with the aim of developing active and selective integrin antagonists. In vitro binding assays established one particular compound with affinity for both the alpha(v)beta(3) and the alpha(v)beta(5) integrins. The synthesis in solution and the in vitro screening of these RGD derivatives, as well as the determination of the conformational properties of the integrin ligands by spectroscopic and computational methods are described.

An advantageous ligand-free protocol for Suzuki couplings is described. The synthetic procedure entails microwave irradiation for the reduction of the reaction times and the use of silica cartridges for the purification. Dihalo-pyrimidine structures, interesting scaffolds in medicinal chemistry, were chosen as test compounds.

Using a convenient and practical route we report the preparation of a series of rigid surrogates of amino acids and dipeptides for application within constrained peptide analogues, and for employment as input for combinatorial science. These substituted 2-oxo-1-azabicycloalkane amino acids have the potential of replicating the backbone geometry and side-chain function of dipeptide residues like serine, lysine, glutamate, and related amino acids.

O-Alkylation of phenol compounds was performed in a continuous flow apparatus under biphasic liquid/liquid conditions and promoted by tetrabutylammonium bromide (TBAB) as a phase-transfer catalyst. The segmented flow that is generated within the flow system is able to afford the desired ethers in high yield and in very short times.

A practical synthetic scheme was developed to prepare both the cis- and trans-fused stereoisomers of N-Boc- l -octahydroindole-2-carboxylic acid ( l -Oic) methyl ester. Key event of the synthetic sequence was the ring-closing metathesis of a suitable diallylated proline derivative. This is the first reported practical synthesis of the trans-fused isomer. Functionalization of the octahydroindole nucleus by electrochemical oxidation followed by acid-catalysed allylation paved the way for the preparation of reverse-turn dipeptide mimics.

International audience; Tetrahedral (TET) aminopeptidases are large polypeptide destruction machines present in prokaryotes and eukaryotes. Here, the rules governing their assembly into hollow 12-subunit tetrahedrons are addressed by using TET2 from Pyrococcus horikoshii (PhTET2) as a model. Point mutations allowed the capture of a stable, catalytically active precursor. Small angle x-ray scattering revealed that it is a dimer whose architecture in solution is identical to that determined by x-ray crystallography within the fully assembled TET particle. Small angle x-ray scattering also showed that the reconstituted PhTET2 dodecameric particle displayed the same quaternary structure and thermal stability as the wild-type complex. The PhTET2 assembly intermediates were characterized by analytical ultracentrifugation, native gel electrophoresis, and electron microscopy. They revealed that PhTET2 assembling is a highly ordered process in which hexamers represent the main intermediate. Peptide degradation assays demonstrated that oligomerization triggers the activity of the TET enzyme toward large polypeptidic substrates. Fractionation experiments in Pyrococcus and Halobacterium cells revealed that, in vivo, the dimeric precursor co-exists together with assembled TET complexes. Taken together, our observations explain the biological significance of TET oligomerization and suggest the existence of a functional regulation of the dimer-dodecamer equilibrium in vivo.

β2-Microglobulin (β2m) is the light chain of the class-I major histocompatibility complex, being also the causing agent of dialysis-related amyloidosis, which results from its accumulation as amyloid material in the skeletal joints. This study describes conformational properties of β2m under two distinct, in vitro amyloidogenic conditions: neutral pH in the presence of 20% 2,2,2-trifluoroethanol (TFE) and acidic pH in the absence of TFE. Species distribution analysis by electrospray ionizationmass spectrometry (ESI-MS) is combined with information obtained by ion mobilitymass spectrometry (IM-MS), fluorescence and circular dichroism (CD) spectroscopy. It is shown that β2m populates quite different conformational ensembles under the two conditions, but both ensembles display a minor fraction of the population in a partially folded state. In spite of similar compactness, these two partially folded forms display different conformations: helical secondary structure is predominant in the species at pH 7.4, 20% TFE, while the low-pH form is mainly random coil. As temperature is increased, the TFE intermediate looses helical structure becoming more similar to the low-pH intermediate. The existence of different conformational ensembles may rationalize the different aggregation propensity displayed by β2m under the two fibrillation conditions analyzed here.

Beta-2 microglobulin (β2m) is the light chain of Class I major histocompatibility complex (MHC-I) complex. β2m is an intrinsically amyloidogenic protein capable of forming amyloid fibrils in vitro and in vivo. β2m displays the typical immunoglobulin-like fold with a disulphide bridge (Cys25-Cys80) cross-linking the two β-sheets. Engineering of the loop comprised between β-strands D and E has shown that mutations in this region affect protein structure, fold stability, folding kinetics and amyloid aggregation properties. Such overall effects have been related to the DE loop backbone structure, which presents a strained conformation in the wild-type (wt) protein, and a type I β-turn in the W60G mutant. Here, we report a biophysical and structural characterization of the K58P-W60G β2m mutant, where a Pro residue has been introduced in the type I β-turn i + 1 position. The K58P-W60G mutant shows improved chemical and temperature stability and faster folding relative to wt β2m. The crystal structure (1.25 Å resolution) shows that the Cys25-Cys80 disulphide bridge is unexpectedly severed, in agreement with electrospray ionization-mass spectrometry (ESI-MS) spectra that indicate that a fraction of the purified protein lacks the internal disulphide bond. These observations suggest a stabilizing role for Pro58, and stress a crucial role for the DE loop in determining β2m biophysical properties.

In the last few years click chemistry reactions, and in particular copper-catalyzed cycloadditions, have been used intensively for the preparation of new bioconjugate molecules and materials applicable to biomedical and pharmaceutical areas. This review will be focused on conjugates of the tripeptide Arg-Gly-Asp formed by means of click chemistry reactions. This sequence is a well known binding motif for specific transmembrane proteins and is involved in cellular adhesion to the extracellular matrix, allowing the selective recognition of the biomolecule or polymer in which it is incorporated.

A practical synthetic scheme was developed to prepare both the cis- and trans-fused stereoisomers of N-Boc- l -octahydroindole-2-carboxylic acid ( l -Oic) methyl ester. Key event of the synthetic sequence was the ring-closing metathesis of a suitable diallylated proline derivative. This is the first reported practical synthesis of the trans-fused isomer. Functionalization of the octahydroindole nucleus by electrochemical oxidation followed by acid-catalysed allylation paved the way for the preparation of reverse-turn dipeptide mimics.

An advantageous ligand-free protocol for Suzuki couplings is described. The synthetic procedure entails microwave irradiation for the reduction of the reaction times and the use of silica cartridges for the purification. Dihalo-pyrimidine structures, interesting scaffolds in medicinal chemistry, were chosen as test compounds.

Beta2-microglobulin (beta2m) is the light chain component of class I major histocompatibility complex (MHC-I). beta2m is an intrinsically amyloidogenic protein that can assemble into amyloid fibrils in vitro and in vivo. Several recent reports suggested that the polypeptide loop comprised between beta-strands D and E of beta2m is important for protein stability and for the protein propensity to aggregate as amyloid fibrils. In particular, the roles of Trp60 for MHC-I assembly and beta2m stability have been highlighted by showing that the beta2m Trp60-->Gly mutant is more stable and less prone to aggregation than the wild type protein. To further analyse such properties, the Trp60-->Cys and Asp59-->Pro beta2m mutants have been expressed, purified, and their crystal structures determined. The stability to thermal denaturation and propensity to fibrillar aggregation have also been analysed. The experimental evidences gathered on the two mutants reinforce the hypothesis that conformational strain in the DE loop can affect beta2m stability and amyloid aggregation properties.

In the scenario of a continuous request for better drugs in shorter times, medicinal chemists must face the challenging task of preparing new patentable molecules, combining high activity and selectivity, drug-likeness and good pharmacokinetic properties. Multiparametric optimization requires a substantial improvement of the efficacy and throughput of the early discovery process, leading to a significant revolution in organic synthesis and chemistry technologies. Chemists are searching for ways to simplify synthetic protocols, for example, by the use of polymer-assisted solution-phase synthesis, microwave-assisted organic synthesis and flow chemistry. Organic synthesis is benefiting of fast and robust reactions, with breakthrough approaches often entailing the privileged use of multicomponent reactions, click chemistry and ring-closing metathesis.

[reaction: see text] An efficient and operationally simple method for the synthesis of functionalized azaoxobicyclo[X.3.0]alkane amino acids has been devised. The key step is an intramolecular nitrone cycloaddition on 5-allyl- or 5-homoallylproline that was found to be completely regio- and stereoselective.

The first example of ring-closing metathesis reaction of dehydroamino acids using ruthenium-based catalyst leading to the azabicyclo[X.Y.0]alkanes has been demonstrated. A preliminary investigation into the scope and limitations of the method will be presented. (C) 2004 Elsevier Ltd. All rights reserved.

Parallel synthesis of a small library of hydroxy functionalized bicyclic lactams with optically pure mimicking dipeptide Pro-Ser has been accomplished via aldol condensation of aldehyde 9 with N-BocGlyCO 2 Et. The configurations of eight scaffolds were established unambiguously by NMR spectroscopy.

By a stereoselective alkylation approach a synthesis of eight enantiopure, sterically constrained C α -tetrasubstituted azabicycloalkane amino acids was carried out.

An efficient and versatile synthetic method for the preparation of new fused bicyclic lactams 3a and 3b is described. The spirane cyclopentane nucleus was easily installed by diallylation of the pyroglutamate derivative 18 followed by ring-closing metathesis (RCM). A more practical and stereoselective method for the allylation of the α-methoxy carbamate 21 , involving the use of InCl3 as a Lewis acid, was developed. In the crucial coupling reaction of the diastereomeric mixture of cis- and trans-pirrolidine derivatives 5a and 5b with N-Cbz vinyl phenylalanine only the cis isomer was found to react. An RCM reaction on the dipeptides 25a and 25b followed by catalytic hydrogenation, gave the final epimeric bicyclic lactams 3a and 3b . The same synthetic sequence on the model compound 7 , lacking the spiro cyclopentane nucleus, is also reported.

A practical approach to the synthesis of a conformationally constrained spiroazabicycloalkane aminoacid scaffold as a reverse-turn inducer dipeptide mimic is described.

The Fmoc-protected lactams 3 and 4 were used to prepare cyclo(Arg-Gly-Asp-lactam) 1 and cyclo(Arg-Gly-Asp-Phe-lactam) 2, which contain the Arg-Gly-Asp (RGD) recognition motif. Their solid-phase synthesis, conformational analysis, and binding to purified αVβ3 and αVβ5 integrins are reported. Compound 1 was found to act as an active and selective inhibitor of the αVβ5 integrin.

A practical approach to the synthesis of a conformationally constrained spiroazabicycloalkane aminoacid scaffold as a reverse-turn inducer dipeptide mimic is described.