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2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten 总被引:5,自引:0,他引:5
The crystal structure of the Fab fragment of the murine monoclonal anti-dinitrophenyl-spin-label antibody AN02 complexed with its hapten has been solved at 2.9 A resolution using a novel molecular replacement method. Prior to translation searches, a large number of the most likely rotation function solutions were subjected to a rigid body refinement against the linear correlation coefficient between intensities of observed and calculated structure factors. First, the overall orientation of the search model and then the orientations and positions of the four Fab domains (VH, VL, CH1 and CL) were refined. This procedure clearly identified the correct orientation of the search model. The refined search model was then subjected to translation searches which unambiguously determined the enantiomer and position in the unit cell of the crystal. The successful search model was refined 2.5 A crystal structure of the Fab fragment of HyHel-5 from which non-matching residues in the variable domains had been removed. HyHel-5 is a murine monoclonal antibody whose heavy and light chains are of the same subclass (gamma 1, kappa, respectively) as AN02. After molecular replacement the structure of the AN02 Fab has been refined using simulated annealing in combination with model building and conjugate gradient refinement to a current crystallographic R-factor of 19.5% for 12,129 unique reflections between 8.0 and 2.9 A. The root-mean-square (r.m.s.) deviation from ideal bond lengths is 0.014 A, and the r.m.s. deviation from ideal bond angles is 3.1 degrees. The electron density reveals the hapten sitting in a pocket formed by the loops of the complementarity determining region. The dinitrophenyl ring of the hapten is sandwiched between the indole rings of Trp96 of the heavy-chain and Trp91 of the light-chain. The positioning of the hapten and general features of the combining site are in good agreement with the results of earlier nuclear magnetic resonance experiments. 相似文献
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Yosef Manik Jessica Leahy Anthony Halog 《The International Journal of Life Cycle Assessment》2013,18(7):1386-1392
Purpose
This study aims to investigate the social implications of palm oil biodiesel via a case study using a life cycle assessment framework.Methods
The case study was conducted in Jambi Province of Indonesia and involved several stakeholders, such as value chain actors, employees, local community members, government, and nongovernmental organization representatives related in palm oil industry. The assessment was carried out using social criteria developed by adopting the Society of Environmental Toxicology and Chemistry/United Nations Environment Programme Code of Practice, supplemented by an expert survey, and supported by literature review. Stakeholders’ perspectives were evaluated by determining the gaps between expected and perceived quality of each social criterion, which are gauged using seven-point Likert scale.Results and discussion
Twenty-four social criteria were developed and aggregated into five social impact categories: human rights, working condition, cultural heritage, social–economic repercussion, and governance. These criteria have been weighted, useful for further application in multicriteria decision analysis. The results of the stakeholders’ survey reveal the critical social hotspots, which are the issues within the impact categories of working conditions and cultural heritage.Conclusions
In order to achieve the social equitability of palm oil biodiesel, which is an important pillar to sustainability, efforts must be put to address these social hotspots through actions in various policy level. 相似文献5.
The genes encoding the lipase (LipA) and lipase chaperone (LipB) from Acinetobacter calcoaceticus RAG-1 were cloned and sequenced. The genes were isolated from a genomic DNA library by complementation of a lipase-deficient transposon mutant of the same strain. Transposon insertion in this mutant and three others was mapped to a single site in the chaperone gene. The deduced amino acid (aa) sequences for the lipase and its chaperone were found to encode mature proteins of 313 aa (32.5kDa) and 347 aa (38.6kDa), respectively. The lipase contained a putative leader sequence, as well as the conserved Ser, His, and Asp residues which are known to function as the catalytic triad in other lipases. A possible trans-membrane hydrophobic helix was identified in the N-terminal region of the chaperone. Phylogenetic comparisons showed that LipA, together with the lipases of A. calcoaceticus BD413, Vibrio cholerae El Tor, and Proteus vulgaris K80, were members of a previously described family of Pseudomonas and Burkholderia lipases. This new family, which we redefine as the Group I Proteobacterial lipases, was subdivided into four subfamilies on the basis of overall sequence homology and conservation of residues which are unique to the subfamilies. LipB, moreover, was found to be a member of an analogous family of lipase chaperones. We propose that the lipases produced by P. fluorescens and Serratia marcescens, which comprise a second sequence family, be referred to as the Group II Proteobacterial lipases. Evidence is provided to support the hypothesis that both the Group I and Group II families have evolved from a combination of common descent and lateral gene transfer. 相似文献
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Amy?Y.?RossmanEmail author M.?Cathie Aime David?F.?Farr Lisa?A.?Castlebury Kristin?R.?Peterson Robert?Leahy 《Mycological Progress》2004,3(4):275-290
The coelomycetous genera Chaetomella and Pilidium were determined to be closely related to each other, yet are recognized as distinct genera based on both morphological observations
and rDNA sequence analyses. Analyses of the SSU and LSU of the nuclear ribosomal RNA genes suggest that Chaetomella and Pilidium along with Sphaerographium tenuirostrum and Synchaetomella lunatospora constitute a distinct lineage within the ascomycetes that is allied with the Leotiomycetes. Chaetomella and Pilidium both produce black pycnidia generally opening by a raphe, acropleurogenous conidiogenous cells, and non-septate, hyaline,
usually fusiform to falcate, rarely ellipsoid, conidia. Pycnidia of Pilidium are smooth while those of Chaetomella have setae of various types. A Hainesia sporodochial synanamorph was observed in cultures of C. oblonga and C. raphigera similar to H. lythri, the synanamorph of P. concavum. Specimens of C. oblonga, type species of Chaetomella, C. acutiseta, C. circinoseta, C. raphigera, Pilidium acerinum, type species of Pilidium, and P. concavum were examined. Diagnoses and illustrations are provided for these species along with a key to the accepted species in both
genera.
Mention of trade names or commercial products in this article is solely for the purpose of providing specific information
and does not imply recommendation or endorsement by the U.S. Department of Agriculture. 相似文献
8.
Leahy M Vaughan P Fanning L Fanning S Sheehan D 《Enzyme and microbial technology》2001,28(7-8):682-688
A recombinant Rhizobium meliloti beta-galactosidase was purified to homogeneity from an Escherichia coli expression system. The gene for the enzyme was cloned into a pKK223-3 plasmid which was then used to transform E. coli JM109 cells. The enzyme was purified 35-fold with a yield of 34% by a combination of DEAE-cellulose (pH 8.0) and two sequential Mono Q steps (at pH 8.0 and 6.0, respectively). The purified enzyme had an apparent molecular mass of 174 kDa and a subunit molecular weight of 88 kDa, indicating that it is a dimer. It was active with both synthetic substrates p-nitrophenyl beta-D-galactopyranoside (PNPG) and o-nitrophenyl beta-D-galactopyranoside (ONPG) with K(m)(PNPG) and K(m)(ONPG) of 1 mM at 25 degrees C. The k(cat)/K(m) ratios for both substrates were approximately 70 mM(-1) sec(-1), indicating no clear preference for either PNPG or ONPG, unlike E. coli beta-galactosidase. After non-denaturing electrophoresis, active beta-galactosidase bands were identified using 5-bromo-4-chloro-3-indolyl beta-D-galactopyranoside (X-gal) or 6-bromo-2-naphthyl beta-D-galactopyranoside (BNG) and diazo blue B. 相似文献
9.
Liu YQ Nevin PW Leahy JL 《American journal of physiology. Endocrinology and metabolism》2000,279(1):E68-E73
Islet beta-cells are the regulatory element of the glucose homeostasis system. When functioning normally, they precisely counterbalance changes in insulin sensitivity or beta-cell mass to preserve normoglycemia. This understanding seems counter to the dogma that beta-cells are regulated by glycemia. We studied 60% pancreatectomy rats (Px) 4 wk postsurgery to elucidate the beta-cell adaptive mechanisms. Nonfasting glycemia and insulinemia were identical in Px and sham-operated controls. There was partial regeneration of the excised beta-cells in the Px rats, but it was limited in scope, with the pancreas beta-cell mass reaching 55% of the shams (40% increase from the time of surgery). More consequential was a heightened glucose responsiveness of Px islets so that glucose utilization and insulin secretion per milligram of islet protein were both 80% augmented at normal levels of glycemia. Investigation of the biochemical basis showed a doubled glucokinase maximal velocity in Px islets, with no change in the glucokinase protein concentration after adjustment for the different beta-cell mass in Px and sham islets. Hexokinase activity measured in islet extracts was also minimally increased, but the glucose 6-phosphate concentration and basal glucose usage of Px islets were not different from those in islets from sham-operated rats. The dominant beta-cell adaptive response in the 60% Px rats was an increased catalytic activity of glucokinase. The remaining beta-cells thus sense, and respond to, perceived hyperglycemia despite glycemia actually being normal. beta-Cell mass and insulin secretion are both augmented so that whole pancreas insulin output, and consequently glycemia, are maintained at normal levels. 相似文献
10.
Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition 总被引:3,自引:0,他引:3
Homer EVH1 (Ena/VASP Homology 1) domains interact with proline-rich motifs in the cytoplasmic regions of group 1 metabotropic glutamate receptors (mGluRs), inositol-1,4,5-trisphosphate receptors (IP3Rs), and Shank proteins. We have determined the crystal structure of the Homer EVH1 domain complexed with a peptide from mGluR (TPPSPF). In contrast to other EVH1 domains, the bound mGluR ligand assumes an unusual conformation in which the side chains of the Ser-Pro tandem are oriented away from the Homer surface, and the Phe forms a unique contact. This unusual binding mode rationalizes conserved features of both Homer and Homer ligands that are not shared by other EVH1 domains. Site-directed mutagenesis confirms the importance of specific Homer residues for ligand binding. These results establish a molecular basis for understanding the biological properties of Homer-ligand complexes. 相似文献