Practical applications of time-averaged restrained molecular dynamics to ligand-receptor systems: FK506 bound to the Q50R,A95H,K98I triple mutant of FKBP-13

Summary The ability of time-averaged restrained molecular dynamics (TARMD) to escape local low-energy conformations and explore conformational space is compared with conventional simulated-annealing methods. Practical suggestions are offered for performing TARMD calculations with ligand-receptor systems, and are illustrated for the complex of the immunosuppressant FK506 bound to Q50R,A95H,K98I triple mutant FKBP-13. The structure of ¹³C-labeled FK506 bound to triple-mutant FKBP-13 was determined using a set of 87 NOE distance restraints derived from HSQC-NOESY experiments. TARMD was found to be superior to conventional simulated-annealing methods, and produced structures that were conformationally similar to FK506 bound to wild-type FKBP-12. The individual and combined effects of varying the NOE restraint force constant, using an explicit model for the protein binding pocket, and starting the calculations from different ligand conformations were explored in detail.Abbreviations DG distance geometry - dmFKBP-12 double-mutant (R42K,H87V) FKBP-12 - FKBP-12 FK506-binding protein (12 kDa) - FKBP-13 FK506-binding protein (13 kDa) - HSQC heteronuclear single-quantum coherence - K_NOE force constant (penalty) for NOE-derived distance restraints - MD molecular dynamics - NOE nuclear Overhauser effect - SA simulated annealing - TARMD molecular dynamics with time-averaged restraints - tmFKBP-13 triple-mutant (Q50R,A95H,K98I) FKBP-13 - wtFKBP-12 wild-type FKBP-12     

Evaluation of coupling conditions for the incorporation of Nα-Fmoc-Tyr(PO3H2)-OH in solid-phase peptide synthesis

Summary In order to minimise the formation of the pyrophosphate derivative of the target peptide when side-chain-unprotected phopshotyrosine is used in solid-phase peptide synthesis, this building block can be incorporated using benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate/1-hydroxybenzotriazole/N-methylmorpholine (1:1:2.3) in the presence of a chaotropic salt (0.4 M LiCl in N-methyl-2-pyrrolidinone).Abbreviations BOP benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate - DIEA diisopropylethylamine - Fmoc 9-fluorenylmethoxycarbony - HATU N-[(dimethylamino)1H-1,2,3-triazolo[4,5-b]pyridin-1-ylmethylene]-N-methylmethan-aminium hexafluorophosphate N-oxide - HOBt 1-hydroxybenzotriazole - HPLC high-performance liquid chromatography - MALDI-TOF matrix-assisted laser-desorption ionization time-of-flight mass spectrometry - NMM N-methylmorpholine - NMP N-methyl-2-pyrrolidinone - Pmc 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl - ® solid support - TFA trifluoroacetic acid - TPTU 2-(2-pyridon-1-yl)-1,1,3,3-tetramethyluroniumfluoroborate. Abbreviations used for amino acids follow the recommendations of the IUPAC-IUB Commission of Biochemical Nomenclature [Eur. J. Biochem., 138 (1984) 9]     

A new mite-plant association: mites living amidst the adhesive traps of a carnivorous plant

Non-antagonistic interactions between arthropods and leaves of insectivorous plants with adhesive traps so far have never been reported. The mites are common prey of such plants, but we have found a new subspecies of the mite Oribatula tibialis living on the leaves of Pinguicula longifolia. Because of its small size and the low glandular density of the host, the mite moves without being trapped by the mucilaginous droplets of the leaf surface. P. longifolia provides shelter and food for the mite, while the plant may also benefit because of its fungivorous and scavenging activities. This new interaction is another dramatic example of widespread miteplant associations.     

Expression of ferredoxin-dependent glutamate synthase in dark-grown pine seedlings

Pine seedlings are able to accumulate chlorophylls and develop green plastids in a light-independent manner. In this work, we have characterized ferredoxin-dependent glutamate synthase (EC 1.4.7.1; Fd-GOGAT), a key enzyme in nitrogen interconversion during this process. Fd-GOGAT has been purified about 170-fold from cotyledons of maritime pine (Pinus pinaster). As occurs in angiosperms, the native enzyme is a single polypeptide with an apparent molecular mass of 163–168 kDa that is confined to the chloroplast stroma. Polyclonal antibodies generated against the purified enzyme were used to immunoscreen a gt11 expression library from Scots pine (Pinus sylvestris) seedlings and partial cDNA clones were isolated and characterized. The clone with the longest cDNA insert (pGOP44) contained the codification for the C-terminal (550 amino acids) of the pine Fd-GOGAT polypeptide. Immunological cross-reactivity and comparative amino sequence analysis revealed that Fd-GOGAT is a well conserved protein in higher plants. Western blot analyses showed that protein was expressed in chloroplast-containing pine tissues and this expression pattern was not affected by exogenously supplied nitrogen. Fd-GOGAT mRNA, polypeptide and enzyme activity accumulated in substantial amounts in dark-grown pine seedlings. The presence of a functional Fd-GOGAT may be important to provide the required glutamate for the biosynthesis of nitrogen compounds during chloroplast biogenesis in the dark.     

Factors involved in capillary growth in the heart

Growth of capillaries in the heart occurs under physiological circumstances during endurance exercise training, exposure to high altitude and/or cold, and changes in cardiac metabolism or heart rate elicited by modification of thyroid hormone levels. Capillary growth in all these conditions can be linked with increased coronary blood flow, decreased heart rate, or both. This paper brings evidence that, although increased blood flow due to long-term administration of coronary vasodilators results in capillary growth, a long-term decrease in heart rate induced by electrical bradycardial pacing in rabbits and pigs, or by chronic administration of a bradycardic drug, alinidine, in rats, stimulates capillary growth with little or no change in coronary blood flow. Decreased heart rate results in increased capillary wall tension, increased end-diastolic volume and increased force of contraction, and thus stretch of the capillary wall. This could lead to release of various growth factors possibly stored in the capillary basement membrane. Correlation was found between capillary density (CD) and the levels of low molecular endothelial cell stimulating angiogenic factor (ESAF) both in rabbit and pig hearts with CD increased by pacing. There was no relation between expression of mRNA for basic fibroblast growth factor and CD in sham-operated and paced rabbit hearts. In contrast, mRNA for TGFß was increased in paced hearts, and the possible role of this factor in the regulation of capillary growth induced by bradycardia is discussed.     

Intercontinental spread of promiscuous mercury-resistance transposons in environmental bacteria

We demonstrate that horizontal spread of mer operons similar to worldwide spread of antibiotic-resistance genes in medically important bacteria occurred in bacteria found in ores, soils and waters. The spread was mediated by different transposons and plasmids. Some of the spreading transposons were damaged in different ways but this did not prevent their further spread. Certain transposons are mosaics composed of segments belonging to distinct sequence types. These mosaics arose as a result of homologous and site-specific recombination. Our data suggest that the mercury-resistance operons of Gram-negative environmental bacteria can be considered as a worldwide population composed of a relatively small number of distinct recombining clones shared, at least partially, by environmental and clinical bacteria.     

Hydrological cycle and interannual variability of the aquatic community in a temporary saline lake (Fuente de Piedra,Southern Spain)

Fuente de Piedra is a shallow, temporary saline lake whoseseasonal behavior is strongly dependent on the annual hydrologicalbudget. In this study, we outline the characteristics of Fuente dePiedra Lake for two years that had different hydrological budgets.The high precipitations in 1989–90 caused the lake not to dry asusual, and decreased both salinity and the amplitude of changes.There were also differences in nutrient dynamics, with generallylower concentrations of soluble reactive phosphorus and ammonium,whereas in the more humid year nitrate showed a distinct maximum inwinter. Winter bloom chlorophyll a concentrations were alsomuch higher in 1989–90 (>600 g l-1) but there wasalso a winter productive phase that was presumably poorly coupledwith consumption processes that predominate in spring. Planktonicassemblages were different between years. Highly halotolerantphytoplankton species (Dunaliella salina and D. viridis) became scarcer, and especially two previouslyunrecorded diatoms (Cyclotella sp. and Chaetoceros sp.)became dominant in the bloom time in the wet year. The speciesrichness of the zooplankton increased in the wet year, with newspecies appearing that were not collected during 1987–88(Branchinectella media, Daphnia mediterranea, Macrothrix sp.,Arctodiaptomus salinus, Cyclops sp., Sigara sp...).There was also a much higher development of macrophytes (Ruppiadrepanensis, Althenia orientalis, Lamprothamnium papulosum)and bird populations, especially flamingoes (Phoenicopterusruber).Important interannual variations in this sort of system pointto the need for long term studies to observe the whole range ofstates that define the lake as an entity.     

Effects of water level fluctuations on phytoplankton in a river-floodplain lake system (Paraná River,Argentina)

Several aspects of community organization wereanalyzed comparatively in a small side-arm of theParaná River (Correntoso) and a shallowfloodplain lake (El Tigre) (31° 41 S and60° 42 W), in relation to the hydrology of thesystem. Taxonomic and morphological composition inthe river differed from that in the lake: the riverhad lower species richness (151 vs 218),different contributions of some Classes to totalspecies number (higher Cyano-, Zygo- andDiatomophyceae vs higher Chlorophyceae), anddiffent proportions of nannoplanktonic algae (67.5%vs 80.7%) and netplanktonic filamentousspecies (18.2% vs 4.2%). Phytoplanktonbiomass, higher in the lake than in the river due tothe retention time, was mostly dominated bynannoplankton and netplankton. Loticphytoplankton was dominated by typical fluvialspecies of Diatomophyceae (R-strategists). Riverconditions seem to maintain a subclimacticcommunity, which was little impacted by the flushingof populations from floodplain lakes. Water levelwas the main factor controlling phytoplanktonbiomass, species diversity (H), evenness (E) andcommunity change rate () in the river. Inthe lake, phytoplankton had an autogenicsuccessional sequence during the isolation phase (C-to S-strategists) and other responses todisturbance, mainly during the flood(R-strategists). Frequent changes in phytoplanktoncomposition, biomass, H, E and , revealed aenvironmental instability in the lake, which may beexplained by interactions of external factors(hydrology and climatology) and those of internalorigin, such as nutrients and grazing.     

Contribution of Mutation and RNA Recombination to the Evolution of a Plant Pathogenic RNA

The nucleotide sequence of 17 variants of the satellite RNA of cucumber mosaic virus (CMV-satRNA) isolated from field-infected tomato plants in the springs of 1989, 1990, and 1991 was determined. The sequence of each of the 17 satRNAs was unique and was between 334 and 340 nucleotides in length; 57 positions were polymorphic. There was much genetic divergence, ranging from 0.006 to 0.141 nucleotide substitutions per site for pairwise comparisons, and averaging 0.074 for any pair. When the polymorphic positions were analyzed relative to a secondary structure model proposed for CMV-satRNAs, it was found that there were significantly different numbers of changes in base-paired and non–base-paired positions, and that mutations that did not disrupt base pairing were preferred at the putatively paired sites. This supports the concept that the need to maintain a functional structure may limit genetic divergence of CMV-satRNA. Phylogenetic analyses showed that the 17 CMV-satRNA variants clustered into two subgroups, I and II, and evolutionary lines proceeding by the sequential accumulation of mutations were apparent. Three satRNA variants were outliers for these two phylogenetic groups. They were shown to be recombinants of subgroup I and II satRNAs by calculating phylogenies for different molecular regions and by using Sawyer's test for gene conversion. At least two recombination events were required to produce these three recombinant satRNAs. Thus, recombinants were found to be frequent (∼17%) in natural populations of CMV-satRNA, and recombination may make an important contribution to the generation of new variants. To our knowledge this is the first report of data allowing the frequency of recombinant isolates in natural populations of an RNA replicon to be estimated. Received: 14 May 1996 / Accepted: 17 July 1996