scholarly journals Structural mechanism of GTPase-powered ribosome-tRNA movement

2021 ◽  
Author(s):  
Valentyn Petrychenko ◽  
Bee-Zen Peng ◽  
Ana C. de A. P. Schwarzer ◽  
Frank Peske ◽  
Marina V. Rodnina ◽  
...  
Keyword(s):  
Large Scale ◽  
Ribosomal Subunit ◽  
Molecular Switches ◽  
Thermal Fluctuations ◽  
23S Rrna ◽  
Gtp Hydrolysis ◽  
Time Resolved ◽  
Structural Mechanism ◽  
Molecular Movement ◽  
Switch Regions

GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP—Pi form stabilizes ribosomal subunit rotation and induces twisting of the sarcin-ricin loop of the 23S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a cascade of rearrangements and a large-scale rotation of EF-G that exerts force on the ribosome and ultimately drives tRNA movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.

scholarly journals Structural mechanism of GTPase-powered ribosome-tRNA movement

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Valentyn Petrychenko ◽  
Bee-Zen Peng ◽  
Ana C. de A. P. Schwarzer ◽  
Frank Peske ◽  
Marina V. Rodnina ◽  
...  
Keyword(s):  
Large Scale ◽  
Thermal Fluctuations ◽  
Small Subunit ◽  
Forward Movement ◽  
Gtp Hydrolysis ◽  
Time Resolved ◽  
Ribosomal Subunits ◽  
Structural Mechanism ◽  
Molecular Movement ◽  
Switch Regions

AbstractGTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP–Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement.

The ribosome as a molecular machine: the mechanism of tRNA–mRNA movement in translocation

2011 ◽  
Vol 39 (2) ◽  
pp. 658-662 ◽  
Author(s):  
Marina V. Rodnina ◽  
Wolfgang Wintermeyer
Keyword(s):  
Ribosomal Subunit ◽  
Elongation Factor ◽  
Thermal Fluctuations ◽  
Spontaneous Movement ◽  
Conformational States ◽  
Gtp Hydrolysis ◽  
Time Resolved ◽  
Directional Bias ◽  
Loosely Coupled ◽  
Dynamic Events

Translocation of tRNA and mRNA through the ribosome is one of the most dynamic events during protein synthesis. In the cell, translocation is catalysed by EF-G (elongation factor G) and driven by GTP hydrolysis. Major unresolved questions are: how the movement is induced and what the moving parts of the ribosome are. Recent progress in time-resolved cryoelectron microscopy revealed trajectories of tRNA movement through the ribosome. Driven by thermal fluctuations, the ribosome spontaneously samples a large number of conformational states. The spontaneous movement of tRNAs through the ribosome is loosely coupled to the motions within the ribosome. EF-G stabilizes conformational states prone to translocation and promotes a conformational rearrangement of the ribosome (unlocking) that accelerates the rate-limiting step of translocation: the movement of the tRNA anticodons on the small ribosomal subunit. EF-G acts as a Brownian ratchet providing directional bias for movement at the cost of GTP hydrolysis.

scholarly journals Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

2021 ◽  
Vol 69 (3) ◽  
Author(s):  
S. J. Eder ◽  
P. G. Grützmacher ◽  
M. Rodríguez Ripoll ◽  
J. F. Belak
Keyword(s):  
Grain Boundary ◽  
Large Scale ◽  
Surface Deformation ◽  
Boundary Migration ◽  
Material Design ◽  
Lattice Rotation ◽  
Time Resolved ◽  
Near Surface ◽  
Color Saturation ◽  
Dynamics Simulations

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

scholarly journals Time-resolved PIV measurements of a deflected submerged jet interacting with liquid-gas and liquid-liquid interfaces

2021 ◽  
Author(s):  
Stefan Puttinger ◽  
Mahdi Saeedipour
Keyword(s):  
Liquid Layer ◽  
Large Scale ◽  
Free Surface Flow ◽  
Industrial Applications ◽  
Liquid Pool ◽  
Surface Flow ◽  
Two Phase ◽  
Time Resolved ◽  
Submerged Jet ◽  
Major Interest

AbstractThis paper presents an experimental investigation on the interactions of a deflected submerged jet into a liquid pool with its above interface in the absence and presence of an additional lighter liquid. Whereas the former is a free surface flow, the latter mimics a situation of two stratified liquids where the liquid-liquid interface is disturbed by large-scale motions in the liquid pool. Such configurations are encountered in various industrial applications and, in most cases, it is of major interest to avoid the entrainment of droplets from the lighter liquid into the main flow. Therefore, it is important to understand the fluid dynamics in such configurations and to analyze the differences between the cases with and without the additional liquid layer. To study this problem, we applied time-resolved particle image velocimetry experiments with high spatial resolution. A detailed data analysis of a small layer beneath the interface shows that although the presence of an additional liquid layer stabilizes the oscillations of the submerged jet significantly, the amount of kinetic energy, enstrophy, and velocity fluctuations concentrated in the proximity of the interface is higher when the oil layer is present. In addition, we analyze the energy distribution across the eigenmodes of a proper orthogonal distribution and the distribution of strain and vortex dominated regions. As the main objective of this study, these high-resolution time-resolved experimental data provide a validation platform for the development of new models in the context of the volume of fluid-based large eddy simulation of turbulent two-phase flows.

scholarly journals Reconfiguration of human evolving large-scale epileptic brain networks prior to seizures: an evaluation with node centralities

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rieke Fruengel ◽  
Timo Bröhl ◽  
Thorsten Rings ◽  
Klaus Lehnertz
Keyword(s):  
Large Scale ◽  
Brain Networks ◽  
Brain Regions ◽  
Brain Network ◽  
Theoretical Concept ◽  
Global Network ◽  
Time Resolved ◽  
Functional Connections ◽  
Node Centrality ◽  
Network Mechanism

AbstractPrevious research has indicated that temporal changes of centrality of specific nodes in human evolving large-scale epileptic brain networks carry information predictive of impending seizures. Centrality is a fundamental network-theoretical concept that allows one to assess the role a node plays in a network. This concept allows for various interpretations, which is reflected in a number of centrality indices. Here we aim to achieve a more general understanding of local and global network reconfigurations during the pre-seizure period as indicated by changes of different node centrality indices. To this end, we investigate—in a time-resolved manner—evolving large-scale epileptic brain networks that we derived from multi-day, multi-electrode intracranial electroencephalograpic recordings from a large but inhomogeneous group of subjects with pharmacoresistant epilepsies with different anatomical origins. We estimate multiple centrality indices to assess the various roles the nodes play while the networks transit from the seizure-free to the pre-seizure period. Our findings allow us to formulate several major scenarios for the reconfiguration of an evolving epileptic brain network prior to seizures, which indicate that there is likely not a single network mechanism underlying seizure generation. Rather, local and global aspects of the pre-seizure network reconfiguration affect virtually all network constituents, from the various brain regions to the functional connections between them.

scholarly journals Whole-Genome Phylogenomic Heterogeneity of Neisseria gonorrhoeae Isolates with Decreased Cephalosporin Susceptibility Collected in Canada between 1989 and 2013

2014 ◽  
Vol 53 (1) ◽  
pp. 191-200 ◽  
Author(s):  
Walter Demczuk ◽  
Tarah Lynch ◽  
Irene Martin ◽  
Gary Van Domselaar ◽  
Morag Graham ◽  
...  
Keyword(s):  
Neisseria Gonorrhoeae ◽  
Large Scale ◽  
Epidemiological Studies ◽  
23S Rrna ◽  
Genome Comparison ◽  
Whole Genome ◽  
Content Type ◽  
Genomic Epidemiology ◽  
High Level ◽  
Sequence Types

A large-scale, whole-genome comparison of CanadianNeisseria gonorrhoeaeisolates with high-level cephalosporin MICs was used to demonstrate a genomic epidemiology approach to investigate strain relatedness and dynamics. Although current typing methods have been very successful in tracing short-chain transmission of gonorrheal disease, investigating the temporal evolutionary relationships and geographical dissemination of highly clonal lineages requires enhanced resolution only available through whole-genome sequencing (WGS). Phylogenomic cluster analysis grouped 169 Canadian strains into 12 distinct clades. While someN. gonorrhoeaemultiantigen sequence types (NG-MAST) agreed with specific phylogenomic clades or subclades, other sequence types (ST) and closely related groups of ST were widely distributed among clades. Decreased susceptibility to extended-spectrum cephalosporins (ESC-DS) emerged among a group of diverse strains in Canada during the 1990s with a variety of nonmosaicpenAalleles, followed in 2000/2001 with thepenAmosaic X allele and then in 2007 with ST1407 strains with thepenAmosaic XXXIV allele. Five genetically distinct ESC-DS lineages were associated withpenAmosaic X, XXXV, and XXXIV alleles and nonmosaic XII and XIII alleles. ESC-DS with coresistance to azithromycin was observed in 5 strains with 23S rRNA C2599T or A2143G mutations. As the costs associated with WGS decline and analysis tools are streamlined, WGS can provide a more thorough understanding of strain dynamics, facilitate epidemiological studies to better resolve social networks, and improve surveillance to optimize treatment for gonorrheal infections.

scholarly journals Halobacterium cutirubrum ribosomes. Properties of the ribosomal proteins and ribonucleic acid

1972 ◽  
Vol 130 (1) ◽  
pp. 103-110 ◽  
Author(s):  
L. P. Visentin ◽  
C. Chow ◽  
A. T. Matheson ◽  
M. Yaguchi ◽  
F. Rollin
Keyword(s):  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Soluble Fraction ◽  
Ribosomal Subunit ◽  
23S Rrna ◽  
Core Particle ◽  
Fractionation Procedure ◽  
Additional Protein ◽  
70S Ribosome ◽  
Low Ionic Strength

1. The 30S ribosomal subunit of the extreme halophile Halobacterium cutirubrum is unstable and loses 75% of its ribosomal protein when the 70S ribosome is dissociated into the two subunits. A stable 30S subunit is obtained if the dissociation of the 70S particle is carried out in the presence of the soluble fraction. 2. A fractionation procedure was developed for the selective removal of groups of proteins from the 30S and 50S subunits. When the ribosomes, which are stable in 4m-K+ and 0.1m-Mg2+, were extracted with low-ionic-strength buffer 75–80% of the 30S proteins and 60–65% of the 50S proteins as well as the 5S rRNA were released. The proteins in this fraction are the most acidic of the H. cutirubrum ribosomal proteins. Further extraction with Li+–EDTA releases additional protein, leaving a core particle containing either 16S rRNA or 23S rRNA and about 5% of the total ribosomal protein. The amino acid composition, mobility on polyacrylamide gels at pH4.5 and 8.7, and the molecular-weight distribution of the various protein fractions were determined. 3. The s values of the rRNA are 5S, 16S and 23S. The C+G contents of the 16S and 23S rRNA were 56.1 and 58.8% respectively and these are higher than C+G contents of the corresponding Escherichia coli rRNA (53.8 and 54.1%).

Effect of Acoustic Feedback on Lagrangian Coherent Structures in a Backward Facing Step Combustor With a Partially Premixed Flame

2017 ◽  
Author(s):  
Ramgopal Sampath ◽  
S. R. Chakravarthy
Keyword(s):  
Coherent Structures ◽  
Large Scale ◽  
Pressure Oscillation ◽  
Velocity Fields ◽  
Premixed Flame ◽  
Time Resolved ◽  
Acoustic Feedback ◽  
Acoustic Characterization ◽  
Partially Premixed ◽  
Partially Premixed Flame

The thermoacoustic oscillations of a partially premixed flame stabilized in a backward facing step combustor are studied at a constant equivalence ratio in long and short combustor configurations corresponding to with and without acoustic feedback respectively. We perform simultaneous time-resolved particle image velocimetry (TR-PIV) and chemiluminescence for selected flow conditions based on the acoustic characterization in the long combustor. The acoustic characterization shows a transition in the dominant pressure amplitudes from low to high magnitudes with an increase in the inlet flow Reynolds number. This is accompanied by a shift in the dominant frequencies. For the intermittent pressure oscillations in the long combustor, the wavelet analysis indicates a switch between the acoustic and vortex modes with silent zones of relatively low-pressure amplitudes. The short combustor configuration indicates the presence of the vortex shedding frequency and an additional band comprising the Kelvin Helmholtz mode. Next, we apply the method of finite-time Lyapunov exponent (FTLE) to the time-resolved velocity fields to extract features of the Lagrangian coherent structures (LCS) of the flow. In the long combustor post transition with the time instants with dominant acoustic mode, a large-scale modulation of the FTLE boundaries over one cycle of pressure oscillation is evident. Further, the FTLEs and the flame boundaries align each other for all phases of the pressure oscillation. In the short combustor, the FTLEs indicate the presence of small wavelength waviness that overrides the large-scale vortex structure, which corresponds to the vortex shedding mode. This behaviour contrasts with the premixed flame in the short combustor reported earlier in which such large scales were found to be seldom present. The presence of the large-scale structures even in the absence of acoustic feedback in a partially premixed flame signifies its inherent unstable nature leading to large pressure amplitudes during acoustic feedback. Lastly, the FTLE boundaries provide the frequency information of the identified coherent structure and also acts as the surrogate flame boundaries that are estimated from just the velocity fields.

Large scale alignment of a lamellar block copolymer thin film via electric fields: a time-resolved SFM study

Soft Matter ◽  
2006 ◽  
Vol 2 (12) ◽  
pp. 1089-1094 ◽  
Author(s):  
Violetta Olszowka ◽  
Markus Hund ◽  
Volker Kuntermann ◽  
Sabine Scherdel ◽  
Larisa Tsarkova ◽  
...  
Keyword(s):  
Thin Film ◽  
Block Copolymer ◽  
Electric Fields ◽  
Large Scale ◽  
Time Resolved ◽  
Large Scale Alignment

scholarly journals An Asymmetric Mechanism in a Symmetric Molecular Machine

2020 ◽  
Author(s):  
Florian Blanc ◽  
Marco Cecchini
Keyword(s):  
Free Energy ◽  
Large Scale ◽  
Technological Development ◽  
Thermal Fluctuations ◽  
Free Energy Calculations ◽  
Molecular Machine ◽  
Free Energy Surface ◽  
Promising Area ◽  
Sequential Mechanism ◽  
External Stimuli

The design of molecular architectures exhibiting functional motions is a promising area for disruptive technological development. Towards this goal, rotaxanes and catenanes, which undergo relative motions of their sub-units in response to external stimuli, are prime candidates. Here, we report on the computational analysis of the contraction/extension of a bistable [c2]-daisy chain rotaxane. Using free energy calculations and transition path optimizations, we explore the free energy landscape governing the functional motions of a prototypical molecular machine with atomic resolution.<br>The calculations reveal a sequential mechanism for contraction/extension in which the asynchronous gliding of each ring is preferred over the concerted movement suggested by chemical intuition. Analysis of the underlying free energy surface indicates that dissymmetric gliding is favored because it entails crossings of much smaller barriers.<br>Our findings illustrate an important design principle for molecular machines, namely that efficient exploitation of thermal fluctuations may be realized by breaking down the large-scale functional motions into smaller steps.

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