Single-particle XFEL 3D reconstruction of ribosome-size particles based on Fourier slice matching: requirements to reach subnanometer resolution

Three-dimensional (3D) structures of biomolecules provide insight into their functions. Using X-ray free-electron laser (XFEL) scattering experiments, it was possible to observe biomolecules that are difficult to crystallize, under conditions that are similar to their natural environment. However, resolving 3D structure from XFEL data is not without its challenges. For example, strong beam intensity is required to obtain sufficient diffraction signal and the beam incidence angles to the molecule need to be estimated for diffraction patterns with significant noise. Therefore, it is important to quantitatively assess how the experimental conditions such as the amount of data and their quality affect the expected resolution of the resulting 3D models. In this study, as an example, the restoration of 3D structure of ribosome from two-dimensional diffraction patterns created by simulation is shown. Tests are performed using the diffraction patterns simulated for different beam intensities and using different numbers of these patterns. Guidelines for selecting parameters for slice-matching 3D reconstruction procedures are established. Also, the minimum requirements for XFEL experimental conditions to obtain diffraction patterns for reconstructing molecular structures to a high-resolution of a few nanometers are discussed.

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Cryomicroscopy of crotoxin complex crystals at 400 KV

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100156109 ◽

1989 ◽

Vol 47 ◽

pp. 826-827

Author(s):

Jaap Brink ◽

Wah Chiu

Keyword(s):

Signal To Noise Ratio ◽

3D Structure ◽

Three Dimensional ◽

Carbon Films ◽

Depth Of Field ◽

Basic Subunit ◽

Ewald Sphere ◽

Diffraction Patterns ◽

Complex Crystals ◽

Acidic Subunit

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

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Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100181026 ◽

1990 ◽

Vol 48 (1) ◽

pp. 454-455

Author(s):

Jose-Maria Carazo ◽

I. Benavides ◽

S. Marco ◽

J.L. Carrascosa ◽

E.L. Zapata

Keyword(s):

3D Reconstruction ◽

3D Structure ◽

Three Dimensional ◽

Software Tools ◽

Mapping Method ◽

Computer Architectures ◽

Parallel Computer ◽

Reconstruction Process ◽

Computing Power ◽

Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

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Electrostatics of Tau Protein by Molecular Dynamics

Biomolecules ◽

10.3390/biom9030116 ◽

2019 ◽

Vol 9 (3) ◽

pp. 116 ◽

Cited By ~ 6

Author(s):

Tarsila Castro ◽

Florentina-Daniela Munteanu ◽

Artur Cavaco-Paulo

Keyword(s):

Molecular Dynamics ◽

3D Structure ◽

Three Dimensional ◽

Dynamics Simulation ◽

Microtubule Assembly ◽

Interaction Sites ◽

Disordered Protein ◽

Fluid Environment ◽

Function Relationship ◽

Insight Into

Tau is a microtubule-associated protein that promotes microtubule assembly and stability. This protein is implicated in several neurodegenerative diseases, including Alzheimer’s. To date, the three-dimensional (3D) structure of tau has not been fully solved, experimentally. Even the most recent information is sometimes controversial in regard to how this protein folds, interacts, and behaves. Predicting the tau structure and its profile sheds light on the knowledge about its properties and biological function, such as the binding to microtubules (MT) and, for instance, the effect on ionic conductivity. Our findings on the tau structure suggest a disordered protein, with discrete portions of well-defined secondary structure, mostly at the microtubule binding region. In addition, the first molecular dynamics simulation of full-length tau along with an MT section was performed, unveiling tau structure when associated with MT and interaction sites. Electrostatics and conductivity were also examined to understand how tau affects the ions in the intracellular fluid environment. Our results bring a new insight into tau and tubulin MT proteins, their characteristics, and the structure–function relationship.

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Put Some Guts into It: Intestinal Organoid Models to Study Viral Infection

Viruses ◽

10.3390/v12111288 ◽

2020 ◽

Vol 12 (11) ◽

pp. 1288 ◽

Cited By ~ 1

Author(s):

Inés García-Rodríguez ◽

Adithya Sridhar ◽

Dasja Pajkrt ◽

Katja C. Wolthers

Keyword(s):

Viral Infection ◽

Cell Lines ◽

Barrier Function ◽

Three Dimensional ◽

3D Models ◽

Cellular Heterogeneity ◽

Two Dimensional ◽

Intestinal Organoids ◽

Insight Into

The knowledge about enteric viral infection has vastly increased over the last eight years due to the development of intestinal organoids and enteroids that suppose a step forward from conventional studies using cell lines. Intestinal organoids and enteroids are three-dimensional (3D) models that closely mimic intestinal cellular heterogeneity and organization. The barrier function within these models has been adapted to facilitate viral studies. In this review, several adaptations (such as organoid-derived two-dimensional (2D) monolayers) and original intestinal 3D models are discussed. The specific advantages and applications, as well as improvements of each model are analyzed and an insight into the possible path for the field is given.

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An in silico structural insights into Plasmodium LytB protein and its inhibition

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273314082096 ◽

2014 ◽

Vol 70 (a1) ◽

pp. C1791-C1791

Author(s):

Rajabrata Bhunya ◽

Suman Nandy ◽

Alpana Seal

Keyword(s):

In Silico ◽

3D Structure ◽

Three Dimensional ◽

Comparative Modeling ◽

Binding Energies ◽

E Coli ◽

Dimethylallyl Diphosphate ◽

In Silico Study ◽

Structural Insights ◽

Insight Into

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.

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Reconstruction of Three-Dimensional Conformations of Bacterial ClpB from High-Speed Atomic-Force-Microscopy Images

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.704274 ◽

2021 ◽

Vol 8 ◽

Author(s):

Bhaskar Dasgupta ◽

Osamu Miyashita ◽

Takayuki Uchihashi ◽

Florence Tama

Keyword(s):

Atomic Force Microscopy ◽

Computational Modeling ◽

High Speed ◽

3D Structure ◽

Three Dimensional ◽

3D Models ◽

Computational Method ◽

Molecular Surface ◽

Force Microscopy ◽

Atomic Force

ClpB belongs to the cellular disaggretase machinery involved in rescuing misfolded or aggregated proteins during heat or other cellular shocks. The function of this protein relies on the interconversion between different conformations in its native condition. A recent high-speed-atomic-force-microscopy (HS-AFM) experiment on ClpB from Thermus thermophilus shows four predominant conformational classes, namely, open, closed, spiral, and half-spiral. Analyses of AFM images provide only partial structural information regarding the molecular surface, and thus computational modeling of three-dimensional (3D) structures of these conformations should help interpret dynamical events related to ClpB functions. In this study, we reconstruct 3D models of ClpB from HS-AFM images in different conformational classes. We have applied our recently developed computational method based on a low-resolution representation of 3D structure using a Gaussian mixture model, combined with a Monte-Carlo sampling algorithm to optimize the agreement with target AFM images. After conformational sampling, we obtained models that reflect conformational variety embedded within the AFM images. From these reconstructed 3D models, we described, in terms of relative domain arrangement, the different types of ClpB oligomeric conformations observed by HS-AFM experiments. In particular, we highlighted the slippage of the monomeric components around the seam. This study demonstrates that such details of information, necessary for annotating the different conformational states involved in the ClpB function, can be obtained by combining HS-AFM images, even with limited resolution, and computational modeling.

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MolAR: Bringing Chemical Structures to Life with Augmented Reality and Machine Learning

10.33774/chemrxiv-2021-jnpgl ◽

2021 ◽

Author(s):

Sukolsak Sakshuwong ◽

Hayley Weir ◽

Umberto Raucci ◽

Todd J. Martínez

Keyword(s):

Machine Learning ◽

Augmented Reality ◽

3D Structure ◽

Three Dimensional ◽

Real Life ◽

Data Bank ◽

Molecular Structures ◽

Chemical Structures ◽

Food And Drink ◽

Research And Education

Visualizing three-dimensional molecular structures is crucial to understanding and predicting their chemical behavior. Existing visualization software, however, can be cumbersome to use, and, for many, hand-drawn skeletal structures remain the preferred method of chemical communication. Although convenient, the static, two-dimensional nature of these drawings can be misleading in conveying the molecule’s 3D structure, not to mention that dynamic movement is completely disregarded. Here, we combine machine learning and augmented reality (AR) to develop MolAR, an immersive mobile application for visualizing molecules in real-world scenes. The application uses deep learning to recognize hand-drawn hydrocarbons structures which it converts into interactive 3D molecules in AR. Users can also “hunt” for chemicals in food and drink to uncover molecules in their real-life environment. A variety of interesting molecules are pre-loaded into the application, and users can visualize molecules in PubChem by providing their name or SMILES string and proteins in the Protein Data Bank by providing their PDB ID. MolAR was designed to be used in both research and education settings, providing an almost barrierless platform to visualize and interact with 3D molecular structures in a uniquely immersive way.

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A novel 3D template for mandible and maxilla reconstruction: Rapid prototyping using stereolithography

Indian Journal of Plastic Surgery ◽

10.4103/0970-0358.173123 ◽

2015 ◽

Vol 48 (03) ◽

pp. 263-273 ◽

Cited By ~ 12

Author(s):

Samir Kumta ◽

Monica Kumta ◽

Leena Jain ◽

Shrirang Purohit ◽

Rani Ummul

Keyword(s):

Rapid Prototyping ◽

Computer Aided Design ◽

Treatment Plan ◽

3D Structure ◽

Three Dimensional ◽

Bone Grafts ◽

3D Models ◽

Mirror Image ◽

Anatomical Model ◽

Patient Counselling

ABSTRACT Introduction: Replication of the exact three-dimensional (3D) structure of the maxilla and mandible is now a priority whilst attempting reconstruction of these bones to attain a complete functional and aesthetic rehabilitation. We hereby present the process of rapid prototyping using stereolithography to produce templates for modelling bone grafts and implants for maxilla/mandible reconstructions, its applications in tumour/trauma, and outcomes for primary and secondary reconstruction. Materials and Methods: Stereolithographic template-assisted reconstruction was used on 11 patients for the reconstruction of the mandible/maxilla primarily following tumour excision and secondarily for the realignment of post-traumatic malunited fractures or deformity corrections. Data obtained from the computed tomography (CT) scans with 1-mm resolution were converted into a computer-aided design (CAD) using the CT Digital Imaging and Communications in Medicine (DICOM) data. Once a CAD model was constructed, it was converted into a stereolithographic format and then processed by the rapid prototyping technology to produce the physical anatomical model using a resin. This resin model replicates the native mandible, which can be thus used off table as a guide for modelling the bone grafts. Discussion: This conversion of two-dimensional (2D) data from CT scan into 3D models is a very precise guide to shaping the bone grafts. Further, this CAD can reconstruct the defective half of the mandible using the mirror image principle, and the normal anatomical model can be created to aid secondary reconstructions. Conclusion: This novel approach allows a precise translation of the treatment plan directly to the surgical field. It is also an important teaching tool for implant moulding and fixation, and helps in patient counselling.

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Three-Dimensional Reconstruction of Coronary Arteries and Its Application in Localization of Coronary Artery Segments Corresponding to Myocardial Segments Identified by Transthoracic Echocardiography

Computational and Mathematical Methods in Medicine ◽

10.1155/2013/783939 ◽

2013 ◽

Vol 2013 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Chunyan Zhong ◽

Yanli Guo ◽

Haiyun Huang ◽

Liwen Tan ◽

Yi Wu ◽

...

Keyword(s):

Coronary Arteries ◽

Transthoracic Echocardiography ◽

3D Structure ◽

Three Dimensional ◽

3D Models ◽

Localization Accuracy ◽

Significant Difference ◽

2D Ultrasound ◽

Ct Data ◽

Contrast Ct

Objectives.To establish 3D models of coronary arteries (CA) and study their application in localization of CA segments identified by Transthoracic Echocardiography (TTE).Methods.Sectional images of the heart collected from the first CVH dataset and contrast CT data were used to establish 3D models of the CA. Virtual dissection was performed on the 3D models to simulate the conventional sections of TTE. Then, we used 2D ultrasound, speckle tracking imaging (STI), and 2D ultrasound plus 3D CA models to diagnose 170 patients and compare the results to coronary angiography (CAG).Results.3D models of CA distinctly displayed both 3D structure and 2D sections of CA. This simulated TTE imaging in any plane and showed the CA segments that corresponded to 17 myocardial segments identified by TTE. The localization accuracy showed a significant difference between 2D ultrasound and 2D ultrasound plus 3D CA model in the severe stenosis group (P<0.05) and in the mild-to-moderate stenosis group (P<0.05).Conclusions.These innovative modeling techniques help clinicians identify the CA segments that correspond to myocardial segments typically shown in TTE sectional images, thereby increasing the accuracy of the TTE-based diagnosis of CHD.

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Enhancement of RGB-D Image Alignment Using Fiducial Markers

Sensors ◽

10.3390/s20051497 ◽

2020 ◽

Vol 20 (5) ◽

pp. 1497 ◽

Cited By ~ 1

Author(s):

Tiago Madeira ◽

Miguel Oliveira ◽

Paulo Dias

Keyword(s):

3D Reconstruction ◽

Three Dimensional ◽

3D Models ◽

Difficult Problem ◽

Image Alignment ◽

Fiducial Markers ◽

Final Model ◽

Optimization Framework ◽

Reconstruction Methods ◽

Alignment Errors

Three-dimensional (3D) reconstruction methods generate a 3D textured model from the combination of data from several captures. As such, the geometrical transformations between these captures are required. The process of computing or refining these transformations is referred to as alignment. It is often a difficult problem to handle, in particular due to a lack of accuracy in the matching of features. We propose an optimization framework that takes advantage of fiducial markers placed in the scene. Since these markers are robustly detected, the problem of incorrect matching of features is overcome. The proposed procedure is capable of enhancing the 3D models created using consumer level RGB-D hand-held cameras, reducing visual artefacts caused by misalignments. One problem inherent to this solution is that the scene is polluted by the markers. Therefore, a tool was developed to allow their removal from the texture of the scene. Results show that our optimization framework is able to significantly reduce alignment errors between captures, which results in visually appealing reconstructions. Furthermore, the markers used to enhance the alignment are seamlessly removed from the final model texture.

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