Analysis of secondary structure in proteins by chemical cross-linking coupled to MS

Chemical cross-linking is an attractive technique for the study of the structure of protein complexes due to its low sample consumption and short analysis time. Furthermore, distance constraints obtained from the identification of cross-linked peptides by MS can be used to construct and validate protein models. If a sufficient number of distance constraints are obtained, then determining the secondary structure of a protein can allow inference of the protein's fold. In this work, we show how the distance constraints obtained from cross-linking experiments can identify secondary structures within the protein sequence. Molecular modeling of alpha helices and beta sheets reveals that each secondary structure presents different cross-linking possibilities due to the topological distances between reactive residues. Cross-linking experiments performed with amine reactive cross-linkers with model alpha helix containing proteins corroborated the molecular modeling predictions. The cross-linking patterns established here can be extended to other cross-linkers with known lengths for the determination of secondary structures in proteins.     

Utilization of d-carnitine by Pseudomonas sp. AK 1

Abstract The degradation of chlorophenols by Alcaligenes eutrophus JMP134 (pJP4) was studied. The strain grew on 2,4,6-trichlorophenol or 2,4,6-tribromophenol as the sole carbon and energy source. Complete degradation of 2,4,6-trichlorophenol was confirmed by chloride release and gas chromatography analysis of supernatants from growth cultures. The 2,3,5-, 2,3,4-, 2,3,6-and 2,4,5-isomers of trichlorophenol did not support growth. However, up to 40% of 2,4,5-trichlorophenol was mineralized during growth of A. eutrophus on chemostats fed with either phenol (0.4 mM) or 2,4,6-trichlorophenol (0.4 mM) plus 2,4,5-trichlorophenol (0.1 mM). Growth on 2,4,6-trihalophenols was also observed in A. Eutrophus JMP222, the strain lacking pJP4, suggesting that this new degradative ability reported for A. eutrophus is not related to pJP4 encoded catabolic functions.     

Early activation of p160ROCK by pressure overload in rat heart

We investigated the effects of acutepressure overload on activation of p160^ROCK in ratmyocardium. Constriction of transverse aorta, controlled to increasepeak systolic pressure of ascending aorta by ~40 mmHg, induced arapid association of RhoA with Dbl-3 and p160^ROCK. Thebinding of p160^ROCK to RhoA was rapidly increased, peakingat 30 min (~3.5-fold), but reduced to lower levels (~1.9-fold) by60 min of pressure overload. The activity of immunoprecipitatedp160^ROCK toward myosin light chain increased ~2.5-foldwithin 10 min but decreased to lower levels (~1.6-fold) after 60 minof pressure overload. Confocal microscopic analysis indicated thatpressure overload induced the formation of aggregates ofp160^ROCK and RhoA along the longitudinal axis of cardiacmyocytes. Immunoelectron microscopic analysis showed that pressureoverload induced the association of p160^ROCK and RhoA toZ-line, T-tubule, and subsarcolemmal areas. The rapid activation ofp160^ROCK by pressure overload and its aggregation insubcellular structures involved in transmission of mechanical forcesuggest a role for this enzyme in the mechanobiochemical transductionin the myocardium.

     

Colchicine attenuates left ventricular hypertrophy but preserves cardiac function of aortic-constricted rats.

To investigate the effects of colchicine on left ventricular (LV) function and hypertrophy (LVH) of rats subjected to constriction of transverse aorta (TAoC), we evaluated SO (sham operated, vehicle; n = 25), SO-T (sham operated, colchicine 0.4 mg/kg body wt ip daily; n = 38), TAoC (vehicle; n = 37), and TAoC-T (TAoC, colchicine; n = 34) on the 2nd, 6th, and 15th day after surgery. Colchicine attenuated LVH of TAoC-T compared with TAoC rats, as evaluated by ratio between LV mass (LV(M)) and right ventricular mass, LV wall thickness, and average diameter of cardiac myocytes. Systolic gradient across TAoC ( approximately 45 mmHg), LV systolic pressure, LV end-diastolic pressure, and rate of LV pressure increase (+dP/dt) were comparable in TAoC-T and TAoC rats. However, the baseline and increases of LV systolic pressure-to-LV(M) and +dP/dt-to-LV(M) ratios induced by phenylephrine infusion were greater in TAoC-T and SO-T compared with SO rats. Baseline and increases of +dP/dt-to-LV(M) ratio were reduced in TAoC compared with SO rats. TAoC rats increased polymerized fraction of tubulin compared with SO, SO-T, and TAoC-T rats. Our results indicate that colchicine treatment reduced LVH to pressure overload but preserved LV function.     

Reactions of pentaammineruthenium complexes with 1,2- and 1,4-dicyanobenzene and cyanobenzamides: evidences of neighboring group participation

The spectral (UV-Vis and IR) and electrochemical behavior of the nitrile bonded complexes [Ru(NH₃)₅L]²⁺ (L = 1,4-dicyanobenzene (1,4-dcb), 1,2-dicyanobenzene (1,2-dcb)), [Ru(NH₃)₅(NHC(OH)-bz-4-CN)]³⁺, [Ru(NH₃)₅(NHC(O)-bz-2-CN)]²⁺ and [Ru(NH₃)₅(NH(C)NHC(O)bz)]³⁺ (NH(C)NHC(O)-bz = 3-imino-1-oxo-isoindoline) are described. Oxidation of [Ru(NH₃)₅L]²⁺, at 0 ? pH ? 6, is followed by hydrolysis of the coordinated nitrile to give amide complexes in which the amide is through the nitrogen, with pH-dependent rate constants. The estimated values of the rate constant of hydrolysis (k_obs) at 25 °C are 2.9 × 10⁻³ s⁻¹ for [Ru(NH₃)₅(1,4-dcb)]³⁺ and 5.6 × 10⁻³ s⁻¹ for [Ru(NH₃)₅(1,2-dcb)]³⁺ at pH 4.65. Reduction of [Ru(NH₃)₅(NHC(O)-bz-4-CN)]²⁺ and [Ru(NH₃)₅(NHC(O)-bz-2-CN)]²⁺ is followed by two reactions, one is an aquation forming [Ru(NH₃)₅(OH₂)]²⁺ and free ligand, and the other an intramolecular linkage isomerization forming [Ru(NH₃)₅(NC-bz-4-NH₂C(O))]²⁺ and [Ru(NH₃)₅(NC-bz-2-NH₂C(O))]²⁺. The oxidized1,2-cyanobenzamide complex [Ru(NH₃)₅(NHC(OH)-bz-2-CN)]³⁺ undergoes an amide to nitrile intramolecular linkage isomerization, followed by a cyclization reaction resulting in [Ru(NH₃)₅(NH-(C)(HN-C(O)-2-bz))]³⁺ ((NH-(C)(HN-C(O)-2-bz)) = 3-imino-1-oxo-isoindoline bonded through the exocyclic nitrogen) (pK_a = 4.3). The rates of these reactions, which occur with neighboring group participation, increase with acidity. The reduced form, [Ru(NH₃)₅(NH-(C)(HN-C(O)-2-bz))]²⁺, is relatively substitution inert.     

Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli

Two proteins (CaiB and CaiD) were found to catalyze the reversible biotransformation of crotonobetaine to L-carnitine in Escherichia coli in the presence of a cosubstrate (e.g., gamma-butyrobetainyl-CoA or crotonobetainyl-CoA). CaiB (45 kDa) and CaiD (27 kDa) were purified in two steps to electrophoretic homogeneity from overexpression strains. CaiB was identified as crotonobetainyl-CoA:carnitine CoA-transferase by MALDI-TOF mass spectrometry and enzymatic assays. The enzyme exhibits high cosubstrate specificity to CoA derivatives of trimethylammonium compounds. In particular, the N-terminus of CaiB shows significant identity with other CoA-transferases (e.g., FldA from Clostridium sporogenes, Frc from Oxalobacter formigenes, and BbsE from Thauera aromatica) and CoA-hydrolases (e.g., BaiF from Eubacterium sp.). CaiD was shown to be a crotonobetainyl-CoA hydratase using MALDI-TOF mass spectrometry and enzymatic assays. Besides crotonobetainyl-CoA CaiD is also able to hydrate crotonyl-CoA with a significantly lower Vmax (factor of 10(3)) but not crotonobetaine. The substrate specificity of CaiD and its homology to the crotonase confirm this enzyme as a new member of the crotonase superfamily. Concluding these results, it was verified that hydration of crotonobetaine to L-carnitine proceeds at the CoA level in two steps: the CaiD catalyzed hydration of crotonobetainyl-CoA to L-carnitinyl-CoA, followed by a CoA transfer from L-carnitinyl-CoA to crotonobetaine, catalyzed by CaiB. When gamma-butyrobetainyl-CoA was used as a cosubstrate (CoA donor), the first reaction is the CoA transfer. The optimal ratios of CaiB and CaiD during this hydration reaction, determined to be 4:1 when crotonobetainyl-CoA was used as cosubstrate and 5:1 when gamma-butyrobetainyl-CoA was used as cosubstrate, are different from that found for in vivo conditions (1:3).     

Treatment with 5-Aza-2'-Deoxycytidine Induces Expression of NY-ESO-1 and Facilitates Cytotoxic T Lymphocyte-Mediated Tumor Cell Killing

Background

NY-ESO-1 belongs to the cancer/testis antigen (CTA) family and represents an attractive target for cancer immunotherapy. Its expression is induced in a variety of solid tumors via DNA demethylation of the promoter of CpG islands. However, NY-ESO-1 expression is usually very low or absent in some tumors such as breast cancer or multiple myeloma. Therefore, we established an optimized in vitro treatment protocol for up-regulation of NY-ESO-1 expression by tumor cells using the hypomethylating agent 5-aza-2''-deoxycytidine (DAC).

Methodology/Principal Findings

We demonstrated de novo induction of NY-ESO-1 in MCF7 breast cancer cells and significantly increased expression in U266 multiple myeloma cells. This effect was time- and dose-dependent with the highest expression of NY-ESO-1 mRNA achieved by the incubation of 10 μM DAC for 72 hours. NY-ESO-1 activation was also confirmed at the protein level as shown by Western blot, flow cytometry, and immunofluorescence staining. The detection and quantification of single NY-ESO-1 peptides presented at the tumor cell surface in the context of HLA-A*0201 molecules revealed an increase of 100% and 50% for MCF7 and U266 cells, respectively. Moreover, the enhanced expression of NY-ESO-1 derived peptides at the cell surface was accompanied by an increased specific lysis of MCF7 and U266 cells by HLA-A*0201/NY-ESO-1(_157–165) peptide specific chimeric antigen receptor (CAR) CD8⁺ T cells. In addition, the killing activity of CAR T cells correlated with the secretion of higher IFN-gamma levels.

Conclusions/Significance

These results indicate that NY-ESO-1 directed immunotherapy with specific CAR T cells might benefit from concomitant DAC treatment.     

Urinary Bladder Dysfunction in Transgenic Sickle Cell Disease Mice

Background

Urological complications associated with sickle cell disease (SCD), include nocturia, enuresis, urinary infections and urinary incontinence. However, scientific evidence to ascertain the underlying cause of the lower urinary tract symptoms in SCD is lacking.

Objective

Thus, the aim of this study was to evaluate urinary function, in vivo and ex vivo, in the Berkeley SCD murine model (SS).

Methods

Urine output was measured in metabolic cage for both wild type and SS mice (25-30 g). Bladder strips and urethra rings were dissected free and mounted in organ baths. In isolated detrusor smooth muscle (DSM), relaxant response to mirabegron and isoproterenol (1nM-10μM) and contractile response to (carbachol (CCh; 1 nM-100μM), KCl (1 mM-300mM), CaCl₂ (1μM-100mM), α,β-methylene ATP (1, 3 and 10 μM) and electrical field stimulation (EFS; 1-32 Hz) were measured. Phenylephrine (Phe; 10nM-100μM) was used to evaluate the contraction mechanism in the urethra rings. Cystometry and histomorphometry were also performed in the urinary bladder.

Results

SS mice present a reduced urine output and incapacity to produce typical bladder contractions and bladder emptying (ex vivo), compared to control animals. In DSM, relaxation in response to a selective β3-adrenergic agonist (mirabegron) and to a non-selective β-adrenergic (isoproterenol) agonist were lower in SS mice. Additionally, carbachol, α, β-methylene ATP, KCl, extracellular Ca²⁺ and electrical-field stimulation promoted smaller bladder contractions in SS group. Urethra contraction induced by phenylephrine was markedly reduced in SS mice. Histological analyses of SS mice bladder revealed severe structural abnormalities, such as reductions in detrusor thickness and bladder volume, and cell infiltration.

Conclusions

Taken together, our data demonstrate, for the first time, that SS mice display features of urinary bladder dysfunction, leading to impairment in urinary continence, which may have an important role in the pathogenesis of the enuresis and infections observed the SCD patients.