scholarly journals Cryo-EM Analyses Permit Visualization of Structural Polymorphism of Biological Macromolecules

2021 ◽  
Vol 1 ◽  
Author(s):  
Wei-Hau Chang ◽  
Shih-Hsin Huang ◽  
Hsin-Hung Lin ◽  
Szu-Chi Chung ◽  
I-Ping Tu
Keyword(s):  
Crystal Packing ◽  
Three Dimensional ◽  
Image Data ◽  
Biological Macromolecules ◽  
Learning Approaches ◽  
Structural Polymorphism ◽  
Structure Information ◽  
Rna Molecules ◽  
Recent Developments ◽  
And Function

The functions of biological macromolecules are often associated with conformational malleability of the structures. This phenomenon of chemically identical molecules with different structures is coined structural polymorphism. Conventionally, structural polymorphism is observed directly by structural determination at the density map level from X-ray crystal diffraction. Although crystallography approach can report the conformation of a macromolecule with the position of each atom accurately defined in it, the exploration of structural polymorphism and interpreting biological function in terms of crystal structures is largely constrained by the crystal packing. An alternative approach to studying the macromolecule of interest in solution is thus desirable. With the advancement of instrumentation and computational methods for image analysis and reconstruction, cryo-electron microscope (cryo-EM) has been transformed to be able to produce “in solution” structures of macromolecules routinely with resolutions comparable to crystallography but without the need of crystals. Since the sample preparation of single-particle cryo-EM allows for all forms co-existing in solution to be simultaneously frozen, the image data contain rich information as to structural polymorphism. The ensemble of structure information can be subsequently disentangled through three-dimensional (3D) classification analyses. In this review, we highlight important examples of protein structural polymorphism in relation to allostery, subunit cooperativity and function plasticity recently revealed by cryo-EM analyses, and review recent developments in 3D classification algorithms including neural network/deep learning approaches that would enable cryo-EM analyese in this regard. Finally, we brief the frontier of cryo-EM structure determination of RNA molecules where resolving the structural polymorphism is at dawn.

Right ventricle and pulmonary arterial pressure

2016 ◽  
Author(s):  
Annemien E. van den Bosch ◽  
Luigi P. Badano ◽  
Julia Grapsa
Keyword(s):  
Clinical Decision Making ◽  
Complex Geometry ◽  
Three Dimensional ◽  
Clinical Decision ◽  
Tissue Doppler ◽  
Left Ventricular ◽  
Doppler Imaging ◽  
Prognostic Information ◽  
Recent Developments ◽  
And Function

Right ventricular (RV) performance plays an important role in the morbidity and mortality of patients with left ventricular dysfunction, congenital heart disease, and pulmonary hypertension. Assessment of RV size, function, and haemodynamics has been challenging because of its complex geometry. Conventional two-dimensional echocardiography is the modality of choice for assessment of RV function in clinical practice. Recent developments in echocardiography have provided several new techniques for assessment of RV dimensions and function, include tissue Doppler imaging, speckle-tracking imaging, and volumetric three-dimensional imaging. However, specific training, expensive dedicated equipment, and extensive clinical validation are still required. Doppler methods interrogating tricuspid inflow and pulmonary artery flow velocities, which are influenced by changes in pre- and afterload conditions, may not provide robust prognostic information for clinical decision-making. This chapter addresses the role of the various echocardiographic modalities used to assess the RV and pulmonary circulation. Special emphasis has been placed on technical considerations, limitations, and pitfalls of image acquisition and analysis.

scholarly journals Barnaba: Software for Analysis of Nucleic Acids Structures and Trajectories

2018 ◽  
Author(s):  
Sandro Bottaro ◽  
Giovanni Bussi ◽  
Giovanni Pinamonti ◽  
Sabine Reißer ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Molecular Simulations ◽  
Network Models ◽  
Molecular Conformations ◽  
Rna Molecules ◽  
Command Line Tool ◽  
Perform Cluster Analysis ◽  
And Function

AbstractRNA molecules are highly dynamic systems characterized by a complex interplay between sequence, structure, dynamics, and function. Molecular simulations can potentially provide powerful insights into the nature of these relationships. The analysis of structures and molecular trajectories of nucleic acids can be non-trivial because it requires processing very high-dimensional data that are not easy to visualize and interpret.Here we introduce Barnaba, a Python library aimed at facilitating the analysis of nucleic acids structures and molecular simulations. The software consists of a variety of analysis tools that allow the user to i) calculate distances between three-dimensional structures using different metrics, ii) back-calculate experimental data from three-dimensional structures, iii) perform cluster analysis and dimensionality reductions, iv) search three-dimensional motifs in PDB structures and trajectories and v) construct elastic network models (ENM) for nucleic acids and nucleic acids-protein complexes.In addition, Barnaba makes it possible to calculate torsion angles, pucker conformations and to detect base-pairing/base-stacking interactions. Barnaba produces graphics that conveniently visualize both extended secondary structure and dynamics for a set of molecular conformations. The software is available as a command-line tool as well as a library, and supports a variety of 1le formats such as PDB, dcd and xtc 1les. Source code, documentation and examples are freely available at https://github.com/srnas/barnaba under GNU GPLv3 license.

Crystallization of Membrane Proteins

1999 ◽  
Author(s):  
F. Reiss-Husson ◽  
D. Picot
Keyword(s):  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein A ◽  
Limited Proteolysis ◽  
Three Dimensional ◽  
Hydrophobic Surface ◽  
Biological Macromolecules ◽  
Recent Developments ◽  
Tight Association ◽  
Membrane Components

Crystallization of membrane proteins is one of the most recent developments in protein crystal growth; in 1980, for the first time, two membrane proteins were successfully crystallized, bacteriorhodopsin (1) and porin (2). Since then, a number of membrane proteins (about 30) yielded three-dimensional crystals. In several cases, the quality of the crystals was sufficient for X-ray diffraction studies. The first atomic structure of a membrane protein, a photosynthetic bacterial reaction centre, was described in 1985 (3), followed by the structure of about ten other membrane protein families. Crystallization of membrane proteins is now an actively growing field, and has been discussed in several recent reviews (4-8). The major difficulty in the study of membrane proteins, which for years hampered their crystallization, comes from their peculiar solubility properties. These originate from their tight association with other membrane components, particularly lipids. Indeed integral membrane proteins contain hydrophobic surface regions buried in the lipid bilayer core, as well as hydrophilic regions with charged or polar residues more or less exposed at the external faces of the membrane. Disruption of the bilayer for isolating a membrane protein can be done in various ways: extraction with organic solvents, use of chaotropic agents, or solubilization by a detergent. The last method is the most frequently used, since it maintains the biological activity of the protein if a suitable detergent is found. This chapter will be restricted to specific aspects of three-dimensional crystallizations done in micellar solutions of detergent. In some cases, it is possible to separate soluble domains from the membrane protein either by limited proteolysis or by genetic engineering. Such protein fragments can then be treated as soluble proteins and so will not be discussed further in this chapter. We refer to Chapter 12 and the review by Kühlbrandt (9) for the methodology of two-dimensional crystallization used for electron diffraction. The general principles discussed in this book for the crystallization of soluble biological macromolecules apply for membrane proteins; the protein solution must be brought to supersaturation by modifying its physical parameters (concentrations of constituents, ionic strength, and so on), so that nucleation may occur.

DIRECTIONAL COHERENCE INTERPOLATION FOR THREE-DIMENSIONAL GRAY-LEVEL IMAGES

2004 ◽  
Vol 04 (04) ◽  
pp. 535-561 ◽  
Author(s):  
YONGMEI MICHELLE WANG ◽  
JINGDAN ZHANG ◽  
ZHUNPING ZHANG ◽  
BAINING GUO
Keyword(s):  
Interpolation Method ◽  
Three Dimensional ◽  
Boundary Surface ◽  
Computation Time ◽  
Image Data ◽  
Gray Level ◽  
Object Boundary ◽  
Structure Information ◽  
Algorithm Efficiency ◽  
Smoothness Term

A novel three-dimensional gray-level interpolation method called the Directional Coherence Interpolation (DCI) is presented in the paper. The principal advantage of the proposed approach is that it leads to significantly higher visual quality in 3D rendering when compared with traditional image interpolation methods. The basis of DCI is a form of directional image-space coherence. DCI interpolates the missing image data along the maximum coherence directions (MCD), which are estimated from the local image intensity yet constrained by a generic smoothness term. In order to further improve both the algorithm efficiency and robustness, we also propose to apply a pyramidal search strategy for MCD estimation. This coarse-to-fine scheme requires less computation time by starting with the reduced amount of data and propagating searching results to finer resolutions. DCI can incorporate image shape and structure information without the prior requirement of explicit representation of object boundary/surface. Extensive experiments were performed on both synthetic and real medical images to evaluate the proposed approaches. The experimental results show that the proposed methods are able to handle general object interpolation, while achieving both accuracy and efficiency in interpolation compared with the existing techniques.

scholarly journals 3D Flexible Refinement: Structure and Motion of Flexible Proteins from Cryo-EM

2021 ◽  
Author(s):  
Ali Punjani ◽  
David J. Fleet
Keyword(s):  
3D Structure ◽  
Rigid Motion ◽  
Image Data ◽  
Deformation Field ◽  
Local Geometry ◽  
Biological Macromolecules ◽  
Conformational Variability ◽  
Structure And Motion ◽  
Flow Generator ◽  
And Function

Single particle cryo-EM excels in determining static structures of biological macromolecules such as proteins. However, many proteins are dynamic, with their motion inherently linked to their function. Recovering the continuous motion and detailed 3D structure of flexible proteins from cryo-EM data has remained an open challenge. We introduce 3D Flexible Refinement (3DFlex), a motion-based deep neural network model of continuous heterogeneity. 3DFlex directly exploits the knowledge that conformational variability of a protein is often the result of physical processes that transport density over space and tend to conserve mass and preserve local geometry. From 2D image data, the 3DFlex model jointly learns a single canonical 3D map, latent coordinate vectors that specify positions on the protein's conformational landscape, and a flow generator that, given a latent position as input, outputs a 3D deformation field. This deformation field convects the canonical map into appropriate conformations to explain experimental images. Applied to experimental data, 3DFlex learns non-rigid motion spanning several orders of magnitude while preserving high-resolution details of secondary structure elements. Further, 3DFlex resolves canonical maps that are improved relative to conventional refinement methods because particle images contribute to the maps coherently regardless of the conformation of the protein in the image. Together, the ability to obtain insight into motion in macromolecules, as well as the ability to resolve features that are usually lost in cryo-EM of flexible specimens, will provide new insight and allow new avenues of investigation into biomolecular structure and function.

scholarly journals ATSAS2.1, a program package for small-angle scattering data analysis

2006 ◽  
Vol 39 (2) ◽  
pp. 277-286 ◽  
Author(s):  
Petr V. Konarev ◽  
Maxim V. Petoukhov ◽  
Vladimir V. Volkov ◽  
Dmitri I. Svergun
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Three Dimensional ◽  
Program Package ◽  
Scattering Data ◽  
Primary Data ◽  
Biological Macromolecules ◽  
Colloidal Solutions ◽  
Angle Scattering ◽  
Recent Developments

The program packageATSAS2.1 for small-angle X-ray and neutron scattering data analysis is presented. The programs included in the package cover the major processing and interpretation steps from primary data reduction to three-dimensional modelling. This system is primarily oriented towards the analysis of biological macromolecules, but could also be used for non-biological isotropic and partially ordered objects (nanoparticle systems, colloidal solutions, polymers in solution and bulk). Recent developments in the programs included inATSAS2.1 are highlighted. The main programs run on multiple hardware platforms, including Windows PC, Linux RedHat and Suse, DEC Alpha, SGI IRIX and Mac OSX.

scholarly journals Methods for merging data sets in electron cryo-microscopy

2019 ◽  
Vol 75 (9) ◽  
pp. 782-791 ◽  
Author(s):  
Max E. Wilkinson ◽  
Ananthanarayanan Kumar ◽  
Ana Casañal
Keyword(s):  
Three Dimensional ◽  
Scaling Factor ◽  
Biological Macromolecules ◽  
Data Sets ◽  
Independent Data ◽  
Pixel Size ◽  
Combine Data ◽  
Data Merging ◽  
Recent Developments

Recent developments have resulted in electron cryo-microscopy (cryo-EM) becoming a useful tool for the structure determination of biological macromolecules. For samples containing inherent flexibility, heterogeneity or preferred orientation, the collection of extensive cryo-EM data using several conditions and microscopes is often required. In such a scenario, merging cryo-EM data sets is advantageous because it allows improved three-dimensional reconstructions to be obtained. Since data sets are not always collected with the same pixel size, merging data can be challenging. Here, two methods to combine cryo-EM data are described. Both involve the calculation of a rescaling factor from independent data sets. The effects of errors in the scaling factor on the results of data merging are also estimated. The methods described here provide a guideline for cryo-EM users who wish to combine data sets from the same type of microscope and detector.

Biostereometrics–The Spatial and Spatio-Temporal Analysis of Body form and Function

1974 ◽  
Vol 18 (1) ◽  
pp. 26-30
Author(s):  
R. E. Herron
Keyword(s):  
Traffic Safety ◽  
Three Dimensional ◽  
Temporal Analysis ◽  
Body Form ◽  
Form And Function ◽  
Sensing Technology ◽  
Biological Form ◽  
Recent Developments ◽  
Spatio Temporal ◽  
And Function

The fact that the human body form is irregular and three-dimensional calls for a revision of the mathematical strategy which underlies modern anthropometry. Traditional linear anthropometric methods are inadequate for many modern research and clinical needs, where comprehensive three-dimensional (or four-dimensional, when the dimension of time is included) information is required. Recent developments in stereometric sensing technology and computer processing have opened up new opportunities to implement stereometric strategies in such areas as traffic safety engineering, consumer product design, fitting of artificial limbs, clothing evaluation and cockpit geometry among others. It is important to understand that the mathematical strategy which underlies biostereometrics– the spatial and spatio-temporal analysis of biological form and function based on principles of analytic geometry–is the main focus of attention in this work; the development and refinement of different stereometric sensors, though essential, is a secondary concern. Already a wide variety of stereometric sensing technology is available and no doubt further methods will be developed as specific needs are better defined. The presentation will include illustrations from over thirty projects carried out during the last six years.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

Structure and function of neural networks in the retina

1988 ◽  
Vol 46 ◽  
pp. 26-27
Author(s):  
Peter Sterling
Keyword(s):  
Ganglion Cells ◽  
Three Dimensional ◽  
Structure And Function ◽  
Synaptic Connections ◽  
Visual Axis ◽  
One Dimensional ◽  
Cat Retina ◽  
Ultrathin Sections ◽  
And Function ◽  
Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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