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Korostelev N. B. Baytalyuk A. A. Maltsev I. V. Orlov A. M. 《Journal of Ichthyology》2020,60(6):891-899
Journal of Ichthyology - The results on the studies on age and growth in Pacific flatnose (fine-scale antimora) Antimora microlepis from the waters of underwater Emperor mounting range (open water... 相似文献
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Understanding the mechanisms of inhibitors of translation termination may inform development of new antibacterials and therapeutics for premature termination diseases. We report the crystal structure of the potent termination inhibitor blasticidin S bound to the ribosomal 70S?release factor 1 (RF1) termination complex. Blasticidin S shifts the catalytic domain 3 of RF1 and restructures the peptidyl transferase center. Universally conserved uridine 2585 in the peptidyl transferase center occludes the catalytic backbone of the GGQ motif of RF1, explaining the structural mechanism of inhibition. Rearrangement of domain 3 relative to the codon-recognition domain 2 provides insight into the dynamics of RF1 implicated in termination accuracy. 相似文献
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Easy-to-use macromolecular viewers, such as UCSF Chimera, are a standard tool in structural biology. They allow rendering and performing geometric operations on large complexes, such as viruses and ribosomes. Dynamical simulation codes enable modeling of conformational changes, but may require considerable time and many CPUs. There is an unmet demand from structural and molecular biologists for software in the middle ground, which would allow visualization combined with quick and interactive modeling of conformational changes, even of large complexes. This motivates MMB-GUI. MMB uses an internal-coordinate, multiscale approach, yielding as much as a 2000-fold speedup over conventional simulation methods. We use Chimera as an interactive graphical interface to control MMB. We show how this can be used for morphing of macromolecules that can be heterogeneous in biopolymer type, sequence, and chain count, accurately recapitulating structural intermediates. We use MMB-GUI to create a possible trajectory of EF-G mediated gate-passing translocation in the ribosome, with all-atom structures. This shows that the GUI makes modeling of large macromolecules accessible to a wide audience. The morph highlights similarities in tRNA conformational changes as tRNA translocates from A to P and from P to E sites and suggests that tRNA flexibility is critical for translocation completion. 相似文献
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Characterization of the capsid protein glycosylation of adeno-associated virus type 2 by high-resolution mass spectrometry
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Murray S Nilsson CL Hare JT Emmett MR Korostelev A Ongley H Marshall AG Chapman MS 《Journal of virology》2006,80(12):6171-6176
Adeno-associated virus type 2 (AAV-2) capsid proteins have eight sequence motifs that are potential sites for O- or N-linked glycosylation. Three are in prominent surface locations, close to the sites of cellular receptor attachment and to neutralizing epitopes on or near protrusions surrounding the three-fold axes, raising the possibility that AAV-2 might use glycosylation as a means of immune escape or for preventing reattachment on release of progeny virus. Peptide mapping and structural analysis by Fourier transform ion cyclotron resonance mass spectrometry demonstrates, however, no glycosylation of the capsid protein for virus prepared in cultured HeLa cells. 相似文献
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Rudiño-Piñera E Ravelli RB Sheldrick GM Nanao MH Korostelev VV Werner JM Schwarz-Linek U Potts JR Garman EF 《Journal of molecular biology》2007,368(3):833-844
An important goal of structural studies of modular proteins is to determine the inter-module orientation, which often influences biological function. The N-terminal domain of human fibronectin (Fn) is composed of a string of five type 1 modules (F1). Despite their small size, to date F1 modules have proved intractable to X-ray structure solution, although there are several NMR structures available. Here, we present the first structures (two X-ray models and an NMR-derived model) of the (2)F1(3)F1 module pair, which forms part of the binding site for Fn-binding proteins from pathogenic bacteria. The crystallographic structure determination was aided by the novel technique of UV radiation damage-induced phasing. The individual module structures are very similar in all three models. In the NMR structure and one of the X-ray structures, a similar but smaller interdomain interface than that observed previously for (4)F1(5)F1 is seen. The other X-ray structure has a different interdomain orientation. This work underlines the benefits of combining X-ray and NMR data in the studies of multi-domain proteins. 相似文献
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Yu. V. Mitrishkin A. Ya. Korostelev V. N. Dokuka R. R. Khayrutdinov 《Plasma Physics Reports》2011,37(4):279-320
Synthesis and simulation of a hierarchical (two-level) magnetic system for controlling a tokamakreactor plasma throughout
the entire divertor discharge stage, including the plasma current ramp-up phase, are carried out. The plasma vertical velocity
is stabilized about zero by using a proportional controller in a scalar control loop. The gain of the controller—the coefficient
that ensures the required stability margins—is found by using a second-order linear model constructed by solving the identification
problem on the basis of numerical experiments carried out with the DINA plasmophysical computer code. The internal cascade
(the lower level of the system) for tracking the scenario currents in the poloidal magnetic field coils is synthesized by
using the complete dynamic channel decoupling method. The external cascade (the upper level of the system) for tracking the
plasma current and shape is synthesized by using the method of pseudoseparation of the control channels and the multidimensional
diagonal proportional-integral controller, with proportional, integrating, and double integrating units connected in parallel
in each channel. In the hierarchical control system, the lower level (the internal cascade) is subordinated to the upper level
(the external cascade). The external cascade acts on the internal one by the signals that set the required currents in the
coils of the central solenoid and of the poloidal magnetic field in order to ensure the required plasma current and shape
in accordance with the output signals from the plant, which are transmitted through the vector feedback channel. The lower
level is aimed exclusively at tracking the reference inputs by tracking the currents in the control coils. An operating mode
of the system under the conditions of current saturation in the control coils is proposed and implemented. Results are presented
from numerical simulations of the two-level (cascade) control system for reference scenario no. 2 of the ITER database (www.iter.org)
with the DINA nonlinear code. 相似文献
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Ravcheev DA Li X Latif H Zengler K Leyn SA Korostelev YD Kazakov AE Novichkov PS Osterman AL Rodionov DA 《Journal of bacteriology》2012,194(5):1145-1157
Redox-sensing repressor Rex was previously implicated in the control of anaerobic respiration in response to the cellular NADH/NAD(+) levels in gram-positive bacteria. We utilized the comparative genomics approach to infer candidate Rex-binding DNA motifs and assess the Rex regulon content in 119 genomes from 11 taxonomic groups. Both DNA-binding and NAD-sensing domains are broadly conserved in Rex orthologs identified in the phyla Firmicutes, Thermotogales, Actinobacteria, Chloroflexi, Deinococcus-Thermus, and Proteobacteria. The identified DNA-binding motifs showed significant conservation in these species, with the only exception detected in Clostridia, where the Rex motif deviates in two positions from the generalized consensus, TTGTGAANNNNTTCACAA. Comparative analysis of candidate Rex sites revealed remarkable variations in functional repertoires of candidate Rex-regulated genes in various microorganisms. Most of the reconstructed regulatory interactions are lineage specific, suggesting frequent events of gain and loss of regulator binding sites in the evolution of Rex regulons. We identified more than 50 novel Rex-regulated operons encoding functions that are essential for resumption of the NADH:NAD(+) balance. The novel functional role of Rex in the control of the central carbon metabolism and hydrogen production genes was validated by in vitro DNA binding assays using the TM0169 protein in the hydrogen-producing bacterium Thermotoga maritima. 相似文献
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