Experimental and theoretical investigations of Dy(III) complex with 2,2′-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study

Abstract

In this study, the interactions of a novel metal complex [Dy(bpy)₂Cl₃.OH₂] (bpy is 2,2'-bipyridine) with fish salmon DNA (FS-DNA) and bovine serum albumin (BSA) were investigated by experimental and theoretical methods. All results suggested significant binding between the Dy(III) complex with FS-DNA and BSA. The binding constants (K_b), Stern-Volmer quenching constants (K_SV) of Dy(III)-complex with FS-DNA and BSA at various temperatures as well as thermodynamic parameters using Van’t Hoff equation were obtained. The experimental results from absorption, ionic strength, iodide ion quenching, ethidium bromide (EtBr) quenching studies and positive ΔH? and ΔS? suggested that hydrophobic groove-binding mode played a predominant role in the binding of Dy(III)-complex with FS-DNA. Indeed, the molecular docking results for DNA-binding were in agreement with experimental data. Besides, the results found from experimental and molecular modeling indicated that the Dy(III)-complex bound to BSA via Van der Waals interactions. Moreover, the results of competitive tests by phenylbutazone, ibuprofen, and hemin (as a site-I, site-II and site-III markers, respectively) considered that the site-III of BSA is the most possible binding site for Dy(III)-complex. In addition, Dy(III) complex was concurrently screened for its antimicrobial activities. The presented data provide a promising platform for the development of novel metal complexes that target nucleic acids and proteins with antimicrobial activity.

Communicated by Ramaswamy H. Sarma     

Modeling of in vivo Proteolytic Degradation of Hemoglobin

Abstract

Based on the amino acid sequences of endogenous peptides and X-ray spatial structure, mechanism of the in vivo proteolly degradation of bovine hemoglobin was analysed. The degradation was shown to be a multi-stage process. Its first stage is determined by the spatial organization of the native protein substrate, and the next stages—;by the distribution of the electrostatic field potential of the protein fragments formed at the earlier stage.     

Isolation and Purification of Human Serum Alpha-1 Acid Glycoprotein

Abstract

Alpha-1 acid glycoprotein (or orosmucoid) was obtained in a pure state from normal human serum by ion exchange chromatography followed by curtain electrophoresis and a final ion exchange chromatography step. Pure α₁ acid glycoprotein (α₁A) has a sedimentation coefficient of 3.1 S and a diffusion coefficient of 5.2 × 10^?7cm² sec^?1, which yields a molecular weight of 44,680 Daltons and an asymmetry factor of 14.6. The αA prepared in the manner here described appears less denatured than the same protein isolated by the Cohn fractionation method.^1,2 ' Alpha-1 A acts as a depressant of phagocytosis³ and is one of the constituents of Mowbray's serum fraction,″which induces a prolongation of skin homografts.     

Erythrocyte agglutination by wheat germ agglutinin: ionic strength dependence of the contact seam topology

Abstract

In this work, we describe a process for production of a Pichia pastoris strain which overproduces large quantities of the human glycine receptor. Subsequent purification yielded functional, uniform protein with expression yields of up to 5 mg per liter cell culture. As the wild-type protein is prone to proteolytic degradation, the labile sites were removed by mutagenesis resulting in an intracellular loop 2 deletion mutant with N-terminal modifications. This variant of the receptor is both stable during purification and storage on ice for up to a week as a complex with an antagonist. The quality of the protein is suitable for biophysical characterization and structural studies. The interaction of the agonist glycine and the antagonist strychnine with purified protein was analyzed by isothermal titration calorimetry. Strychnine binding is driven enthalpically with a K_D of 138 ± 55 nM, a ΔH of ?9708 ± 1195 cal/mol and a ΔS of ?1.0 ± 4.1 cal/mol/K, whereas glycine binding is driven by entropy with a K_D of 3.2 ± 0.8 μM, a ΔH of ?2228 ± 1012 cal/mol and ΔS of 17.7 ± 2.8 cal/mol/K. Strychnine and glycine binding is competitive with a stoichiometry of one ligand molecule to one pentameric glycine receptor.     

PTK2/FAK regulates UPS impairment via SQSTM1/p62 phosphorylation in TARDBP/TDP-43 proteinopathies

ABSTRACT

TARDBP/TDP-43 (TAR DNA binding protein) proteinopathies are a common feature in a variety of neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and Alzheimer disease (AD). However, the molecular mechanisms underlying TARDBP-induced neurotoxicity are largely unknown. In this study, we demonstrated that TARDBP proteinopathies induce impairment in the ubiquitin proteasome system (UPS), as evidenced by an accumulation of ubiquitinated proteins and a reduction in proteasome activity in neuronal cells. Through kinase inhibitor screening, we identified PTK2/FAK (PTK2 protein tyrosine kinase 2) as a suppressor of neurotoxicity induced by UPS impairment. Importantly, PTK2 inhibition significantly reduced ubiquitin aggregates and attenuated TARDBP-induced cytotoxicity in a Drosophila model of TARDBP proteinopathies. We further identified that phosphorylation of SQSTM1/p62 (sequestosome 1) at S403 (p-SQSTM1 [S403]), a key component in the autophagic degradation of poly-ubiquitinated proteins, is increased upon TARDBP overexpression and is dependent on the activation of PTK2 in neuronal cells. Moreover, expressing a non-phosphorylated form of SQSTM1 (SQSTM1^S403A) significantly repressed the accumulation of insoluble poly-ubiquitinated proteins and neurotoxicity induced by TARDBP overexpression in neuronal cells. In addition, TBK1 (TANK binding kinase 1), a kinase that phosphorylates S403 of SQSTM1, was found to be involved in the PTK2-mediated phosphorylation of SQSTM1. Taken together, our data suggest that the PTK2-TBK1-SQSTM1 axis plays a critical role in the pathogenesis of TARDBP by regulating neurotoxicity induced by UPS impairment. Therefore, targeting the PTK2-TBK1-SQSTM1 axis may represent a novel therapeutic intervention for neurodegenerative diseases with TARDBP proteinopathies.Abbreviations: ALP: macroautophagy/autophagy lysosomal pathway; ALS: amyotrophic lateral sclerosis; ATXN2: ataxin 2; BafA1: bafilomycin A₁; cCASP3: cleaved caspase 3; CSNK2: casein kinase 2; FTLD: frontotemporal lobar degeneration; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; OPTN: optineurin; PTK2/FAK: PTK2 protein tyrosine kinase 2; SQSTM1/p62: sequestosome 1; TARDBP/TDP-43: TAR DNA binding protein; TBK1: TANK binding kinase 1; ULK1: unc-51 like autophagy activating kinase 1; UPS: ubiquitin-proteasome system.     

Unraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach

Abstract

Most of the drugs binding to human serum albumin (HSA) are transported to various parts of the body. Here, we have studied the molecular interaction between HSA and synthesized uridine derivatives, 1-[(3R, 4S, 5?R)-2-methyl-3, 4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dion.)(C-MU); [(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxy-4-methyl-tetrahydrofuran-2-yl] methyl methyl phosphochloridate (CM-MU) and [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-2-methyl-3,4-dihydroxyoxolan-2-yl] methyl dihydrogen phosphate (P-MU). Cytotoxic studies of these synthesized compounds with mouse macrophages (RAW 246.7) and HeLa cells (human cervical cancer cells) and binding mechanism of these uridine derivatives with HSA were performed. Subsequently, fluorescence quenching was observed upon titration of uridine derivatives with HSA via static mode of quenching, and the binding constants (K_2-C-MU = 4?±?0.03?×?10⁴M^?1, K_5-CM-MU = 1.95?±?0.03?×?10⁴ M^?1 and K_5-P-MU =1.56?±?0.03?×?10⁴ M^?1) were found to be in sync with the computational results. Further, molecular displacement and molecular docking data revealed that all the derivatives are binding in the subdomain IIA and IIB regions of HSA. The protein secondary structure of complexes was determined by circular dichroism, indicating partial unfolding of the protein upon addition of the uridine derivatives. Furthermore, atomic force microscopy data reveal the change in topology upon binding of 2-C-MU, 5-CM-MU and 5-P-MU with HSA, indicating change in the microenvironment around tryptophan region. Additionally, cytotoxicity studies on HeLa and Raw Cell lines suggested that these molecules have significant anti-proliferative and anti-inflammatory properties. Hence, the study may be of help for development of new drugs based on uridine derivatives which may be helpful for combating various potential diseases.

Communicated by Ramaswamy H. Sarma     

Burkholderia xenovorans LB400联苯双加氧酶及突变体对DDTs的降解

DDTs（dichlorodiphenyltrichloroethane,1,1,1-三氯-2,2-双氯苯基乙烷）是一种典型的持久性有机污染物,曾在疟疾防治和农业除虫方面被广泛应用。虽然包括我国在内的很多国家已经禁止使用DDTs,但目前对环境中DDTs的检测发现它仍然广泛存在且具有新的输入源。DDTs的持续存在对近海生态系统和人类健康具有一定危害,因此它所造成的环境污染问题仍然值得关注。由于Rieske型芳香羟化双加氧酶能够起始多种持久性污染物的降解,过去的几十年里一直是芳香化合物降解领域的焦点。[目的] 为探讨联苯双加氧酶对DDTs的降解特性及机制,本研究选取了食异生素伯克霍尔德氏菌LB400（Burkholderia xenovorans）联苯双加氧酶及突变体对p,p''-DDT和o,p''-DDT的降解过程进行研究。[方法] 以BphAE_LB400为亲本,通过两步定点突变将283位的丝氨酸突变为蛋氨酸,获得突变体BphAE_S283M。通过比较亲本酶与突变体对DDTs的催化性能,模拟突变蛋白结构和分子对接等方法,探究其降解特性及机制。[结果] BphAE_LB400和突变体BphAE_S283M都无法降解对位的p,p''-DDT,但突变体BphAE_S283M可以代谢o,p''-DDT并产生2个立体异构体。对接p,p''-DDT的BphAE_LB400和BphAE_S283M的结构分析表明,BphAE_LB400和BphAE_S283M中p,p''-DDT的反应环均不与原晶体结构中的联苯反应环重合。而对接o,p''-DDT的BphAE_S283M的结构分析表明o,p''-DDT的反应环与晶体结构中的联苯反应环距离很近,且2、3位的碳原子与单核铁原子催化中心的距离在0.5 nm以内,此外,BphAE_S283M的催化腔表面积和体积比BphAE_LB400更大,这很可能有助于BphAE_S283M与o,p''-DDT的结合。[结论] 283位氨基酸是影响BphAE_LB400对DDTs的催化代谢能力的关键氨基酸残基,它可以通过调节反应碳原子与催化中心的距离以及催化腔的大小来影响底物特异性。本次研究进一步阐明了283位氨基酸残基的影响机理,为更有效修复DDTs污染提供理论依据和技术支持。     

Molecular dynamics analysis of the effects of GTP,GDP and benzimidazole derivative on structural dynamics of a cell division protein FtsZ from Mycobacterium tuberculosis

Abstract

The prevailing multi-drug resistance in Mycobacterium tuberculosis continues to remain one of the main challenges to combat tuberculosis. Hence, it becomes imperative to focus on novel drug targets. Filamenting temperature-sensitive mutant Z (FtsZ) is an essential cell division protein, a eukaryotic tubulin homologue and a promising drug target. During cytokinesis, FtsZ polymerises in the presence of GTP to form Z-ring and recruits other proteins at this site that eventually lead to the formation of daughter cells. Benzimidazoles were experimentally shown to inhibit Mtb-FtsZ, with one of the benzimidazole derivatives, M1, being reported to have the minimum inhibitory concentration (MIC) value of 3.13 µg/mL. In the present study, mechanism of destabilisation of FtsZ in the presence of M1 was computationally investigated in the presence of its substrate GTP/GDP employing molecular dynamics (MD) simulation analysis, principal component analysis (PCA), molecular mechanics combined with the generalised Born and surface area continuum salvation (MM-GBSA) and density functional theory (DFT). From the analyses, it is proposed that binding of M1 in the inter-domain cleft induces structural changes in the GTP-binding region that affect GTP binding, thus switching the preference of this protein towards depolymerised state and eventually inhibiting the cell division. Hence, this study provides mechanistic insights into the design of novel benzimidazole inhibitors against Mtb-FtsZ.

Communicated by Ramaswamy H. Sarma     

Presence of D2-dofamine Receptors in Human Term Placenta

Abstract

We studied the binding of [³H]-spiperone on human term placental membranes. This binding reached plateau level after 30 min incubation at 37°C and was reversed (t_1/2 ～ 5 min) by addition of an excess of unlabeled spiperone. Scatchard analysis of saturation experiments with increasing doses of [³H]-spiperone (0–25 nM) showed one class of high affinity binding sites with a dissociation constant (Kd) of 14 ± 2 nM and a maximal binding capacity (Bmax) of 222 ± 9 fmoles/mg protein. The affinity of 5 competitors was determined in competitive binding assays. The D₂-dopamine antagonists were the most potent inhibitors: Ki for spiperone and haloperidol were 8 ± 2 and 56 ± 22 nM respectively. Dopamine inhibited [³H]-spiperone binding with a Ki of 570 ± 50 μM whereas Schering 23390 (D₁ antagonist) and propranolol (β-adrenergic antagonist) were without effect. The binding was also inhibited by 100 μM GTPγS (38 ± 8% inhibition), indicating that the dopamine receptor is coupled with a GTP binding protein. These results demonstrate for the first time the presence of D₂-dopamine receptors in human placenta.     

Cholinergic Binding to the Receptor Proteolipid from Torpedo Electroplax Separated by Ion Exchange Chromatography

Abstract

Proteolipids (i.e., hydrophobic proteins) have been extracted with chloroform-methanol (2:1) from lyophilized Torpedo electroplax, and fractionated on a DEAE-cellulose column. The elution system consisted of the same solvent and a gradient of the hydrophobic ion ptoluene sulfonate (0.1–100mM). The three fractions obtained (I, II and III) have different content of protein, lipid P, and reducing sugars. The amino acid composition shows a higher proportion of hydrophobic residues in I and more charged ones in fractions II and III. Polyacryl amide gel electrophoresis of fraction I shows a single major band of 39 kdaltons; in fractions II and III a major band of 42 kdaltons and fainter bands in the range 62–68 kdaltons are observed.

Fraction I has the highest specific binding for [³H]-acetylcholine (7.1 nmol/mg protein) and [³H]α-bungarotoxin (5.2 nmol/mg protein). The nicotinic nature of this proteolipid was demonstrated by blocking experiments. The Scatchard plot showed two affinity sites for [³H]-acetylcholine (Kd₁ = 3nM and Kd₂ = 1.1 μm). 4-(N-maleimido) pheny1 [³H]trimethylammonium specifically labeled the 39 kdaltons band.

The possible factors involved in the fractionation of proteolipids are discussed. The findings suggest that the 39 kdaltons polypeptide contains the receptor site for acetylcholine and that the other proteolipid components may play a different function in the membrane.     

Rat Kidney Histamine N-Methyltransferase: Purification and Partial Characterization

Abstract

Histamine N-methyltransferase (HMT, EC 2.1.1.8) was purified 8,420-fold In 44% yield from rat kidney. The basic steps in the purification included differential centrlfugation, calcium phosphate adsorption, DEAE cellulose chromatography, and affinity chromatography on an S-adenosylhomocysteine-agarose matrix. The resulting protein was homogeneous as determined by gel electrophoresis and was stable for at least five months at ?80°C. The apparent molecular weight of the enzyme was found to be 31,500 as determined by gel filtration through Sephadex G-100 and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The Isoelectric point of the enzyme was determined to be 5.4. The K_m's for histamine and S-adenosyl-L-methionine were 12.4 ± 1.3 μM and 10.2 ±0.5 μM, respectively. When S-adenosyl-L-methionlne was the variable substrate, the K₁'s for S-adenosyl-L-homocysteine and S-adenosyl-D-homocys-teine were 31.9 ± 3.4 μM and 32.0 ± 3.5 μM, respectively. When histamine was the variable substrate, the K₁ for S-adenosyl-L-homocysteine was 11.8 ± 0.6 μM. Comparison of physico-chemical and catalytic properties of the rat kidney and the guinea pig enzymes suggest that these proteins have similar structural and catalytic characteristics.     

RNA结合蛋白QKI-5对乳腺癌细胞MCF-7增殖的影响研究

目的:检测RNA结合蛋白QKI-5在乳腺癌细胞中的表达水平以及对癌细胞增殖能力的抑制作用。方法:通过免疫印迹实验检测QKI-5在不同乳腺癌细胞株中的表达水平,通过慢病毒感染构建能够稳定过表达QKI-5基因的细胞株,使用MTT,流式细胞仪检测细胞周期来观察过表达QKI-5对细胞增殖能力及周期的影响。结果:MCF-7细胞在三株乳腺癌细胞中QKI-5表达水平相对最低,MTT实验结果显示与对照相比,过表达QKI-5的MCF-7细胞增殖能力出现显著降低P0.05,同时细胞周期检测显示过表达QKI-5的MCF-7细胞组出现了明显的G1期阻滞,进入S期G2/M期细胞减少。结论:在乳腺癌中QKI-5的高表达可能通过抑制癌细胞周期致使细胞增殖变缓,从而导致肿瘤生长受限。     

Binding Interactions of Antagonists with 5‐Hydroxytryptamine3A Receptor Models

Abstract

Homology modeling was performed on the N‐terminal extracellular regions of human, mouse, and guinea pig 5‐hydroxytryptamine type 3A receptors (5‐HT₃R) based on the 24% sequence homology with and on the crystal structure of the snail acetylcholine binding protein (AChBP). Docking of 5‐HT₃ antagonists granisetron, tropisetron, ondansetron, dolasetron ('setrons), and (+)‐tubocurarine suggests an aromatic binding cleft behind a hydrophilic vestibule. Several intra‐ and interface interactions, H‐bonds, and salt bridges stabilize the pentameric structure and the binding cleft. The planar rings of antagonists are intercalated between aromatic side‐chains (W183‐Y234, Y143‐Y153). S227 donates H‐bonds to the carbonyl groups of 'setrons. The tertiary ammonium ions interact with E236, N128 or E129, and/or W90 (cation‐π interaction). This offers a molecular explanation of the pharmacophore models of 5‐HT₃R antagonists. Docking artifacts suggest some ambiguities in the binding loops A and C of the 5‐HT_3AR models. Lower potencies of (+)‐tubocurarine for human, and those of tropisetron for guinea pig 5‐HT_3ARs can be attributed to steric differences of I/S230 in the binding cleft and to distinct binding interactions with E229 and S227, respectively. Ligand binding interferes with crucial intra‐ and interface interactions along the binding cleft.     

Decreased paraoxonase 2 enzymatic activity in monocyte/macrophages cells. A comparative in vivo and in vitro study for diabetes

Aim: To investigate peripheral blood monocytes/macrophages (Mo/M?) paraoxonase 2 (PON2) in diabetes and the factors modulating its activity.

Methods: One hundred and eighteen patients with newly diagnosed uncomplicated type 2 diabetes mellitus were compared regarding clinical, biochemical and oxidative stress parameters with 80 healthy subjects. The capacity of the peripheral blood mononuclear cells (PBMNC) to release pro-oxidants and to neutralise them was determined by measuring the respiratory burst (RB) and the intracellular antioxidant enzyme PON2. In vitro experiments were conducted on a differentiated monocytes cell line (dU937) that was exposed to serum deprivation followed by addition of isolated lipoproteins (VLDL or LDL).

Results: Paraoxonase 2 activity in Mo/M? was significantly lower in type 2 diabetes patients (0.042?±?0.044 vs 0.165?±?0.133U lactonase activity/mg protein in controls, p?1c) and insulin resistance (HOMA-IR). In multivariate regression models, 15–34% of the PON2 variance was explained by diabetes. The in vitro addition of VLDL normalised the RB of serum deprived dU937 cells, S? (to 82?±?18% of the cells incubated with serum, S+) and PON2 activity (from 0.524?±?0.061 in S???to 0.298?±?0.048?U/mg protein). In contrast, when LDL was added, the RB remained lower (61?±?12% of S+, p?=?.03) and PON2 higher (0.580?±?0.030?U/mg protein, p?=?.003).

Conclusions: The decrease in monocyte/macrophage PON2 enzymatic activity observed in type 2 diabetes cannot be totally explained by abdominal obesity and insulin resistance. The underlying molecular mechanisms need to be identified.     

Heparin binding to antithrombin III: Variation in binding sites and affinity

Heparin fractions of different molecular weights and anticoagulant activities were prepared by chromatography on protamine-Sepharose, and the association constants and stoichiometry for binding to antithrombin III were determined by measurement of enhancement of tryptophan fluorescence. A 7,900 molecular weight heparin preparation bound to antithrombin III with a stoichiometry of close to 2:1, whereas 14,300 and 21,600 molecular weight fractions bound at approximately 1:1 with the protein. Apparent association constants were 0.66 × 10⁶ M^?1 for the low molecular weight preparation and 2.89 × 10⁶ M^?1 for the high molecular weight material. Maximal fluorescence enhancement was greater with the higher molecular weight heparin. These results suggest a model of heparin-antithrombin III binding in which two sites on antithrombin III can accommodate one large heparin molecule with high affinity or two smaller molecules with low affinity.     

Lipid-regulated degradation of HMG-CoA reductase and Insig-1 through distinct mechanisms in insect cells

In mammalian cells, levels of the integral membrane proteins 3-hydroxy-3-methylglutaryl-CoA reductase and Insig-1 are controlled by lipid-regulated endoplasmic reticulum-associated degradation (ERAD). The ERAD of reductase slows a rate-limiting step in cholesterol synthesis and results from sterol-induced binding of its membrane domain to Insig-1 and the highly related Insig-2 protein. Insig binding bridges reductase to ubiquitin ligases that facilitate its ubiquitination, thereby marking the protein for cytosolic dislocation and proteasomal degradation. In contrast to reductase, Insig-1 is subjected to ERAD in lipid-deprived cells. Sterols block this ERAD by inhibiting Insig-1 ubiquitination, whereas unsaturated fatty acids block the reaction by preventing the protein''s cytosolic dislocation. In previous studies, we found that the membrane domain of mammalian reductase was subjected to ERAD in Drosophila S2 cells. This ERAD was appropriately accelerated by sterols and required the action of Insigs, which bridged reductase to a Drosophila ubiquitin ligase. We now report reconstitution of mammalian Insig-1 ERAD in S2 cells. The ERAD of Insig-1 in S2 cells mimics the reaction that occurs in mammalian cells with regard to its inhibition by either sterols or unsaturated fatty acids. Genetic and pharmacologic manipulations coupled with subcellular fractionation indicate that Insig-1 and reductase are degraded through distinct mechanisms that are mediated by different ubiquitin ligase complexes. Together, these results establish Drosophila S2 cells as a model system to elucidate mechanisms through which lipid constituents of cell membranes (i.e., sterols and fatty acids) modulate the ERAD of Insig-1 and reductase.