A "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain: structural basis and relevance to the XLP syndrome

The SH2 domain protein SAP/SH2D1A, encoded by the X-linked lymphoproliferative (XLP) syndrome gene, associates with the hematopoietic cell surface receptor SLAM in a phosphorylation-independent manner. By screening a repertoire of synthetic peptides, the specificity of SAP/SH2D1A has been mapped and a consensus sequence motif for binding identified, T/S-x-x-x-x-V/I, where x represents any amino acid. Remarkably, this motif contains neither a Tyr nor a pTyr residue, a hallmark of conventional SH2 domain-ligand interactions. The structures of the protein, determined by NMR, in complex with two distinct peptides provide direct evidence in support of a "three-pronged" binding mechanism for the SAP/SH2D1A SH2 domain in contrast to the "two-pronged" binding for conventional SH2 domains. Differences in the structures of the two complexes suggest considerable flexibility in the SH2 domain, as further confirmed and characterized by hydrogen exchange studies. The structures also explain binding defects observed in disease-causing SAP/SH2D1A mutants and suggest that phosphorylation-independent interactions mediated by SAP/SH2D1A likely play an important role in the pathogenesis of XLP.     

Sequence reversed peptide from CaMKK binds to calmodulin in reversible Ca2+ -dependent manner

Calmodulin (CaM) is a highly versatile Ca(2+) signaling transducer known to regulate over a hundred proteins. In this paper, we further demonstrate the versatility of CaM binding by showing that it binds to a synthetic peptide (revCKKp) made by reversing the amino acid sequence of the CaM-binding peptide (CKKp) from CaM-dependent protein kinase kinase (CaMKK) (residues 438-463). Sequence comparison between revCKKp and other CaM-binding peptides (CBPs) from the CaM target databank showed that revCKKp does not resemble any existing classes of CBPs, except CKKp [M. Zhang, T. Yuan, Molecular mechanisms of calmodulin's functional versatility, Biochem. Cell Biol. 76 (1998) 313-323; S.W. Vetter, E. Leclerc, Novel aspects of calmodulin target recognition and activation, Eur. J. Biochem. 270 (2003) 404-414]. Furthermore, computational modeling showed that revCKKp could bind CaM in a similar manner to CKKp. Lastly, we experimentally showed that our synthetic revCKKp binds to CaM in a reversible Ca(2+)-dependent manner.     

NMR dynamics-derived insights into the binding properties of a peptide interacting with an SH2 domain

The signal transduction protein phospholipase C-gamma1 (PLC-gamma1) is activated when its C-terminal SH2 domain (PLCC) binds the phosphorylated Tyr-1021 site (pTyr-1021) in the beta-platelet-derived growth factor receptor (PDGFR). To better understand the contributions that dynamics make to binding, we have used NMR relaxation experiments to investigate the motional properties of backbone amide and side chain methyl groups in a peptide derived from the pTyr-1021 site of PDGFR, both free and in complex with the PLCC SH2 domain. The free peptide has relaxation properties that are typical for a small, unstructured polymer, while the backbone of the bound peptide is least flexible for residues in the central portion of the binding site with the amplitude of pico- to nanosecond time scale motions increasing toward the C-terminus of the peptide. The increase in large amplitude motion toward the end of the pY1021 peptide is consistent with the bound peptide existing as an ensemble of states with C-terminal residues having the broadest distribution of backbone conformations, while residues in the central binding site are the most restricted. Deuterium spin relaxation experiments establish that the protein-peptide interface is highly dynamic, and this mobility may play an important role in modulating the affinity of the interaction.     

Removal of the N-linked glycan structure from the peanut peroxidase prxPNC2: influence on protein stability and activity

Lines of transgenic tobacco have been generated that are transformed with either the wild-type peanut peroxidase prxPNC2 cDNA, driven by the CaMV35S promoter (designated 35S::prxPNC2-WT) or a mutated PNC2 cDNA in which the asparagine residue (Asn189) associated with the point of glycan attachment (Asn189) has been replaced with alanine (designated 35S::prxPNC2-M). PCR, using genomic DNA as template, has confirmed the integration of the 35S::prxPNC2-WT and 35S:prxPNC2-M constructs into the tobacco genome, and western analysis using anti-PNC2 antibodies has revealed that the prxPNC2-WT protein product (PNC2-WT) accumulates with a molecular mass of 34,670 Da, while the prxPNC2-M protein product (PNC2-M) accumulates with a molecular mass of 32,600 Da. Activity assays have shown that both PNC2-WT and PNC2-M proteins accumulate preferentially in the ionically-bound cell wall fraction, with a significantly higher relative accumulation of the PNC2-WT isoenzyme in the ionically-bound fraction when compared with the PNC2-M isoform. Kinetic analysis of the partially purified PNC2-WT isozyme revealed an affinity constant (apparent Km) of 11.2 mM for the reductor substrate guaiacol and 1.29 mM for H2O2, while values of 11.9 mM and 1.12 mM were determined for the PNC2-M isozyme. A higher Arrenhius activation energy (Ea) was determined for the PNC2-M isozyme (22.9 kJ mol(-1)), when compared with the PNC2-WT isozyme (17.6 kJ mol(-1)), and enzyme assays have determined that the absence of the glycan influences the thermostability of the PNC2-M isozyme. These results are discussed with respect to the proposed roles of N-linked glycans attached to plant peroxidases.     

Revision of Dolabraulax Quicke (Hymenoptera: Braconidae) with the description of three new species from south India

The braconine genus, Dolabraulax Quicke is reported for the first time from the Indian sub-continent and three new species, namely D. aruni Ranjith sp. nov., D. athirae Ranjith sp. nov. and D. jalalae Ranjith sp. nov. are described and illustrated. A key to all species of Dolabraulax is provided and its generic diagnosis is revised.     

Changes in the accumulation of alkenones and lipids under nitrogen limitation and its relation to other energy storage metabolites in the haptophyte alga <Emphasis Type="Italic">Emiliania huxleyi</Emphasis> CCMP 2090

Alkenones are long-chain methyl/ethyl ketones (mainly in length of C₃₇-C₃₉) with two to four trans-unsaturated bonds produced by several kinds of marine haptophytes such as Emiliania huxleyi (coccolithophore). The physiological functions and metabolic profile of alkenones are not well known yet. In this study, we focused on elucidating how alkenones contribute to energy storage and cellular carbon partitioning in relation to other cellular components. For the purpose, we analyzed the changes in carbon allocation among various cell components like lipids, alkenones, proteins, and polysaccharides between cells exposed to N-sufficient (+N) and N-limited conditions (?N) in E. huxleyi CCMP 2090. Finally, the alkenones were found to function as main storage lipids and their accumulation was clearly increased by ?N, whereas triacylglycerols (TAGs) were barely detected under any N conditions. The mobilization of carbons into alkenones was stimulated by ?N from 15% under +N to 27% under ?N. However, photosynthetic C allocation into other components was suppressed by ?N, showing that percent C allocation into fatty acids, proteins, and polysaccharides was decreased from 9, 46, and 6.8% under +N to 7, 25, and 4.5% under ?N, respectively. In addition, fatty acids such as 16:0, 18:0, 18:1, and 18:2 became dominant under ?N while 18:5 became dominant under +N conditions, with no significant change in 22:6. This study revealed that alkenones function as primary carbon storage pools especially under ?N condition in E. huxleyi CCMP 2090 and that N supply triggers a dynamic change in carbon metabolism by modifying membrane lipid composition and regulating carbon allocation preferences.     

Going Beyond Lithium Hybrid Capacitors: Proposing a New High‐Performing Sodium Hybrid Capacitor System for Next‐Generation Hybrid Vehicles Made with Bio‐Inspired Activated Carbon

A novel sodium hybrid capacitor (NHC) is constructed with an intercalation‐type sodium material [carbon coated‐Na₃V₂(PO₄)₃, C‐NVP] and high surface area‐activated carbon derived from an eco‐friendly resource cinnamon sticks (CDCs) in an organic electrolyte. This novel NHC possesses a combination of high energy and high power density, along with remarkable electrochemical stability. In addition, the C‐NVP/CDC system outperforms present, well‐established lithium hybrid capacitor systems in all areas, and can thus be added to the list of candidates for future electric vehicles. A careful optimization of mass balance between electrode materials enables the C‐NVP/CDC cell to exhibit extraordinary capacitance performance. This novel NHC produces an energy density of 118 Wh kg^?1 at a specific power of 95 W kg^?1 and retains an energy density of 60 Wh kg^?1 with high specific power of 850 W kg^?1. Furthermore, a discharge capacitance of 53 F g^?1 is obtained from the C‐NVP/CDC cell at a 1 mA cm^?2 current density, along with 95% capacitance retention, even after 10 000 cycles. The sluggish kinetics of the Na ion battery system is successfully overcome by developing a stable, high‐performing NHC system.     

Rubrivivaxin,a new cytotoxic and cyclooxygenase-I inhibitory metabolite from <Emphasis Type="Italic">Rubrivivax benzoatilyticus</Emphasis> JA2

A new phenol terpenoid ester metabolite was isolated from the culture supernatant of Rubrivivax benzoatilyticus JA2 when the organism grown on L-phenylalanine as sole source of nitrogen under photoheterotrophic condition. The compound was characterized by HPLC, LCMS, IR, NMR (¹H, ¹³C) and Mass spectrometry, as a 3, 4-dihydroxybenzoyl-terpenoid ester [IUPAC: 3, 4-dihydroxy, 5-carboxy, 3-methylpentyl ester], which has a molecular mass (m/z) of 298 and we designated as rubrivivaxin. The significance of cyclooxygenase-I (COX-I) inhibitory, antimicrobial, cytotoxic activities against U937 (Human leukemic monocyte lymphoma) and Jurkat (T lymphocyte) cell lines conferred by rubrivivaxin.     

Calnexin Improves the Folding Efficiency of Mutant Rhodopsin in the Presence of Pharmacological Chaperone 11-cis-Retinal

The lectin chaperone calnexin (Cnx) is important for quality control of glycoproteins, and the chances of correct folding of a protein increase the longer the protein interacts with Cnx. Mutations in glycoproteins increase their association with Cnx, and these mutant proteins are retained in the endoplasmic reticulum. However, until now, the increased interaction with Cnx was not known to increase the folding of mutant glycoproteins. Because many human diseases result from glycoprotein misfolding, a Cnx-assisted folding of mutant glycoproteins could be beneficial. Mutations of rhodopsin, the glycoprotein pigment of rod photoreceptors, cause misfolding resulting in retinitis pigmentosa. Despite the critical role of Cnx in glycoprotein folding, surprisingly little is known about its interaction with rhodopsin or whether this interaction could be modulated to increase the folding of mutant rhodopsin. Here, we demonstrate that Cnx preferentially associates with misfolded mutant opsins associated with retinitis pigmentosa. Furthermore, the overexpression of Cnx leads to an increased accumulation of misfolded P23H opsin but not the correctly folded protein. Finally, we demonstrate that increased levels of Cnx in the presence of the pharmacological chaperone 11-cis-retinal increase the folding efficiency and result in an increase in correct folding of mutant rhodopsin. These results demonstrate that misfolded rather than correctly folded rhodopsin is a substrate for Cnx and that the interaction between Cnx and mutant, misfolded rhodopsin, can be targeted to increase the yield of folded mutant protein.