Structure Refinement at Atomic Resolution

2017 ◽  
pp. 549-563 ◽  
Author(s):  
Mariusz Jaskolski
Keyword(s):  
Structure Refinement ◽  
Atomic Resolution

scholarly journals Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ray Yu-Ruei Wang ◽  
Yifan Song ◽  
Benjamin A Barad ◽  
Yifan Cheng ◽  
James S Fraser ◽  
...  
Keyword(s):  
Structure Refinement ◽  
Atomic Resolution ◽  
Large Radius ◽  
Macromolecular Assemblies ◽  
Automated Method ◽  
Large Size ◽  
Biological Phenomena ◽  
Determination Process ◽  
Improve Model ◽  
Model Geometry

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3–4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

scholarly journals Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta

2016 ◽  
Author(s):  
Ray Yu-Ruei Wang ◽  
Yifan Song ◽  
Benjamin A Barad ◽  
Yifan Cheng ◽  
James S Fraser ◽  
...  
Keyword(s):  
Structure Refinement ◽  
Atomic Resolution ◽  
Large Radius ◽  
Macromolecular Assemblies ◽  
Automated Method ◽  
Large Size ◽  
Biological Phenomena ◽  
Determination Process ◽  
Improve Model ◽  
Model Geometry

AbstractCryo-EM has revealed many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions accurately positioning individual atoms remains challenging and may be error-prone. Manually refining thousands of amino acids – typical in a macromolecular assembly – is tedious and time-consuming. We present an automated method that can improve the atomic details in models manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining or improving the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

scholarly journals Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

2020 ◽  
Author(s):  
Mingchen Chen ◽  
Xun Chen ◽  
Shikai Jin ◽  
Wei Lu ◽  
Xingcheng Lin ◽  
...  
Keyword(s):  
Large Scale ◽  
Structure Refinement ◽  
Protein Structures ◽  
Local Environment ◽  
Structural Features ◽  
Atomic Resolution ◽  
Structural Quality ◽  
Atomic Packing ◽  
Dynamics Simulations

1AbstractRecent advances in machine learning, bioinformatics and the understanding of the folding problem have enabled efficient predictions of protein structures with moderate accuracy, even for targets when there is little information from templates. All-atom molecular dynamics simulations provide a route to refine such predicted structures, but unguided atomistic simulations, even when lengthy in time, often fail to eliminate incorrect structural features that would allow the structure to become more energetically favorable owing to the necessity of making large scale motions and overcoming energy barriers for side chain repacking. In this study, we show that localizing packing frustration at atomic resolution by examining the statistics of the energetic changes that occur when the local environment of a site is changed allows one to identify the most likely locations of incorrect contacts. The global statistics of atomic resolution frustration in structures that have been predicted using various algorithms provide strong indicators of structural quality when tested over a database of 20 targets from previous CASP experiments. Residues that are more correctly located turn out to be more minimally frustrated than more poorly positioned sites. These observations provide a diagnosis of both global and local quality of predicted structures, and thus can be used as guidance in all-atom refinement simulations of the 20 targets. Refinement simulations guided by atomic packing frustration turn out to be quite efficient and significantly improve the quality of the structures.

Effect of strain on ADF-STEM high-resolution images

1991 ◽  
Vol 49 ◽  
pp. 666-667
Author(s):  
M. Kelly ◽  
D.M. Bird
Keyword(s):  
High Resolution ◽  
Strong Influence ◽  
Intensity Variation ◽  
Dark Field ◽  
Atomic Resolution ◽  
Strain Fields ◽  
High Resolution Image ◽  
Annular Dark Field ◽  
High Resolution Images ◽  
Interesting Alternative

It is well known that strain fields can have a strong influence on the details of HREM images. This, for example, can cause problems in the analysis of edge-on interfaces between lattice mismatched materials. An interesting alternative to conventional HREM imaging has recently been advanced by Pennycook and co-workers where the intensity variation in the annular dark field (ADF) detector is monitored as a STEM probe is scanned across the specimen. It is believed that the observed atomic-resolution contrast is correlated with the intensity of the STEM probe at the atomic sites and the way in which this varies as the probe moves from cell to cell. As well as providing a directly interpretable high-resolution image, there are reasons for believing that ADF-STEM images may be less suseptible to strain than conventional HREM. This is because HREM images arise from the interference of several diffracted beams, each of which is governed by all the excited Bloch waves in the crystal.

Electron crystallographic determination of the 3-D structure of staurolite at atomic resolution

1991 ◽  
Vol 49 ◽  
pp. 540-541
Author(s):  
Kenneth H. Downing ◽  
Hu Meisheng ◽  
Hans-Rudolf Went ◽  
Michael A. O'Keefe
Keyword(s):  
High Resolution ◽  
Three Dimensional ◽  
High Resolution Electron Microscopy ◽  
Atomic Resolution ◽  
Dimensional Structure ◽  
Structure Information ◽  
Resolution Electron ◽  
Scattering Effects ◽  
High Resolution Images ◽  
Effects Of Radiation

With current advances in electron microscope design, high resolution electron microscopy has become routine, and point resolutions of better than 2Å have been obtained in images of many inorganic crystals. Although this resolution is sufficient to resolve interatomic spacings, interpretation generally requires comparison of experimental images with calculations. Since the images are two-dimensional representations of projections of the full three-dimensional structure, information is invariably lost in the overlapping images of atoms at various heights. The technique of electron crystallography, in which information from several views of a crystal is combined, has been developed to obtain three-dimensional information on proteins. The resolution in images of proteins is severely limited by effects of radiation damage. In principle, atomic-resolution, 3D reconstructions should be obtainable from specimens that are resistant to damage. The most serious problem would appear to be in obtaining high-resolution images from areas that are thin enough that dynamical scattering effects can be ignored.

Scanning tunneling microscopy of E. coli RNA polymerase deposited onto an Au substrate by an electrochemical process

1991 ◽  
Vol 49 ◽  
pp. 378-379
Author(s):  
Rebecca W. Keller ◽  
Carlos Bustamante ◽  
David Bear
Keyword(s):  
Scanning Tunneling Microscope ◽  
Biological Sample ◽  
Substrate Surface ◽  
Electrochemical Process ◽  
Atomic Resolution ◽  
Scanning Tunneling ◽  
Tunneling Microscopy ◽  
Tunneling Microscope ◽  
E Coli ◽  
Preparation Techniques

Under ideal conditions, the Scanning Tunneling Microscope (STM) can create atomic resolution images of different kinds of samples. The STM can also be operated in a variety of non-vacuum environments. Because of its potentially high resolution and flexibility of operation, it is now being applied to image biological systems. Several groups have communicated the imaging of double and single stranded DNA.However, reproducibility is still the main problem with most STM results on biological samples. One source of irreproducibility is unreliable sample preparation techniques. Traditional deposition methods used in electron microscopy, such as glow discharge and spreading techniques, do not appear to work with STM. It seems that these techniques do not fix the biological sample strongly enough to the substrate surface. There is now evidence that there are strong forces between the STM tip and the sample and, unless the sample is strongly bound to the surface, it can be swept aside by the tip.

An atomic resolution study of a carbide phase in platinum

1992 ◽  
Vol 50 (1) ◽  
pp. 20-21
Author(s):  
M.J. Witcomb ◽  
M.A. O'Keefe ◽  
CJ. Echer ◽  
C. Nelson ◽  
J.H. Turner ◽  
...  
Keyword(s):  
Solid Solution ◽  
Carbon Atom ◽  
Carbide Phase ◽  
Structural Changes ◽  
Critical Role ◽  
Alloy System ◽  
Atomic Resolution ◽  
Excess Carbon ◽  
Interstitial Carbon ◽  
Resolution Study

Under normal circumstances, Pt dissolves only a very small amount of interstitial carbon in solid solution. Even so, an appropriate quench/age treatment leads to the formation of stable Pt2C {100} plate precipitates. Excess (quenched-in) vacancies play a critical role in the process by accommodating the volume and structural changes that accompany the transformation. This alloy system exhibits other interesting properties. Due to a large vacancy/carbon atom binding energy, Pt can absorb excess carbon at high temperatures in a carburizing atmosphere. In regions rich in carbon and vacancies, another carbide phase, Pt7C which undergoes an order-disorder reaction was formed. The present study of Pt carburized at 1160°C and aged at 515°C shows that other carbides in the PtxC series can be produced.

Faceted antiphase boundaries in GaAs grown on Ge

1987 ◽  
Vol 45 ◽  
pp. 314-315
Author(s):  
N.-H. Cho ◽  
S. McKernan ◽  
C.B. Carter ◽  
K. Wagner
Keyword(s):  
Cross Section ◽  
Atomic Resolution ◽  
Face Centered Cubic ◽  
Electrical Behavior ◽  
Sphalerite Structure ◽  
Antiphase Boundaries ◽  
Transmission Electron ◽  
Face Centered ◽  
Quality Material ◽  
Simulated Images

Interest has recently increased in the possibility of growing III-V compounds epitactically on non-polar substrates to produce device quality material. Antiphase boundaries (APBs) may then develop in the GaAs epilayer because it has sphalerite structure (face-centered cubic with a two-atom basis). This planar defect may then influence the electrical behavior of the GaAs epilayer. The orientation of APBs and their propagation into GaAs epilayers have been investigated experimentally using both flat-on and cross-section transmission electron microscope techniques. APBs parallel to (110) plane have been viewed at the atomic resolution and compared to simulated images.Antiphase boundaries were observed in GaAs epilayers grown on (001) Ge substrates. In the image shown in Fig.1, which was obtained from a flat-on sample, the (110) APB planes can be seen end-on; the faceted APB is visible because of the stacking fault-like fringes arising from a lattice translation at this interface.

Atomic resolution AEM (ARAEM) of oxide superconductors

1992 ◽  
Vol 50 (1) ◽  
pp. 74-75
Author(s):  
Vinayak P. Dravid ◽  
H. Zhang ◽  
L.D. Marks ◽  
J.P. Zhang
Keyword(s):  
Electron Microscope ◽  
Field Emission ◽  
Atomic Resolution ◽  
Oxide Superconductors ◽  
Electron Holography ◽  
Analytical Electron ◽  
Analytical Electron Microscope ◽  
Point To Point ◽  
Single Instrument ◽  
Better Than

A 200 kV cold field emission gun atomic resolution analytical electron microscope (ARAEM, Hitachi HF-2000) has been recently installed at Northwestern. The ARAEM offers an unprecedented combination of atomic structure imaging of better than 0.20 nm nominal point-to-point resolution and about 0.10 nm line resolution, alongwith nanoscale analytical capabilities and electron holography in one single instrument. The ARAEM has been fully functional/operational and this paper presents some illustrative examples of application of ARAEM techniques to oxide superconductors. Additional results will be presented at the meeting.

STM of freeze-fracture replicas: Problems and promises

1993 ◽  
Vol 51 ◽  
pp. 68-69
Author(s):  
J. T. Woodward ◽  
J. A. N. Zasadzinski
Keyword(s):  
Scanning Tunneling Microscope ◽  
Organic Materials ◽  
Freeze Fracture ◽  
Atomic Resolution ◽  
Scanning Tunneling ◽  
Tunneling Microscope ◽  
Molecular Scale ◽  
Organic Surfaces ◽  
Metal Layers ◽  
Conductive Surfaces

The Scanning Tunneling Microscope (STM) offers exciting new ways of imaging surfaces of biological or organic materials with resolution to the sub-molecular scale. Rigid, conductive surfaces can readily be imaged with the STM with atomic resolution. Unfortunately, organic surfaces are neither sufficiently conductive or rigid enough to be examined directly with the STM. At present, nonconductive surfaces can be examined in two ways: 1) Using the AFM, which measures the deflection of a weak spring as it is dragged across the surface, or 2) coating or replicating non-conductive surfaces with metal layers so as to make them conductive, then imaging with the STM. However, we have found that the conventional freeze-fracture technique, while extremely useful for imaging bulk organic materials with STM, must be modified considerably for optimal use in the STM.

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