Identification of critical residues in loop E in the 5-HT3ASR binding site

Background  

The serotonin type 3 receptor (5-HT₃R) is a member of a superfamily of ligand gated ion channels. All members of this family share a large degree of sequence homology and presumably significant structural similarity. A large number of studies have explored the structure-function relationships of members of this family, particularly the nicotinic and GABA receptors. This information can be utilized to gain additional insights into specific structural and functional features of other receptors in this family.     

A novel method for screening the glutathione transferase inhibitors

Background  

Glutathione transferases (GSTs) belong to the family of Phase II detoxification enzymes. GSTs catalyze the conjugation of glutathione to different endogenous and exogenous electrophilic compounds. Over-expression of GSTs was demonstrated in a number of different human cancer cells. It has been found that the resistance to many anticancer chemotherapeutics is directly correlated with the over-expression of GSTs. Therefore, it appears to be important to find new GST inhibitors to prevent the resistance of cells to anticancer drugs. In order to search for glutathione transferase (GST) inhibitors, a novel method was designed.     

Anti-cancer activity of novel dibenzo[b,f]azepine tethered isoxazoline derivatives

Background  

Nef is an HIV-1 accessory protein essential for viral replication and AIDS progression. Nef interacts with a multitude of host cell signaling partners, including members of the Src kinase family. Nef preferentially activates Hck, a Src-family kinase (SFK) strongly expressed in macrophages and other HIV target cells, by binding to its regulatory SH3 domain. Recently, we identified a series of kinase inhibitors that preferentially inhibit Hck in the presence of Nef. These compounds also block Nef-dependent HIV replication, validating the Nef-SFK signaling pathway as an antiretroviral drug target. Our findings also suggested that by binding to the Hck SH3 domain, Nef indirectly affects the conformation of the kinase active site to favor inhibitor association.     

Aquaporin-11: A channel protein lacking apparent transport function expressed in brain

Background  

The aquaporins are a family of integral membrane proteins composed of two subfamilies: the orthodox aquaporins, which transport only water, and the aquaglyceroporins, which transport glycerol, urea, or other small solutes. Two recently described aquaporins, numbers 11 and 12, appear to be more distantly related to the other mammalian aquaporins and aquaglyceroporins.     

Archazolid and apicularen: Novel specific V-ATPase inhibitors

Background  

V-ATPases constitute a ubiquitous family of heteromultimeric, proton translocating proteins. According to their localization in a multitude of eukaryotic membranes, they energize many different transport processes. Since their malfunction is correlated with various diseases in humans, the elucidation of the properties of this enzyme for the development of selective inhibitors and drugs is one of the challenges in V-ATPase research.     

Where are genes in paulingite? Mathematical principles of formation of inorganic materials on the atomic level

By means of the concept of universal optimum and general principles of inorganic gene, structures of paulingite-related zeolites and minerals have been constructed. The structures of zeolite Rho and paulingite are considered as members of zeolite family generated by the work of 4-colored cellular automaton (CA). The ideal symmetry of the members of the family is cubic, space group $Im \bar 3mBy means of the concept of universal optimum and general principles of inorganic gene, structures of paulingite-related zeolites and minerals have been constructed. The structures of zeolite Rho and paulingite are considered as members of zeolite family generated by the work of 4-colored cellular automaton (CA). The ideal symmetry of the members of the family is cubic, space group , a = 15 + 10n [?], where n is a number of the CA cycle (n = 0 for zeolite Rho and 2 for paulingite). A new hypothetical zeolite of the family with n = 1 is predicted and named ISC-1 (Institute of Silicate Chemistry-1); atomic coordinates and theoretical X-ray powder diffraction pattern have been calculated. It appears to be very probable that universal optimum contains all necessary information for its material realization (sharp configurations) and construction of materials with certain type of interaction potential (even with restrictions existing in theory for this potential).

V. Ya. ShevchenkoEmail:

     

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

Background

The inorganic (P_i) phosphate transporter (PiT) family comprises known and putative Na⁺- or H⁺-dependent P_i-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with P_i to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na⁺-dependent P_i (NaP_i) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins.

Results

We show that the human PiT2 histidine, H₅₀₂, and the human PiT1 glutamate, E₇₀, - both conserved in eukaryotic PiT family members - are critical for P_i transport function. Noticeably, human PiT2 H₅₀₂ is located in the C-terminal PiT family signature sequence, and human PiT1 E₇₀ is located in ProDom domains characteristic for all PiT family members. A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR₂₅₄-V₄₈₃), was found to be a fully functional P_i transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL₁₈₃-V₄₈₃) did also support P_i transport albeit at very low levels.

Conclusions

The results suggest that the overall structure of the P_i-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship.     

High affinity binding of hydrophobic and autoantigenic regions of proinsulin to the 70 kDa chaperone DnaK

Background  

Chaperones facilitate proper folding of peptides and bind to misfolded proteins as occurring during periods of cell stress. Complexes of peptides with chaperones induce peptide-directed immunity. Here we analyzed the interaction of (pre)proinsulin with the best characterized chaperone of the hsp70 family, bacterial DnaK.     

Development of a sensitive non-radioactive protein kinase assay and its application for detecting DYRK activity in <Emphasis Type="Italic">Xenopus laevis</Emphasis> oocytes

Background  

Although numerous non-radioactive methods are in use to measure the catalytic activity of protein kinases, most require specialized equipment and reagents and are not sufficiently sensitive for the detection of endogenous kinase activity in biological samples. Kinases of the DYRK family have important functions in developmental and pathophysiological processes in eukaryotic organisms including mammals. We aimed to develop a highly sensitive, low-tech assay suitable to determine the activity of DYRK family kinases in tissues or cells from diverse sources.     

Identification and characterization of a bacterial glutamic peptidase

Background  

Glutamic peptidases, from the MEROPS family G1, are a distinct group of peptidases characterized by a catalytic dyad consisting of a glutamate and a glutamine residue, optimal activity at acidic pH and insensitivity towards the microbial derived protease inhibitor, pepstatin. Previously, only glutamic peptidases derived from filamentous fungi have been characterized.     

Functional redundancy between <Emphasis Type="Italic">trans</Emphasis>-Golgi network SNARE family members in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Background

Vesicle fusion is an essential process for maintaining the structure and function of the endomembrane system. Fusion is mediated by t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) fusion proteins on the target membrane and v-SNAREs on the vesicle membrane; v-and t-SNAREs interact with each other, driving vesicle fusion with the target membrane. The Arabidopsis thaliana trans-Golgi network resident SNAREs SYP41 and VTI12, along with YKT61/62, have been shown to function in vesicle fusion in vitro, consistent with immunoprecipitation results showing their interaction in Arabidopsis cell extracts. Conflicting published results have indicated that SYP4 family members are either functionally redundant or have distinct and essential functions; the reason for this discrepancy is unclear.

Results

Here we used a proteoliposome fusion assay to demonstrate that SYP42 and SYP43 can substitute for SYP41 in driving lipid mixing, providing support for functional overlap between family members. Previous reports have also suggested that VTI11 and VTI12 SNAREs show partial overlap in function, despite having mostly distinct localizations and binding partners. We show that VTI11 can substitute for VTI12 in in vitro lipid mixing reactions, providing molecular support for the genetic evidence for partial functional redundancy in vivo.

Conclusions

Our data provide biochemical evidence for functional overlap in membrane fusion between members of the SYP4 or VTI1 SNARE groups, supporting previous genetic data suggesting redundancy.

     

A biocatalytic approach for regioselective monoacetylation of 3-aryloxy-1,2-propanediols by porcine pancreatic lipase

Abstract  

Among the various lipases screened for the regioselective monoacetylation of 3-aryloxy-1,2-propanediols, porcine pancreatic lipase was found to afford a higher yield. The selectivity for the monoacetylation process was maximized by using different organic solvents and diisopropyl ether gave the highest conversion to monoacetylated product (ca. 98%). The optimized reaction afforded excellent yields of the monoacetylated product with regioselectivity at the terminal hydroxyl group in the presence of various aryl substituents in the starting material.     

Components of the ubiquitin-proteasome pathway compete for surfaces on Rad23 family proteins

Background  

The delivery of ubiquitinated proteins to the proteasome for degradation is a key step in the regulation of the ubiquitin-proteasome pathway, yet the mechanisms underlying this step are not understood in detail. The Rad23 family of proteins is known to bind ubiquitinated proteins through its two ubiquitin-associated (UBA) domains, and may participate in the delivery of ubiquitinated proteins to the proteasome through docking via the Rad23 ubiquitin-like (UBL) domain.     

Comparison of the receptor FGFRL1 from sea urchins and humans illustrates evolution of a zinc binding motif in the intracellular domain

Background  

FGFRL1, the gene for the fifth member of the fibroblast growth factor receptor (FGFR) family, is found in all vertebrates from fish to man and in the cephalochordate amphioxus. Since it does not occur in more distantly related invertebrates such as insects and nematodes, we have speculated that FGFRL1 might have evolved just before branching of the vertebrate lineage from the other invertebrates (Beyeler and Trueb, 2006).     

A computational study of oxygen-termination of a (6,0) boron nitride nanotube

Abstract  

We performed density functional theory (DFT) calculations to investigate the properties of electronic structures of representative armchair and zigzag silicon carbide nanotubes (SiCNTs). The model structures were optimized and the NMR parameters were calculated at the sites of silicon-29 and carbon-13 atoms in these structures. Our results indicated that different electronic environments could be detected by using the atoms of nanotubes in which the atoms of tips, especially for zigzag SiCNT, exhibit distinctive properties among other atoms.     

The acidic domains of the Toc159 chloroplast preprotein receptor family are intrinsically disordered protein domains

Background  

The Toc159 family of proteins serve as receptors for chloroplast-destined preproteins. They directly bind to transit peptides, and exhibit preprotein substrate selectivity conferred by an unknown mechanism. The Toc159 receptors each include three domains: C-terminal membrane, central GTPase, and N-terminal acidic (A-) domains. Although the function(s) of the A-domain remains largely unknown, the amino acid sequences are most variable within these domains, suggesting they may contribute to the functional specificity of the receptors.     

A synthesis of diethyl alkylsulfanylmethylmalonates catalyzed by KOH in an ionic liquid

Abstract  

1-Ethyl-3-methylimidazolium bromide was used as a green recyclable alternative to volatile organic solvents for KOH catalyzed three-component synthesis of diethyl alkylsulfanylmethylmalonates from aldehydes, diethyl malonate, and alkylthiols.     

Derivatives of 5-nitro-1H-benzo[de]isoquinoline-1,3(2H)-dione: design, synthesis, and biological activity

Abstract  

A series of mono and bis-2-(2-(dimethylamino)-ethyl)-5-nitro-1H-benzo[de]isoquinoline-1,3(2H)-diones with different amino side chains, a novel family of antitumor agents, has been designed and synthesized. Their antitumor activity was evaluated against HeLa, A549, P388, HL-60, MCF-7, HCT-8, and A375 cancer cell lines in vitro. Preliminary results showed that most of the derivatives had antitumor activity comparable with that of mitonafide, with IC ₅₀ values of 10⁻⁶–10⁻⁵ M. More importantly, the derivatives had distinct antitumor selectivity against different cancer cell lines. This work provided a novel class of mitonafide-based lead compounds with improved antitumor selectivity against cancer cell lines for further optimization.