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61.
Manfred Tacker Walter Fontana Peter F. Stadler Peter Schuster 《European biophysics journal : EBJ》1994,23(1):29-38
We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a landscape of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies.
Correspondence to: P. Schuster 相似文献
62.
The three-dimensional structure of the photosynthetic reaction center fromRhodobacter sphaeroides is described. The reaction center is a transmembrane protein that converts light into chemical energy. The protein has three subunits: L, M, and H. The mostly helical L and M subunits provide the scaffolding and the finely tuned environment in which the chromophores carry out electron transfer. The details of the protein-chromophore interactions are from studies of a trigonal crystal form that diffracted to 2.65-Å resolution. Functional studies of the multi-subunit complex by site-specific replacement of key amino acid residues are summarized in the context of the molecular structure.This work was supported in part by the U.S. Department of Energy, Office of Health and Environmental Research, under Contract No. W-31-109-ENG-38 and by Public Health Service Grant GM36598. 相似文献
63.
Robert G. Gregerson Susan S. Miller Mary Petrowski J. Stephen Gantt Carroll P. Vance 《Plant molecular biology》1994,25(3):387-399
Genomic clones encoding two isozymes of aspartate aminotransferase (AAT) were isolated from an alfalfa genomic library and their DNA sequences were determined. The AAT1 gene contains 12 exons that encode a cytosolic protein expressed at similar levels in roots, stems and nodules. In nodules, the amount of AAT1 mRNA was similar at all stages of development, and was slightly reduced in nodules incapable of fixing nitrogen. The AAT1 mRNA is polyadenylated at multiple sites differing by more than 250 bp. The AAT2 gene contains 11 exons, with 5 introns located in positions identical to those found in animal AAT genes, and encodes a plastid-localized isozyme. The AAT2 mRNA is polyadenylated at a very limited range of sites. The transit peptide of AAT2 is encoded by the first two and part of the third exon. AAT2 mRNA is much more abundant in nodules than in other organs, and increases dramatically during the course of nodule development. Unlike AAT1, expression of AAT2 is significantly reduced in nodules incapable of fixing nitrogen. Phylogenetic analysis of deduced AAT proteins revealed 4 separate but related groups of AAT proteins; the animal cytosolic AATs, the plant cytosolic AATs, the plant plastid AATs, and the mitochondrial AATs. 相似文献
64.
Lisa T. Garber R. Curtis Haltiwanger Drake S. Eggleston 《Letters in Peptide Science》1994,1(3):127-133
Summary Continuing a line of investigations on methods for formation and growth of high-quality crystals of peptides, the glycylglycine sequence has been crystallized by evaporation methods as a salt with 1,5-naphthalenedisulfonic acid. The structure of the peptide is highly extended, and is conformationally quite similar to the structures which have been characterized for other zwitterionic and salt forms of this sequence. Thus, crystallization as a salt with this sulfonic acid has imposed no undue influence upon the molecular conformation. These results offer further indication that the preparation of peptide sulfonate salts, particularly with arene templates, may have broad general utility for crystallization of interesting sequences which until now have not been approachable in their zwitterionic forms. 相似文献
65.
Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy. 总被引:1,自引:1,他引:0 下载免费PDF全文
E. Ab G. K. Schuurman-Wolters M. H. Saier J. Reizer M. Jacuinod P. Roepstorff K. Dijkstra R. M. Scheek G. T. Robillard 《Protein science : a publication of the Protein Society》1994,3(2):282-290
The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand. 相似文献
66.
Habitat structure,conspecific presence and spatial variation in the recruitment of a temperate reef fish 总被引:2,自引:0,他引:2
Phillip S. Levin 《Oecologia》1993,94(2):176-185
Pronounced spatial variation in recruitment occurs in many marine invertebrate and fish populations and is thought to be critical to the demography of these species. In this study I examined the importance of habitat structure and the presence of conspecific residents to spatial variation in larval settlement and recruitment in a temperate fish Tautogolabrus adspersus. I define settlement as the movement of individuals from the water column to the benthic habitat, while I refer to recruitment as numbers of individuals surviving some arbitrary period of time after settlement. Experiments in which standard habitats were stocked with conspecifics showed that resident conspecifics were not an important factor contributing to small-scale variability in recruitment. Further correlative analyses demonstrated that large-scale variation in recruitment could not be explained by variability in older age classes. By contrast, manipulations of macroalgal structure within a kelp bed demonstrated that recruitment was significantly higher in habitats with a dense understory of foliose and filamentous algae than in habitats with only crustose algae. Understory algae varied in their pattern of disperison among sites, and the dispersion of fish matched that of the plants. In order to determine the effects of differences in patterns of algal dispersion on the demography of associated T. adspersus populations, I used experimental habitat units to manipulate patterns of dispersion. Settlement was significantly greater to randomly placed versus clumped habitats; however, no differences in recruitment between random and clumped habitats were detected. Because recruitment is a function of the numbers of settlers minus the subsequent loss of settlers, rates of mortality or migration must have been higher in the randomly placed habitats. These results are counter to the current paradigm for reef fishes which suggests that larval settlement is the crucial demographic process producing variability in population abundance. In this experiment patterns of settlement were modified by varying the patch structure of the habitat.Contribution number 278 from the Center for Marine Biology, University of New Hampshire 相似文献
67.
Size structure of the metazoan community in a Piedmont stream 总被引:1,自引:0,他引:1
N. LeRoy Poff Margaret A. Palmer Paul L. Angermeier Robert L. Vadas Jr. Christine C. Hakenkamp Alexa Bely Peter Arensburger Andrew P. Martin 《Oecologia》1993,95(2):202-209
We characterized the size structure of virtually the entire metazoan community in a fourth order, sandybottomed Piedmont stream during late summer. Our study, the first to sample across all habitat types and sizes of metazoans in an aquatic ecosystem, indicates that at the community level, stream size spectra may be bimodal for the benthos or trimodal when fish are included. Animals spanning 10 orders of magnitude in dry mass (from gastrotrichs to fish) were quantitatively collected from nine habitat types. The bimodal benthic size spectrum was characterized by a meiofaunal component (mostly oligochaetes and micro-crustacea) and a macrobenthic component (mostly the introduced asiatic clam, Corbicula fluminea). Insects contributed little to overall standing crop. Size-specific contribution to whole-community metabolism was assessed using allometric equations for respiration, and we found a distinctly bimodal distribution across the entire metazoan size range, with peaks in the meiofaunal and benthic macrofaunal size ranges. Our bimodal benthic size spectrum is similar to that observed for marine benthos but not to other freshwater benthic systems, possibly because the entire range of habitat types and/or animal sizes were not sampled in the latter. Numerous factors may influence size spectra in stream ecosystems, including local geomorphic (habitat) conditions, water level fluctuations, species introductions, and predation processes. 相似文献
68.
A population of a viperid snake,Trimeresurus flavoviridis, was studied over 10 years by removal trapping on a small subtropical island in Japan. The sex ratio of trapped individuals changed seasonally, but was not biased to either sex in the whole sample of 258 individuals. The age of each individual was estimated through the size structure and the age-size relationship. The minimum number of individuals at the beginning of the study was estimated through accumulating older individuals trapped in the subsequent years. By assuming an annual natural survival rate in the course of this accumulation, an age structure was simulated which led to calculate a resulted natural survival rate. The assumed rate of 0.62 fitted best to the resulted one. The annual trapped proportion estimated on the simulated absolute number of individuals was higher in older individuals than in younger ones with the overall mean of 16%. 相似文献
69.
H. T. Wright 《Journal of molecular evolution》1993,36(2):136-143
Summary The serpins are a large family of eukaryotic proteins, many but not all of whose members are proteinase inhibitors. Most members of this family show relatively low sequence identity, but crystal structures determined for 6 different serpins are closely similar. The intron positions of 11 serpins, and the intron sizes in 9 of these 11, have been determined. There is considerable diversity in number, position, and size of introns among these serpins, though subsets show clear similarity or identity. Dendrograms derived from comparisons of DNA and amino acid sequences and of intron positions for the 11 serpins differ from each other and from dendrograms previously derived from protein sequences. These dendrograms are difficult to reconcile exclusively with a loss of introns from a large primordial set during the evolution of the serpin family. The tertiary structure of the serpins does support the idea that this protein family arose from an early recombination event which fused the amino and carboxyl domains. The structure of the carboxyl domain also suggests that an insertion subsequent to the fusion event contributed two strands of -sheet, which complemented three -sheet strands of the amino domain, to complete -sheet A, which is the central secondary structure feature of the serpins. Few of the introns lie between regions of secondary or tertiary structure, and it seems more likely that many were acquired subsequent to the early events of serpin evolution and have undergone multiple insertions, deletions, and migrations since, subject to the constraint of the serpin structure.Abbreviations Api
-1-proteinase inhibitor (human)
- Aci
-1-antichymotrypsin (human)
- Agt
angiotensinogen (rat)
- Oah
ovalbumin (chicken)
- Gyh
gene y (chicken)
- At3
antithrombin 3 (human)
- Pi1
plasminogen activator inhibitor 1—endothelial (human)
- Pi2
plasminogen activator inhibitor 2—placental (human)
- Cli
Cl inhibitor (human)
- Apl
antiplasmin (human)
- Bz4
Z protein (barley). 相似文献
70.
Parthasarathy Manavalan Alan E. Smith John M. McPherson 《Journal of Protein Chemistry》1993,12(3):279-290
A sequence comparison of the two membrane-associated (MA) domains of the cystic fibrosis transmembrane conductance regulator (CFTR), multidrug resistance transporter (MDR), and -factor pheromone export system (STE6) proteins, each of which are believed to contain a total of 12 transmembrane (TM) segments, reveals significant amino acid homology and length conservation in the loop regions that connect individual TM sequences. Similar structural homology is observed between these proteins, hemolysin B (HLYB) and the major histocompatibility-linked peptide transporter, HAM1, the latter two which contain a single MA domain composed of six TM segments. In addition, there are specific sequences that are conserved within the TM segments of the five different membrane proteins. This observation suggests that the folding topologies of the MA domains of MDR, STE6, and CFTR in the plasma membrane are likely to be very similar. The sequence analysis also reveals that there are three characteristic motifs (a pair of aromatic residues, LTLXXXXXXP and GXXL) that are conserved in MDR, STE6, HLYB, HAM1, but not in CFTR. We propose that although CFTR may be evolutionarily related to these other membrane proteins, it belongs to a separate subclass. 相似文献