Crystal structure and mechanism of human lysine-specific demethylase-1

The reversible methylation of specific lysine residues in histone tails is crucial in epigenetic gene regulation. LSD1, the first known lysine-specific demethylase, selectively removes monomethyl and dimethyl, but not trimethyl modifications of Lys4 or Lys9 of histone-3. Here, we present the crystal structure of LSD1 at 2.9-A resolution. LSD1 forms a highly asymmetric, closely packed domain structure from which a long helical 'tower' domain protrudes. The active site cavity is spacious enough to accommodate several residues of the histone tail substrate, but does not appear capable of recognizing the different methylation states of the substrate lysine. This supports the hypothesis that trimethylated lysine is chemically rather than sterically discriminated. We present a biochemical analysis of LSD1 mutants that identifies crucial residues in the active site cavity and shows the importance of the SWIRM and tower domains for catalysis.     

Quantitative determination of nuclear pore complexes in cycling cells with differing DNA content

The number of pore complexes per nucleus was determined for a wide variety of cultured cells selected for their variable DNA content over a range of 1-5,6000. The pore number was compared to DNA content, nuclear surface area, and nuclear volume. Values for pore frequency (pores/square micrometer) were relatively constant in the species studied. When the pore to DNA ratio was plotted against the DNA content, there was a remarkable correlation which decreased exponentially for the cells of vertebrae origin. Exceptions were the heteroploid mammalian cells which had the same ratio as the diploid mammalian cells despite higher DNA content. The results are interpreted to mean that neither the nuclear surface, the nuclear volume, nor the DNA content alone determines the pore number of the nucleus, but rather an as yet undetermined combination of different factors. The surface and volume of vertebrate nuclei do not decrease with decreasing DNA content below a given value. The following speculation is suggested to account for the anomalous size changes of the nucleus relative to DNA content in vertebrates. Species with small DNA complements have a relatively large proportion of active chromatin which determines the limits of the physical parameters of the nucleus. The amount of active chromatin maybe the same for at least the vertebrates with low DNA content, At high DNA content, the nuclear parameters may be determined by the relatively high proportion of inactive condensed chromatin which increases the nuclear surface and volume.     

Protein Disorder and Short Conserved Motifs in Disordered Regions Are Enriched near the Cytoplasmic Side of Single-Pass Transmembrane Proteins

Intracellular juxtamembrane regions of transmembrane proteins play pivotal roles in cell signalling, mediated by protein-protein interactions. Disordered protein regions, and short conserved motifs within them, are emerging as key determinants of many such interactions. Here, we investigated whether disorder and conserved motifs are enriched in the juxtamembrane area of human single-pass transmembrane proteins. Conserved motifs were defined as short disordered regions that were much more conserved than the adjacent disordered residues. Human single-pass proteins had higher mean disorder in their cytoplasmic segments than their extracellular parts. Some, but not all, of this effect reflected the shorter length of the cytoplasmic tail. A peak of cytoplasmic disorder was seen at around 30 residues from the membrane. We noted a significant increase in the incidence of conserved motifs within the disordered regions at the same location, even after correcting for the extent of disorder. We conclude that elevated disorder within the cytoplasmic tail of many transmembrane proteins is likely to be associated with enrichment for signalling interactions mediated by conserved short motifs.     

Numerical modelling of simulated blood flow in idealized composite arterial coronary grafts: transient flow

In composite arterial coronary grafts (CACGs), transport phenomena and geometry may considerably alter blood flow dynamics. CACGs aim at revascularizing pathological arteries according to the human anatomy. However, the exact mechanisms causing the failure of coronary bypass grafting are not yet well elucidated. In the present study, computational fluid dynamics (CFD) techniques are applied for the simulation of multi-branched CACGs under physiologically realistic inflow waveforms. The numerical solution is obtained by a finite-volume method formulated in non-orthogonal, curvilinear coordinates and a multi-grid approach. The geometrical models, consisting of idealized and rigid vessels, include the typical T- and a rather new pi-graft configuration. The stenotic effect is also investigated by comparing computational results for three different degrees of area constriction, namely 25%, 50% and 75%, as well as the case without stenosis. Different grafting distances and various inflow rate ratios are imposed, to give an insight into haemodynamical alterations of CACGs and to study the process of restenosis. The results focus on the interaction between the grafts and coronary flows in terms of spatial and temporal variations of velocity and wall shear stress (WSS) distribution. Prominent variations among the different geometries, concerning the velocity profiles and secondary flow motion, are shown. Moreover, the residual flow emerging from different degrees of area constriction shows that low and oscillating shear stresses may arise for even moderate stenotic fields.     

2-Chlorotrityl chloride resin. Studies on anchoring of Fmoc-amino acids and peptide cleavage

The esterification of 2-chlorotrityl chloride resin with Fmoc-amino acids in the presence of DIEA is studied under various conditions. High esterification yields are obtained using 0.6 equiv. Fmoc-amino acid/mmol resin in DCM or DCE, in 25 min, at room temperature. The reaction proceeds without by product formation even in the case of Fmoc-Asn and Fmoc-Gln. The quantitative and easy cleavage of amino acids and peptides from 2-chlorotrityl resin, by using AcOH/TFE/DCM mixtures, is accomplished within 15-60 min at room temperature, while t-butyl type protecting groups remain unaffected. Under these exceptionally mild conditions 2-chlorotrityl cations generated during the cleavage of amino acids and peptides from resin do not attack the nucleophilic side chains of Trp, Met, and Tyr.     

Effect of X-Asp (or Asn)-Phe-Nh2 (where X; H, Met) peptides on human platelet aggregation in vitro.

A series of di- and tripeptides containing aspartic or asparagine as N-terminal or intermediate amino acid were synthesized and tested for their effect on human platelet aggregation in vitro. It was found that only Met-Asp(or Asn)-Phe-NH2 inhibited platelet aggregation induced by collagen, ADP or adrenaline. Asn-Phe-NH2 and to a small extent Asp-Phe-NH2 presented strong aggregatory activity at low concentrations (at 0.5 mM or lower than this). All the other peptides tested, did not show any effect on platelet aggregation even at the concentration of 10 mM.     

Novel synthetic RGD analogs incorporating salicylic acid derivatives show antiplatelet activity in vitro

Continuing our investigational efforts for more active GpIIb/IIIa inhibitors we have synthesized four novel RGD (Arg-Gly-Asp) analogs incorporating salicylic acid derivatives at their N-terminal amino group using the solid phase synthesis.The synthesized compounds 5-Cl-2-HO-C₆H₃-CO-Arg-Gly-Asp(OBzl)-NH₂and 5-Br-2-HO-C₆H₃-CO-Arg-Gly-Asp(OBzl)-NH₂ were tested for their inhibitory activity on human platelet aggregationin vitro and found to be potent inhibitors of the platelet aggregation with 75 and 67% inhibitory activity respectively. In order to confirm our results flow cytometry with monoclonal antibodies against GpIb, GpIIb/IIIa, GpIIIa and GMP140receptors was used.     

High frequency of copy number variations (CNVs) in the chromosome 11p15 region in patients with Beckwith–Wiedemann syndrome

Beckwith–Wiedemann syndrome (BWS), an overgrowth and tumor predisposition syndrome is clinically heterogeneous. Its variable presentation makes molecular diagnosis particularly important for appropriate counseling of patients with respect to embyronal tumor risk and recurrence risk. BWS is characterized by macrosomia, omphalocele, and macroglossia. Additional clinical features can include hemihyperplasia, embryonal tumors, umbilical hernia, and ear anomalies. BWS is etiologically heterogeneous arising from dysregulation of one or both of the chromosome 11p15.5 imprinting centers (IC) and/or imprinted growth regulatory genes on chromosome 11p15.5. Most BWS cases are sporadic and result from loss of maternal methylation at imprinting center 2 (IC2), gain of maternal methylation at imprinting center 1 (IC1) or paternal uniparental disomy (UPD). Heritable forms of BWS (15 %) have been attributed mainly to mutations in the growth suppressor gene CDKN1C, but have also infrequently been identified in patients with copy number variations (CNVs) in the chromosome 11p15.5 region. Four hundred and thirty-four unrelated BWS patients referred to the molecular diagnostic laboratory were tested by methylation-specific multiplex ligation-dependent probe amplification. Molecular alterations were detected in 167 patients, where 103 (62 %) showed loss of methylation at IC2, 23 (14 %) had gain of methylation at IC1, and 41 (25 %) showed changes at both ICs usually associated with paternal UPD. In each of the three groups, we identified patients in whom the abnormalities in the chromosome 11p15.5 region were due to CNVs. Surprisingly, 14 patients (9 %) demonstrated either deletions or duplications of the BWS critical region that were confirmed using comparative genomic hybridization array analysis. The majority of these CNVs were associated with a methylation change at IC1. Our results suggest that CNVs in the 11p15.5 region contribute significantly to the etiology of BWS. We highlight the importance of performing deletion/duplication testing in addition to methylation analysis in the molecular investigation of BWS to improve our understanding of the molecular basis of this disorder, and to provide accurate genetic counseling.     

Methionine catabolism in Saccharomyces cerevisiae

The catabolism of methionine to methionol and methanethiol in Saccharomyces cerevisiae was studied using (13)C NMR spectroscopy, GC-MS, enzyme assays and a number of mutants. Methionine is first transaminated to alpha-keto-gamma-(methylthio)butyrate. Methionol is formed by a decarboxylation reaction, which yields methional, followed by reduction. The decarboxylation is effected specifically by Ydr380wp. Methanethiol is formed from both methionine and alpha-keto-gamma-(methylthio)butyrate by a demethiolase activity. In all except one strain examined, demethiolase was induced by the presence of methionine in the growth medium. This pathway results in the production of alpha-ketobutyrate, a carbon skeleton, which can be re-utilized. Hence, methionine catabolism is more complex and economical than the other amino acid catabolic pathways in yeast, which use the Ehrlich pathway and result solely in the formation of a fusel alcohol.