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Roman G. Efremov Dmitry I. Gulyaev Gerard Vergoten Nikolai N. Modyanov 《Journal of Protein Chemistry》1992,11(6):665-675
A new computer-aided molecular modeling approach based on the concept of three-dimensional (3D) molecular hydrophobicity potential has been developed to calculate the spatial organization of intramembrane domains in proteins. The method has been tested by calculating the arrangement of membrane-spanning segments in the photoreaction center ofRhodopseudomonas viridis and comparing the results obtained with those derived from the X-ray data. We have applied this computational procedure to the analysis of interhelical packing in membrane moiety of Na+, K+-ATPase. The work consists of three parts. In Part I, 3D distributions of electrostatic and molecular hydrophobicity potentials on the surfaces of transmembrane helical peptides were computed and visualized. The hydrophobic and electrostatic properties of helices are discussed from the point of view of their possible arrangement within the protein molecule. Interlocation of helical segments connected with short extramembrane loops found by means of optimization of their hydrophobic/hydrophilic contacts is considered in Part II. The most probable 3D model of packing of helical peptides in the membrane domain of Na+, K+-ATPase is discussed in the final part of the work. 相似文献
3.
Victor N. Mikheev Dmitry S. Pavlov Daria Pakulska 《Environmental Biology of Fishes》1992,35(4):351-360
Synopsis Swimming speed and swimming path of goldfish and tetra larvae were studied in aquaria containing food patches composed of decapsulated cysts and immobilized nauplii of Artemia salina or sparsely distributed prey. The mean swimming speed of starved larvae in the medium without food was about four times higher than the speed of larvae feeding in a patch. Satiated larvae swam about 1.5 times slower than hungry fish. Consumption of single prey items by starved larvae caused the following sequence of swimming responses: handling pause (cessation of swimming), slow swimming in a restricted area, and fast swimming (approximately twice as fast as hungry larvae before encountering food) accompanied by a widening of the area searched (area increased searching). Mean swimming speed was constant over a broad range (101–103 ind·1–1 of food density, although at extreme (high or low) values of food density it depended on swimming responses of the predator. Frequency of visits to the different parts of the aquarium strongly depended on encounters of hungry fish with food particles or patches. 相似文献
4.
Dmitry V. Beletsky 《Hydrobiologia》1996,322(1-3):75-80
The results of numerical modelling of large-scale circulation in Lakes Onega and Ladoga are presented, with primary emphasis on the temporal variability of currents with time scales of days. Some typical circulation patterns have been inferred from model calculations. They reflect the existence of different dynamic regimes in the lakes, namely, forced and free circulation regimes. The forced circulation regime is the well-known wind-induced double-gyre circulation accompanied by coastal upwelling and downwelling. A case of double-gyre circulation in Lake Onega was investigated in particular detail. The second dynamic regime is a free response (or a relaxation) of the stratified lake to wind cessation, and is connected closely with the evolution of wind-induced upwelling and thermal front propagation. Diagnostic calculations demonstrate that the regime of relaxation supports the restoration of cyclonic circulation in Lake Onega. Barotropic circulation patterns in Lake Ladoga were calculated with the emphasis on prevailing winds from west to south-east. Our calculations show that the bottom relief of Lake Ladoga causes asymmetry in the double-gyre circulation patterns. In particular, approximately equal cyclonic and anticyclonic circulation cells appearing in the case of southerly wind transform to a single dominant cyclonic cell and several small anticyclonic cells in the case of westerly wind. We also found especially strong sensitivity of the sense of rotation of the largest gyre to the east-west components of the wind vector. 相似文献
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Tatyana V Ovchinnikova Zakhar O Shenkarev Zoya A Yakimenko Natalia V Svishcheva Andrey A Tagaev Dmitry A Skladnev Alexander S Arseniev 《Journal of peptide science》2003,9(11-12):817-826
Zervamicin IIB is a member of the alpha-aminoisobutyric acid containing peptaibol antibiotics. A new procedure for the biosynthetic preparation of the uniformly 13C- and 15N-enriched peptaibol is described This compound was isolated from the biomass of the fungus-producer Emericellopsis salmosynnemata strain 336 IMI 58330 obtained upon cultivation in the totally 13C, 15N-labelled complete medium. To prepare such a medium the autolysed biomass and the exopolysaccharides of the obligate methylotrophic bacterium Methylobacillus flagellatus KT were used. This microorganism was grown in totally 13C, 15N-labelled minimal medium containing 13C-methanol and 15N-ammonium chloride as the only carbon and nitrogen sources. Preliminary NMR spectroscopic analysis indicated a high extent of isotope incorporation (> 90%) and led to the complete 13C- and 15N-NMR assignment including the stereospecific assignment of Aib residues methyl groups. The observed pattern of the structurally important secondary chemical shifts of 1H(alpha), 13C=O and 13C(alpha) agrees well with the previously determined structure of zervamicin IIB in methanol solution. 相似文献
8.
Dmitry E. Nolde Alexander G. Sobol Kirill A. Pluzhnikov Eugene V. Grishin Alexander S. Arseniev 《Journal of biomolecular NMR》1995,5(1):1-13
Summary Two-dimensional 1H NMR techniques were used to determine the spatial structure of ectatomin, a toxin from the venom of the ant Ectatomma tuberculatum. Nearly complete proton resonance assignments for two chains of ectatomin (37 and 34 amino acid residues, respectively) were
obtained using 2D TOCSY, DQF-COSY and NOESY experiments. The cross-peak volumes in NOESY spectra were used to define the local
structure of the protein and generate accurate proton-proton distance constraints employing the MARDIGRAS program. Disulfide
bonds were located by analyzing the global fold of ectatomin, calculated with the distance geometry program DIANA. These data,
combined with data on the rate of exchange of amide protons with deuterium, were used to obtain a final set of 20 structures
by DIANA. These structures were refined by unrestrained energy minimization using the CHARMm program. The resulting rms deviations
over 20 structures (excluding the mobile N- and C-termini of each chain) are 0.75 ? for backbone heavy atoms, and 1.25 ? for
all heavy atoms. The conformations of the two chains are similar. Each chain consists of two α-helices and a hinge region
of four residues; this forms a hairpin structure which is stabilized by disulfide bridges. The hinge regions of the two chains
are connected together by a third disulfide bridge. Thus, ectatomin forms a four-α-helical bundle structure. 相似文献
9.
Nikita Biziaev Elizaveta Sokolova Dmitry V. Yanvarev Ilya Yu Toropygin Alexey Shuvalov Tatiana Egorova Elena Alkalaeva 《The Journal of biological chemistry》2022,298(7)
The nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts that are unfavorable for translation termination have been described; however, the exact molecular mechanism that mediates their effects remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. We developed an approach to estimate the level of stop codon readthrough in the absence of eukaryotic release factors (eRFs). In this system, the stop codon is recognized by the suppressor or near-cognate tRNAs. We observed that in the absence of eRFs, readthrough occurs in a 3′ nucleotide context-dependent manner, and the main factors determining readthrough efficiency were the type of stop codon and the sequence of the 3′ nucleotides. Moreover, the efficiency of translation termination in weak 3′ contexts was almost equal to that in the tested standard context. Therefore, the ability of eRFs to recognize stop codons and induce peptide release is not affected by mRNA context. We propose that ribosomes or other participants of the elongation cycle can independently recognize certain contexts and increase the readthrough of stop codons. Thus, the efficiency of translation termination is regulated by the 3′ nucleotide context following the stop codon and depends on the concentrations of eRFs and suppressor/near-cognate tRNAs. 相似文献