Simulation analysis of structures on the reaction pathway of RNAse A

1990 ◽  
Vol 112 (10) ◽  
pp. 3826-3831 ◽  
Author(s):  
Karen Haydock ◽  
Carmay Lim ◽  
Axel T. Brunger ◽  
Martin Karplus
Keyword(s):  
Simulation Analysis ◽  
Reaction Pathway ◽  
Rnase A

Structural insight into precursor tRNA processing by yeast ribonuclease P

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. eaat6678 ◽  
Author(s):  
Pengfei Lan ◽  
Ming Tan ◽  
Yuebin Zhang ◽  
Shuangshuang Niu ◽  
Juan Chen ◽  
...  
Keyword(s):  
Metal Ion ◽  
Simulation Analysis ◽  
Reaction Pathway ◽  
Rnase P ◽  
Ribonuclease P ◽  
Measuring Device ◽  
Catalytic Center ◽  
Cryo Electron Microscopy ◽  
Phosphate Backbone ◽  
Protein Components

Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5′-leader of pre–transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo–electron microscopy structures of Saccharomyces cerevisiae RNase P alone and in complex with pre-tRNAPhe. The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a “measuring device” with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3′ leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion SN2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5′-leader of pre-tRNA is processed by eukaryotic RNase P.

Portein-gold labelling of ultrathin sections of wheat spot mosaic-affected wheat plants

1990 ◽  
Vol 48 (3) ◽  
pp. 680-681
Author(s):  
K. S. Zaychuk ◽  
M. H. Chen ◽  
C. Hiruki
Keyword(s):  
Osmium Tetroxide ◽  
Rnase A ◽  
Leaf Ultrastructure ◽  
Double Membrane ◽  
Young Root ◽  
Leaf Tissues ◽  
Membrane Bound ◽  
Ultrathin Sections ◽  
Gold Labelling ◽  
Electron Dense Core

Wheat spot mosaic (WSpM), which frequently occurs with wheat streak mosaic virus was first reported in 1956 from Alberta. Singly isolated, WSpM causes chlorotic spots, chlorosis, stunting, and sometimes death of the wheat plants. The vector responsible for transmission is the eriophyid mite, Eriophyes tulipae Kiefer. The examination of leaf ultrastructure by electron microscopy has revealed double membrane bound bodies (DMBB’s) 0.1-0.2 μm in diameter. Dispersed fibrils within these bodies suggested the presence of nucleic acid. However, neither ribosomes characteristic of bacteria, mycoplasma and the psittacosis group of organisms nor an electron dense core characteristic of many viruses was commonly evident.In an attempt to determine if the DMBB’s contain nucleic acids, RNase A, DNase I, and lactoferrin protein were conjugated with 10 nm colloidal gold as previously described. Young root and leaf tissues from WSpM-affected wheat plants were fixed in glutaraldehyde, postfixed in osmium tetroxide,and embedded in Spurr’s resin.

Computer simulation study about the dependence of amorphous silicon photonic waveguides efficiency on the material quality

2020 ◽  
Vol 90 (3) ◽  
pp. 30502
Author(s):  
Alessandro Fantoni ◽  
João Costa ◽  
Paulo Lourenço ◽  
Manuela Vieira
Keyword(s):  
Amorphous Silicon ◽  
High Throughput Screening ◽  
Simulation Analysis ◽  
Low Cost ◽  
Deposition Process ◽  
Large Area ◽  
Sidewall Roughness ◽  
Sensing Applications ◽  
Fabrication Defects ◽  
The Impact

Amorphous silicon PECVD photonic integrated devices are promising candidates for low cost sensing applications. This manuscript reports a simulation analysis about the impact on the overall efficiency caused by the lithography imperfections in the deposition process. The tolerance to the fabrication defects of a photonic sensor based on surface plasmonic resonance is analysed. The simulations are performed with FDTD and BPM algorithms. The device is a plasmonic interferometer composed by an a-Si:H waveguide covered by a thin gold layer. The sensing analysis is performed by equally splitting the input light into two arms, allowing the sensor to be calibrated by its reference arm. Two different 1 × 2 power splitter configurations are presented: a directional coupler and a multimode interference splitter. The waveguide sidewall roughness is considered as the major negative effect caused by deposition imperfections. The simulation results show that plasmonic effects can be excited in the interferometric waveguide structure, allowing a sensing device with enough sensitivity to support the functioning of a bio sensor for high throughput screening. In addition, the good tolerance to the waveguide wall roughness, points out the PECVD deposition technique as reliable method for the overall sensor system to be produced in a low-cost system. The large area deposition of photonics structures, allowed by the PECVD method, can be explored to design a multiplexed system for analysis of multiple biomarkers to further increase the tolerance to fabrication defects.

Application of Coupled Structural Acoustic Analysis and Sensitivity Calculations to a Tire Noise Problem

2012 ◽  
Vol 40 (1) ◽  
pp. 25-41 ◽  
Author(s):  
H. M. R. Aboutorabi ◽  
L. Kung
Keyword(s):  
Performance Improvement ◽  
Acoustic Analysis ◽  
Simulation Analysis ◽  
Analysis Method ◽  
Vehicle Manufacturer ◽  
Element Analysis ◽  
Equipment Manufacturer ◽  
Tire Noise ◽  
Fea Modeling ◽  
Testing Instruments

Abstract REFERENCE: H. M. R. Aboutorabi and L. Kung, “Application of Coupled Structural Acoustic Analysis and Sensitivity Calculations to a Tire Noise Problem,” Tire Science and Technology, TSTCA, Vol. 40, No. 1, January – March 2012, pp. 25–41. ABSTRACT: Tire qualification for an original equipment (OE) program consists of several rounds of submissions by the tire manufacturer for evaluation by the vehicle manufacturer. Tires are evaluated both subjectively, where the tire performance is rated by an expert driver, and objectively, where sensors and testing instruments are used to measure the tire performance. At the end of each round of testing the evaluation results are shared and requirements for performance improvement for the next round are communicated with the tire manufacturer. As building and testing is both expensive and time consuming predictive modeling and simulation analysis that can be applied to the performance of the tire is of great interest and value. This paper presents an application of finite element analysis (FEA) modeling along with experimental verification to solve tire noise objections at certain frequencies raised by an original equipment manufacturer (OEM) account. Coupled structural-acoustic analysis method was used to find modal characteristics of the tire at the objectionable frequencies. Sensitivity calculations were then carried out to evaluate the strength of contribution from each tire component to the identified modes. Based on these findings changes to the construction were proposed and implemented that addressed the noise issue.

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