Local Maximum Absorption Method for Structure Fitting in CryoEM

2011 ◽  
Vol 460-461 ◽  
pp. 77-82
Author(s):  
Gui Hua Shan ◽  
Jun Liu ◽  
Xue Bin Chi
Keyword(s):  
Domain Knowledge ◽  
Local Maximum ◽  
Atomic Model ◽  
Absorption Method ◽  
Cryo Electron Microscopy ◽  
Novel Structure ◽  
Fitting Method ◽  
Automatic Alignment ◽  
Density Map ◽  
Fitting In

Cryo-electron microscopy (CryoEM) is a very important method for studying the structures of macromolecules. Structure fitting is one of the key problems in CryoEM technique. We propose a novel structure fitting method for automatic alignment of the atomic model and CryoEM density map. Based on the domain knowledge, 3D density map is presented by local maximum points. And the atomic model is presented by atoms with high density value. According to characteristic of CryoEM density map, these atoms must correspond to one of the local maximum, then employ absolute orientation algorithm to calculate the rotation matrix and transfer vector. To show the efficiency of our method, we apply the algorithm on two pairs of test data.

scholarly journals High-Order Polynomial Fitting Assistance for Fast Double-Peak Finding in Brillouin-Distributed Sensing

Sensors ◽  
2020 ◽  
Vol 21 (1) ◽  
pp. 187
Author(s):  
Marcelo A. Soto ◽  
Alin Jderu ◽  
Dorel Dorobantu ◽  
Marius Enachescu ◽  
Dominik Ziegler
Keyword(s):  
Optical Fibers ◽  
High Order ◽  
Polynomial Fitting ◽  
Gaussian Fitting ◽  
Peak Finding ◽  
Fitting Method ◽  
Fold Reduction ◽  
Order Polynomial ◽  
Fitting In ◽  
Distributed Brillouin Sensor

A high-order polynomial fitting method is proposed to accelerate the computation of double-Gaussian fitting in the retrieval of the Brillouin frequency shifts (BFS) in optical fibers showing two local Brillouin peaks. The method is experimentally validated in a distributed Brillouin sensor under different signal-to noise ratios and realistic spectral scenarios. Results verify that a sixth-order polynomial fitting can provide a reliable initial estimation of the dual local BFS values, which can be subsequently used as initial parameters of a nonlinear double-Gaussian fitting. The method demonstrates a 4.9-fold reduction in the number of iterations required by double-Gaussian fitting and a 3.4-fold improvement in processing time.

scholarly journals The structure of the yeast Ctf3 complex

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Stephen M Hinshaw ◽  
Andrew N Dates ◽  
Stephen C Harrison
Keyword(s):  
Electron Microscopy ◽  
Cell Cycle ◽  
High Resolution ◽  
Atomic Model ◽  
Kinetochore Assembly ◽  
Cryo Electron Microscopy ◽  
Molecular Interpretation ◽  
Spindle Microtubules ◽  
And Function ◽  
Assembly Site

Kinetochores are the chromosomal attachment points for spindle microtubules. They are also signaling hubs that control major cell cycle transitions and coordinate chromosome folding. Most well-studied eukaryotes rely on a conserved set of factors, which are divided among two loosely-defined groups, for these functions. Outer kinetochore proteins contact microtubules or regulate this contact directly. Inner kinetochore proteins designate the kinetochore assembly site by recognizing a specialized nucleosome containing the H3 variant Cse4/CENP-A. We previously determined the structure, resolved by cryo-electron microscopy (cryo-EM), of the yeast Ctf19 complex (Ctf19c, homologous to the vertebrate CCAN), providing a high-resolution view of inner kinetochore architecture (Hinshaw and Harrison, 2019). We now extend these observations by reporting a near-atomic model of the Ctf3 complex, the outermost Ctf19c sub-assembly seen in our original cryo-EM density. The model is sufficiently well-determined by the new data to enable molecular interpretation of Ctf3 recruitment and function.

An Improved Iterative Polynomial Fitting Algorithm for Baseline Correction in X-Ray Spectrum

2021 ◽  
Vol 105 ◽  
pp. 90-98
Author(s):  
Xiao Yu Jiang ◽  
Qing Ya Wang ◽  
Mu Qiang Xu ◽  
Jun Hao
Keyword(s):  
Fluorescence Spectrum ◽  
Soil Analysis ◽  
Simulated Data ◽  
Real Data ◽  
Polynomial Fitting ◽  
X Ray ◽  
Iterative Processes ◽  
Fitting Method ◽  
Fitting Algorithm ◽  
Fitting In

An iterative polynomial fitting method is proposed for the estimate of the baseline of the X-ray fluorescence spectrum signal. The new method generates automatic thresholds by comparing the X-ray fluorescence spectrum signal with the calculated signal from polynomial fitting in the iterative processes. The signal peaks are cut out consecutively in the iterative processes so the polynomial fitting will finally give a good estimation of the baseline. Simulated data and real data from the soil analysis spectrum are used to demonstrate the feasibility of the proposed method.

scholarly journals Cryo-EM structure of phosphodiesterase 6 reveals insights into the allosteric regulation of type I phosphodiesterases

2019 ◽  
Vol 5 (2) ◽  
pp. eaav4322 ◽  
Author(s):  
Sahil Gulati ◽  
Krzysztof Palczewski ◽  
Andreas Engel ◽  
Henning Stahlberg ◽  
Lubomir Kovacik
Keyword(s):  
Conformational Changes ◽  
Second Messengers ◽  
Structural Features ◽  
Full Length ◽  
Type I ◽  
Regulatory Domains ◽  
Catalytic Domains ◽  
Cryo Electron Microscopy ◽  
Density Map ◽  
G Protein Coupled

Cyclic nucleotide phosphodiesterases (PDEs) work in conjunction with adenylate/guanylate cyclases to regulate the key second messengers of G protein–coupled receptor signaling. Previous attempts to determine the full-length structure of PDE family members at high-resolution have been hindered by structural flexibility, especially in their linker regions and N- and C-terminal ends. Therefore, most structure-activity relationship studies have so far focused on truncated and conserved catalytic domains rather than the regulatory domains that allosterically govern the activity of most PDEs. Here, we used single-particle cryo–electron microscopy to determine the structure of the full-length PDE6αβ2γ complex. The final density map resolved at 3.4 Å reveals several previously unseen structural features, including a coiled N-terminal domain and the interface of PDE6γ subunits with the PDE6αβ heterodimer. Comparison of the PDE6αβ2γ complex with the closed state of PDE2A sheds light on the conformational changes associated with the allosteric activation of type I PDEs.

Early treatment of trans-tibial amputees: retrospective analysis of early fitting and elastic bandaging

2005 ◽  
Vol 29 (1) ◽  
pp. 3-12 ◽  
Author(s):  
A. D. van Velzen ◽  
M. J. Nederhand ◽  
C. H. Emmelot ◽  
M. J. Ijzerman
Keyword(s):  
Wound Healing ◽  
Knee Flexion ◽  
Plaster Cast ◽  
Flexion Contracture ◽  
Pressure Sores ◽  
Fitting Method ◽  
Increased Risk ◽  
In Trans ◽  
Fitting In ◽  
Discharge From Hospital

This study investigates the effects of early fitting in trans-tibial amputees. The assumption is that compared to elastic bandaging, the use of a rigid dressing in early fitting will result in quicker wound healing and earlier ambulation. A retrospective file search was carried out in three different hospitals, analysing the time to first prosthesis, the incidence of local and general complications and the functional outcome after discharge from hospital. Each of the hospitals used a different method of postoperative care: elastic bandaging, immediate postoperative application of the plaster cast or delayed application of the plaster cast within one week post amputation. In comparison to the elastic bandaging method (N=52), the use of a rigid dressing in the early fitting method (immediate and delayed, N=97) resulted in a statistically significant shorter period from amputation to the delivery of a first regular prosthesis (110 days vs 50 days) and a decreased risk of knee flexion contracture. Although, differences in local complications were not observed, the risk of pressure sores in other places than the stump was increased in early fitting. Instead of further reducing the time to first prosthesis by immediate fitting, the use of delayed fitting resulted in a statistically significant shorter period from amputation to the delivery of a first regular prosthesis (56 vs 40 days). However, delayed fitting was associated with an increased risk for reamputation. In conclusion, this study indicates that early fitting by use of a rigid dressing after trans-tibial amputation is the treatment of choice. If it is possible to apply a plaster cast in the operating room, the authors would prefer the immediate fitting method.

scholarly journals Fibril structure of amyloid-β(1–42) by cryo–electron microscopy

Science ◽  
2017 ◽  
Vol 358 (6359) ◽  
pp. 116-119 ◽  
Author(s):  
Lothar Gremer ◽  
Daniel Schölzel ◽  
Carla Schenk ◽  
Elke Reinartz ◽  
Jörg Labahn ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Senile Plaques ◽  
Amyloid Β ◽  
Amyloid Β Protein ◽  
Dimer Interface ◽  
Cryo Electron Microscopy ◽  
Fibril Structure ◽  
Β Protein ◽  
Density Map ◽  
Main Component

Amyloids are implicated in neurodegenerative diseases. Fibrillar aggregates of the amyloid-β protein (Aβ) are the main component of the senile plaques found in brains of Alzheimer’s disease patients. We present the structure of an Aβ(1–42) fibril composed of two intertwined protofilaments determined by cryo–electron microscopy (cryo-EM) to 4.0-angstrom resolution, complemented by solid-state nuclear magnetic resonance experiments. The backbone of all 42 residues and nearly all side chains are well resolved in the EM density map, including the entire N terminus, which is part of the cross-β structure resulting in an overall “LS”-shaped topology of individual subunits. The dimer interface protects the hydrophobic C termini from the solvent. The characteristic staggering of the nonplanar subunits results in markedly different fibril ends, termed “groove” and “ridge,” leading to different binding pathways on both fibril ends, which has implications for fibril growth.

A Research of GPS Height Fitting in Mountainous Terrain by CPSO Optimization FLS-SVM

2013 ◽  
Vol 336-338 ◽  
pp. 2339-2343 ◽  
Author(s):  
Yong Gan ◽  
Xin Xin Liu ◽  
Yuan Pan Zheng
Keyword(s):  
Support Vector Machine ◽  
Small Sample ◽  
Least Square ◽  
Support Vector ◽  
Mountainous Area ◽  
Machine Model ◽  
Normal Height ◽  
Fitting Method ◽  
Fitting In ◽  
The Impact

For the problem of data limited in the mountainous area, a method of FLS-SVM (Fuzzy Least Square Vector Machine) that supporting small sample data and having high noise ability was put forward. The CPSO(chaos particle swarm optimization algorithm) is adopted to optimize the parameters of least squares support vector machine algorithm, and to avoid the uncertainty of artificial parameter selection. Meanwhile, considering the impact of terrain, the terrain correction is introduced to the support vector machine model. The experimental results show that the model can get higher precision fitting effect compared with traditional fitting method such as PSO-LSSVM and GA-LSSVM, and suitable for the SRTM application of getting normal height.

scholarly journals The 4.4 Å structure of the giant Melbournevirus virion belonging to the Marseilleviridae family

2021 ◽  
Author(s):  
Raymond N Burton-Smith ◽  
Hemanth K N Reddy ◽  
Martin Svenda ◽  
Chantal Abergel ◽  
Kenta Okamoto ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Capsid Protein ◽  
Major Capsid Protein ◽  
Capsid Proteins ◽  
Atomic Model ◽  
Penton Base ◽  
Cryo Electron Microscopy ◽  
Internal Membrane ◽  
Structural Details ◽  
Giant Viruses

Members of Marseilleviridae, one family of icosahedral giant viruses classified in 2012 have been identified worldwide in all types of environments. The virion shows a characteristic internal membrane extrusion at the five-fold vertices of the capsid, but its structural details need to be elucidated. We now report the 4.4 Å cryo-electron microscopy structure of the Melbournevirus capsid. An atomic model of the major capsid protein (MCP) shows a unique cup structure on the trimer that accommodates additional proteins. A polyalanine model of the penton base protein shows internally extended N- and C-terminals, which indirectly connect to the internal membrane extrusion. The Marseilleviruses share the same orientational organisation of the MCPs as PBCV-1 and CroV, but do not appear to possess a protein akin to the ″tape measure″ of these viruses. Minor capsid proteins named PC-β, zipper, and scaffold are proposed to control the dimensions of the capsid during assembly.

scholarly journals The structure of the yeast Ctf3 complex

2019 ◽  
Author(s):  
Stephen M. Hinshaw ◽  
Andrew N. Dates ◽  
Stephen C. Harrison
Keyword(s):  
Electron Microscopy ◽  
Cell Cycle ◽  
High Resolution ◽  
Atomic Model ◽  
Kinetochore Assembly ◽  
Cryo Electron Microscopy ◽  
Molecular Interpretation ◽  
Spindle Microtubules ◽  
And Function ◽  
Assembly Site

ABSTRACTKinetochores are the chromosomal attachment points for spindle microtubules. They are also signaling hubs that control major cell cycle transitions and coordinate chromosome folding. Most well-studied eukaryotes rely on a conserved set of factors, which are divided among two loosely-defined groups, for these functions. Outer kinetochore proteins contact microtubules or regulate this contact directly. Inner kinetochore proteins designate the kinetochore assembly site by recognizing a specialized nucleosome containing the H3 variant Cse4/CENP-A. We previously determined the structure, resolved by cryo-electron microscopy (cryo-EM), of the yeast Ctf19 complex (Ctf19c, homologous to the vertebrate CCAN), providing a high-resolution view of inner kinetochore architecture. We now extend these observations by reporting a near-atomic model of the Ctf3 complex, the outermost Ctf19c sub-assembly seen in our original cryo-EM density. The model is sufficiently well-determined by the new data to enable molecular interpretation of Ctf3 recruitment and function.

scholarly journals Structure of a cytochrome-based bacterial nanowire

2018 ◽  
Author(s):  
David J. Filman ◽  
Stephen F. Marino ◽  
Joy E. Ward ◽  
Lu Yang ◽  
Zoltán Mester ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Electron Transport ◽  
Long Range ◽  
Biological Significance ◽  
New Materials ◽  
Electrically Conductive ◽  
Cryo Electron Microscopy ◽  
Novel Structure ◽  
Bacterial Nanowires

AbstractElectrically conductive pili from Geobacter species, termed bacterial “nanowires”, are intensely studied for their biological significance and potential in the development of new materials. We have characterized a unique nanowire from conductive G. sulfurreducens pili preparations by cryo-electron microscopy composed solely of the c-type cytochrome OmcS. We present here, at 3.4 Å resolution, a novel structure of a cytochrome-based filament and discuss its possible role in long-range biological electron transport.Summary sentenceCryo-electron microscopy reveals the remarkable assembly of a c-type cytochrome into filaments comprising a heme-based bacterial nanowire.

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