Three-dimensional structure of the ribonuclease T1 2'-GMP complex at 1.9-A resolution

The complex formed between the enzyme ribonuclease T1 (EC 3.1.27.3) and its specific inhibitor 2'-guanylic acid (2'-GMP) has been refined to R = 0.180 using x-ray diffraction data to 1.9-A resolution. The protein molecule displays a compact fold; a 4.5 turn alpha-helix packed over an antiparallel beta-pleated sheet shields most of the hydrophobic interior of the protein against the solvent. The extended pleated sheet structure of ribonuclease T1 is composed of three long and four short strands building up a two-stranded minor beta-sheet near the amino terminus and a five-stranded major sheet in the interior of the protein molecule. In the complex with ribonuclease T1, the inhibitor 2'-guanylic acid adopts the syn-conformation and C2'-endo sugar pucker. Binding of the nucleotide is mainly achieved through amino acid residues 38-46 of the protein. The catalytically active amino acid residues of ribonuclease T1 (His40, Glu58, Arg77, and His92) are located within the major beta-sheet which, as evident from the analysis of atomic temperature factors, provides an environment of minimal local mobility. The geometry of the active site is consistent with a mechanism for phosphodiester hydrolysis where, in the transesterification step, His40 and/or Glu58 act as a general base toward the ribose 2'-hydroxyl group and His92, as a general acid, donates a proton to the leaving 5'-hydroxyl group.     

Assessment of the potential germ cell mutagenicity of industrial and plant protection chemicals as part of an integrated study of genotoxicity in vitro and in vivo

An approach is described that enables the germ cell mutagenicity of chemicals to be assessed as part of an integrated assessment of genotoxic potential. It is recommended, first, that the genotoxicity of a chemical be defined by appropriate studies in vitro. This should involve use of the Salmonella mutation assay and an assay for the induction of chromosomal aberrations, but supplementary assays may be indicated in specific instances. If negative results are obtained from these 2 tests there is no need for the conduct of additional tests. Agents considered to be genotoxic in vitro should then be assessed for genotoxicity to rodents. This will usually involve the conduct of a bone marrow cytogenetic assay, and in the case of negative results, a genotoxicity test in an independent tissue. Agents found to be non-genotoxic in vivo are regarded as having no potential for germ cell mutagenicity. Agents found to be genotoxic in vivo may either be assumed to have potential as germ cell mutagens, or their status in this respect may be defined by appropriate germ cell mutagenicity studies. The basis of the approach, which is supported by the available experimental data, is that germ cell mutagens will be evident as somatic cell genotoxins in vivo, and that these will be detected as genotoxins in vitro given appropriate experimentation. The conduct of appropriate and adequate studies is suggested to be of more value than the conduct of a rigid set of prescribed tests.     

The emission of corrosive vapours by wood. Hot - water - extracted O - acetylated hemicelluloses from sweet chestnut (Castanea sativa) and wych elm (Ulmus glabrau) and a discussion of O-acetyl-group changes occurring in these woods during incubation at 48° and 100% relative humidity

1. O-Acetylated polysaccharides were obtained from green wood of both sweet chestnut and wych elm by treatment of the residue remaining after dimethyl sulphoxide extraction with water at 98 degrees . This gives a mixture of polysaccharides containing xylose, galactose, glucose and uronic acids. Analysis of these and their fractionated products suggest that only xylans in green sweet chestnut and green wych elm are O-acetylated. 2. The isolated O-acetylated xylans are not representative of the total O-acetylated xylans occurring in sweet chestnut and wych elm. 3. Application of the method developed by Bouveng for the location of O-acetyl groups to all four O-acetylated xylans obtained in this series of investigations by dimethyl sulphoxide extraction showed that those from sweet chestnut and wych elm, under the same conditions of incubation, lost: 74.2 and 43.4% of acetyl groups respectively, at C-2; 58.0 and 28.5% of acetyl groups respectively at C-3; 41.8 and 82.2% of acetyl groups respectively at C-2 and C-3. 4. A consideration of electronic and steric factors indicates that there does not appear to be a purely chemical reason for the difference in loss of O-acetyl groups between sweet chestnut and wych elm. It is suggested that the location of O-acetylated xylans in the wood cell walls and the presence of extractive may play some part in this difference.     

Responses of breeding duck populations to changes in food supply

We describe the main results of a monitoring study at Lake Myvatn, northern Iceland, begun in 1975. The aims were to find factors that limit production of young and cause changes in density of breeding ducks of several species. We estimated numbers of ducks in spring, before nesting, numbers of ducklings produced, and numbers moulting. Chironomid and simuliid dipterans were monitored with window traps. In all duck species studied, production of young was correlated with food abundance. Reproductive performance determined subsequent changes in spring population density of Eurasian Wigeon, Tufted Duck, Greater Scaup, Common Scoter and Harlequin Duck. The spring population of Barrow's Goldeneye apparently did not respond to variation in reproductive success. Moulting numbers of male Tufted Duck were related to chironomid abundance, but not those of Scaup and Barrow's Goldeneye. Moulting numbers were not associated with previous reproductive output.     

Long-term changes in benthic Cladocera populations in Lake Myvatn, Iceland

Benthic Cladocera were monitored at five sites in Lake Myvatn, Iceland, over a decade (1990–1999), as part of a programme documenting the population fluctuations of animals at different trophic levels in the lake. The species composition remained relatively stable over the first seven years, but in 1997 the population of Eurycercus lamellatus was greatly reduced at all sites. The following year saw a mass occurrence of Alona rectangula and Alonella nana that were previously abundant only locally and rare at most sites. Alona affinis, A. quadrangularis, Acroperus harpae and Chydorus sphaericus were not affected. In 1999 the Cladocera assemblages returned to the pre-1997 situation. The shift was from large-bodied epibenthic and planktonic species (Eurycercus, Daphnia) to small infaunal (Alona rectangula) and ubiquitous (Alonella nana) species. Medium sized (Alona, Acroperus) and some small cladocerans (Chydorus) were not affected. The course of events was reminiscent of a trophic cascade caused by a change in size-selective predation pressure. If so, the impact of a predatory fish population (three-spined stickleback, Gasterosteus aculeatus) depended on whether cyclic chironomid populations were in a high or a low phase. The change in the Cladocera coincided with profound changes in the sediment characteristics associated with low chironomid abundance. We suggest that the relative competitive ability of the Cladocera species is reversed when the sediment has become homogeneous and nutrient-poor after overexploitation by the dominant, tube building and detritivorous chironomid Tanytarsus gracilentus.     

Structural insights for fatty acid binding in a Lys49-phospholipase A2: crystal structure of myotoxin II from Bothrops moojeni complexed with stearic acid

The crystal structure of dimeric Lys49-phospholipase A2 myotoxin-II from Bothrops moojeni (MjTX-II) co-crystallized with stearic acid (C(18)H(36)O(2)) has been determined at a resolution of 1.8 A. The electron density maps permitted the unambiguous inclusion of six stearic acid molecules in the refinement. Two stearic acid molecules could be located in the substrate-binding cleft of each monomer in positions, which favor the interaction of their carboxyl groups with active site residues. The way of binding of stearic acids to this Lys49-PLA(2)s is analogous to phospholipids and transition state analogues to catalytically active PLA(2)s. Two additional stearic acid molecules were located at the dimer interface region, defining a hitherto unidentified acyl-binding site on the protein surface. The strictly conserved Lys122 for Lys49-PLA(2)s may play a fundamental role for stabilization of legend-protein complex. The comparison of MjTX-II/satiric acid complex with other Lys-PLA(2)s structures whose putative fatty acids were located at their active site is also analysed. Molecular details of the stearic acid/protein interactions provide insights to binding in group I/II PLA(2)s, and to the possible interactions of Lys49-PLA(2)s with target membranes.     

Simplified modeling of fed-batch alcoholic fermentation of sugarcane blackstrap molasses

Simplified modeling based on material balances for biomass, ethanol and substrate was used to describe the kinetics of fed-batch alcohol fermentation of sugarcane blackstrap molasses. Maintenance requirements were previously shown to be of particular significance in this system, owing to the use of massive inoculum to minimize inhibitions; therefore, they were taken into consideration for kinetic modeling. Average values of biomass and ethanol yields, productivities, and substrate consumption rates, calculated at the end of runs performed either at constant or exponentially varying flow rates, demonstrated that all of these parameters were influenced by the initial sugar-feeding rate, F(o)S(o). Under conditions of substrate shortage (F(o)S(o) 相似文献   

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7A resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved beta-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA.     

Crystallization and preliminary X-ray diffraction analysis of suramin, a highly charged polysulfonated napthylurea, complexed with a myotoxic PLA2 from Bothrops asper venom

Suramin is a highly charged polysulfonated napthylurea that interferes in a number of physiologically relevant processes such as myotoxicity, blood coagulation and several kinds of cancers. This synthetic compound was complexed with a myotoxic Lys49 PLA(2) from Bothrops asper venom and crystallized by the hanging-drop vapor diffusion method at 18 degrees C. The crystals belong to the orthorhombic space group P2(1)2(1)2(1), with unit cell parameters a=49.05, b=63.84 and c=85.67 angstroms. Diffraction data was collected to 1.78 angstroms.     

Structure of tick anticoagulant peptide at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at 1.6 A resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 A, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 A. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (Cys5T-Cys15T) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 A to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 A with the guanidinium group forming a cation-pi-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 A in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N-terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.