Porotectosilicate Structure Determination from Model Building

1981 ◽  
pp. 49-61 ◽  
Author(s):  
George T. Kokotailo ◽  
John L. Schlenker
Keyword(s):  
Structure Determination ◽  
Model Building

Parakeet hemoglobin – its crystal structure and oxygen affinity in relation to some avian hemoglobins

2020 ◽  
Vol 27 ◽  
Author(s):  
S.M. Jaimohan ◽  
M.D. Naresh ◽  
A.B. Mandal
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Oxygen Affinity ◽  
Diffusion Method ◽  
Data Set ◽  
X Ray ◽  
Loop Region ◽  
Psittacula Krameri

Background: “Avians” often show efficient oxygen management to meet the demands of their metabolism. Hemoglobin, a transporter protein consists of four non-covalently linked subunits contain haem binding hydrophobic pocket serves as a site of allosteric cooperativity. The physiology and anatomy of both mammals and avian are functionally different, in birds, the respiratory system formed by small air sacs that serve as tidal ventilation for the lungs and have no significant exchange across their cells. Parakeet (Psittacula Krameri) a tropical and non-migrating species and it is easily adapted to living in disturbed habitat. The sequence analysis reveals that α and β chain of parakeet hemoglobin highly similar grey lag goose and bar headed goose hemoglobin respectively. Thus it has been tempted us to study in to analyzing the sequence and structural comparison of this hemoglobin to find out the physiological capabilities of parakeet hemoglobin. Objective: The structure determination studies of parakeet hemoglobin by X-ray diffraction. The sequence and structure are compared with goose, chicken and human Hb, emphasizing the role of amino acids in the subunit contacts that facilitate survival by low oxygen demand. Methods: The Hb was purified and crystallized by hanging drop vapor diffusion method using poly ethylene glycol (PEG) 3350 and sodium phosphate buffer. X-ray diffracted data set was collected at 3Å resolution, the data was processed in Automar and molecular replacement, refinements, model building was carried out in CCP4i program package. The final refined model was deposited in protein data bank with accession id 2zfb. Results: The tertiary structure of Parakeet Hb is compared with the met form of BHG Hb (1c40) and oxy form of GLG (1faw) and oxy form of human Hbs (1hho). Superimposing parakeet Hb α1β1 subunit with ‘R’ state human Hb shows an r.m.s.d of 0.98 Å and for BHG and GLG Hb, the r.m.s.d shows 0.72 and 0.61 Å. The replacement of α115Asp in parakeet Hb as against the α115Glu in human Hb results in the movement of GH corners. The amino acid proline at α50 present only in Parakeet Hb and Chicken HbD and not present in any other avian family which includes human Hb. The residue α78Thr located in EF corner loop region, which slightly diverge when superimposing with human and BHG Hb and also replacement of α113Asn present only in Parakeet Hb placed near the FG helix corner. Conclusion: The present study describes the structure determination of parakeet hemoglobin and its structural features to understand its oxygen affinity characteristics. The crystals were obtained by buffered low-salt conditions, like those of chicken HbD, carbonmonoxy and cyanomet human Hb. The present study reveals several interesting and unique modifications in the finer aspects of the quaternary structure of parakeet Hb, which are involved in oxygen affinity characteristics and the α1β1 subunit contacts. Crystallization of parakeet Hb with allosteric effectors like Inositol pentaphosphate may bring further understanding of the influence of physiological and environmental factors on the quaternary structure.

A fragmentation and reassembly method forab initiophasing

2015 ◽  
Vol 71 (2) ◽  
pp. 304-312 ◽  
Author(s):  
Rojan Shrestha ◽  
Kam Y. J. Zhang
Keyword(s):  
Ab Initio ◽  
Structure Determination ◽  
Model Building ◽  
De Novo ◽  
Sequence Information ◽  
Molecular Replacement ◽  
Protein Targets ◽  
Current State ◽  
Viable Approach ◽  
Automated Model Building

Ab initiophasing withde novomodels has become a viable approach for structural solution from protein crystallographic diffraction data. This approach takes advantage of the known protein sequence information, predictsde novomodels and uses them for structure determination by molecular replacement. However, even the current state-of-the-artde novomodelling method has a limit as to the accuracy of the model predicted, which is sometimes insufficient to be used as a template for successful molecular replacement. A fragment-assembly phasing method has been developed that starts from an ensemble of low-accuracyde novomodels, disassembles them into fragments, places them independently in the crystallographic unit cell by molecular replacement and then reassembles them into a whole structure that can provide sufficient phase information to enable complete structure determination by automated model building. Tests on ten protein targets showed that the method could solve structures for eight of these targets, although the predictedde novomodels cannot be used as templates for successful molecular replacement since the best model for each target is on average more than 4.0 Å away from the native structure. The method has extended the applicability of theab initiophasing byde novomodels approach. The method can be used to solve structures when the bestde novomodels are still of low accuracy.

scholarly journals Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

2021 ◽  
Vol 118 (41) ◽  
pp. e2115001118
Author(s):  
Xudong Wu ◽  
Tom A. Rapoport
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
De Novo ◽  
Binding Protein ◽  
Protein A ◽  
Fab Fragment ◽  
Binding Domains ◽  
Binding Interface ◽  
Small Proteins

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: 1) a Fab fragment of an antibody directed against the nanobody and 2) a nanobody-binding protein A fragment fused to maltose binding protein and Fab-binding domains. The overall ensemble of ∼120 kDa, called Legobody, does not perturb the nanobody–target interaction, is easily recognizable in EM images due to its unique shape, and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23-kDa membrane protein, resulting in a map at 3.2-Å overall resolution with density sufficient for de novo model building, and for the 22-kDa receptor-binding domain (RBD) of SARS-CoV-2 spike protein, resulting in a map at 3.6-Å resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

Porotectosilicate Structure Determination from Model Building

1980 ◽  
Vol 24 ◽  
pp. 49-61
Author(s):  
George T. Kokotailo ◽  
John L. Schlenker
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Model Building ◽  
Stacking Faults ◽  
Isomorphous Substitution ◽  
Crystalline Materials ◽  
Model Crystal ◽  
Small Crystals ◽  
Crystal Twinning

AbstractPorotectosilicates are a class of siliceous crystalline materials which includes both zeolites and materials which resemble zeolites in crystal structure, but may or may not have ion exchange capability. The framework structures of these porotectosilicates are comprised of “T” atoms tetrahedrally coordinated to oxygen, where “T” can be Al, Si or any other element capable of isomorphous substitution for silicon. The occurrence of small crystals and the additional problems introduced by the presence of stacking faults and crystal twinning make structure determination of porotectosilicates by conventional approaches difficult.The industrial significance of these materials has led to the development of a technique which permits the determination of their structure. The method involves the construction of appropriate hypothetical models, a DLS refinement followed by computation of a Smith plot for comparison with the experimental powder pattern. Model crystal structures may now be refined using the Rietveld technique. It is expected that this technique will contribute significantly to the solution of porotectosilicate structures which are difficult--if not impossible--to establish by other techniques.

scholarly journals Deep learning enables the atomic structure determination of the Fanconi Anemia core complex from cryoEM

IUCrJ ◽  
2020 ◽  
Vol 7 (5) ◽  
pp. 881-892
Author(s):  
Daniel P. Farrell ◽  
Ivan Anishchenko ◽  
Shabih Shakeel ◽  
Anna Lauko ◽  
Lori A. Passmore ◽  
...  
Keyword(s):  
Deep Learning ◽  
Fanconi Anemia ◽  
Structure Determination ◽  
Model Building ◽  
Protein Complexes ◽  
Structural Features ◽  
Coarse Grained ◽  
Core Complex ◽  
Distance Distributions

Cryo-electron microscopy of protein complexes often leads to moderate resolution maps (4–8 Å), with visible secondary-structure elements but poorly resolved loops, making model building challenging. In the absence of high-resolution structures of homologues, only coarse-grained structural features are typically inferred from these maps, and it is often impossible to assign specific regions of density to individual protein subunits. This paper describes a new method for overcoming these difficulties that integrates predicted residue distance distributions from a deep-learned convolutional neural network, computational protein folding using Rosetta, and automated EM-map-guided complex assembly. We apply this method to a 4.6 Å resolution cryoEM map of Fanconi Anemia core complex (FAcc), an E3 ubiquitin ligase required for DNA interstrand crosslink repair, which was previously challenging to interpret as it comprises 6557 residues, only 1897 of which are covered by homology models. In the published model built from this map, only 387 residues could be assigned to the specific subunits with confidence. By building and placing into density 42 deep-learning-guided models containing 4795 residues not included in the previously published structure, we are able to determine an almost-complete atomic model of FAcc, in which 5182 of the 6557 residues were placed. The resulting model is consistent with previously published biochemical data, and facilitates interpretation of disease-related mutational data. We anticipate that our approach will be broadly useful for cryoEM structure determination of large complexes containing many subunits for which there are no homologues of known structure.

scholarly journals Use of noncrystallographic symmetry for automated model building at medium to low resolution

2012 ◽  
Vol 68 (4) ◽  
pp. 446-453 ◽  
Author(s):  
Tim Wiegels ◽  
Victor S. Lamzin
Keyword(s):  
Crystal Structure ◽  
Electron Density ◽  
Structure Determination ◽  
Model Building ◽  
Average Length ◽  
Automatic Detection ◽  
Test Cases ◽  
Molecular Fragments ◽  
Novel Method ◽  
Automated Model Building

A novel method is presented for the automatic detection of noncrystallographic symmetry (NCS) in macromolecular crystal structure determination which does not require the derivation of molecular masks or the segmentation of density. It was found that throughout structure determination the NCS-related parts may be differently pronounced in the electron density. This often results in the modelling of molecular fragments of variable length and accuracy, especially during automated model-building procedures. These fragments were used to identify NCS relations in order to aid automated model building and refinement. In a number of test cases higher completeness and greater accuracy of the obtained structures were achieved, specifically at a crystallographic resolution of 2.3 Å or poorer. In the best case, the method allowed the building of up to 15% more residues automatically and a tripling of the average length of the built fragments.

Graphical user interface for the program FraGen

2019 ◽  
Vol 52 (6) ◽  
pp. 1455-1459
Author(s):  
Chao Wang ◽  
Yueju Wei ◽  
Bing Yang ◽  
Yi Li
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Structure Determination ◽  
High Efficiency ◽  
Model Building ◽  
Real Space ◽  
Space Structure ◽  
Experimental Results ◽  
Building Structure ◽  
Xrd Patterns

FraGen is a real-space structure determination program capable of building structure models of inorganic extended frameworks. Despite its high efficiency in model building, it does not have a graphical user interface (GUI), which makes the input of instructions and the interpretation of results rather difficult. In this work, a Python GUI for FraGen has been developed. Using FraGen-GUI, users can easily prepare their instruction files for FraGen and visualize the corresponding output directly. More importantly, it can be used to remove duplicate models generated by FraGen, add bridging atoms that are missing in FraGen simulations and simulate XRD patterns for comparison with experimental results.

scholarly journals Direct phase selection of initial phases from single-wavelength anomalous dispersion (SAD) for the improvement of electron density andab initiostructure determination

2014 ◽  
Vol 70 (9) ◽  
pp. 2331-2343 ◽  
Author(s):  
Chung-De Chen ◽  
Yen-Chieh Huang ◽  
Hsin-Lin Chiang ◽  
Yin-Cheng Hsieh ◽  
Hong-Hsiang Guan ◽  
...  
Keyword(s):  
Electron Density ◽  
Structure Determination ◽  
Model Building ◽  
Correlation Coefficients ◽  
Selection Method ◽  
Anomalous Dispersion ◽  
Biological Macromolecules ◽  
Phase Selection ◽  
Phase Errors ◽  
Density Maps

Optimization of the initial phasing has been a decisive factor in the success of the subsequent electron-density modification, model building and structure determination of biological macromolecules using the single-wavelength anomalous dispersion (SAD) method. Two possible phase solutions (ϕ1and ϕ2) generated from two symmetric phase triangles in the Harker construction for the SAD method cause the well known phase ambiguity. A novel direct phase-selection method utilizing the θDSlist as a criterion to select optimized phases ϕamfrom ϕ1or ϕ2of a subset of reflections with a high percentage of correct phases to replace the corresponding initial SAD phases ϕSADhas been developed. Based on this work, reflections with an angle θDSin the range 35–145° are selected for an optimized improvement, where θDSis the angle between the initial phase ϕSADand a preliminary density-modification (DM) phase ϕDMNHL. The results show that utilizing the additional direct phase-selection step prior to simple solvent flattening without phase combination using existing DM programs, such asRESOLVEorDMfromCCP4, significantly improves the final phases in terms of increased correlation coefficients of electron-density maps and diminished mean phase errors. With the improved phases and density maps from the direct phase-selection method, the completeness of residues of protein molecules built with main chains and side chains is enhanced for efficient structure determination.

Structure solution of zeolites from powder diffraction data

2004 ◽  
Vol 219 (12) ◽  
Author(s):  
Allen W. Burton
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Structure Determination ◽  
Structure Elucidation ◽  
Model Building ◽  
Direct Methods ◽  
Powder Diffraction Data ◽  
Zeolite Structure ◽  
Structure Solution

AbstractThis article reviews methods in structure determination of zeolites from powder diffraction data. First, examples of different model building techniques are discussed. Then the applications and limitations of conventional direct methods in zeolite structure solution are examined. Methods for partitioning overlapping peak intensities are also discussed, and examples are given to illustrate improvements in structure elucidation when these techniques are applied.

scholarly journals Cryo-EM structure determination of small proteins by nanobody-binding scaffolds (Legobodies)

2021 ◽  
Author(s):  
Xudong Wu ◽  
Tom A Rapoport
Keyword(s):  
Structure Determination ◽  
Model Building ◽  
De Novo ◽  
Binding Protein ◽  
Protein A ◽  
Fab Fragment ◽  
Binding Domains ◽  
Binding Interface ◽  
Small Proteins

We describe a general method that allows structure determination of small proteins by single-particle cryo-electron microscopy (cryo-EM). The method is based on the availability of a target-binding nanobody, which is then rigidly attached to two scaffolds: (1) a Fab-fragment of an antibody directed against the nanobody, and (2) a nanobody-binding protein A fragment fused to maltose-binding protein and Fab-binding domains. The overall ensemble of ~120 kDa, called Legobody, does not perturb the nanobody-target interaction and facilitates particle alignment in cryo-EM image processing. The utility of the method is demonstrated for the KDEL receptor, a 23 kDa membrane protein, resulting in a map at 3.2 Angstrom overall resolution with density sufficient for de novo model building, and for the 22 kDa RBD of SARS-CoV2 spike protein, resulting in a map at 3.6 Angstrom overall resolution that allows analysis of the binding interface to the nanobody. The Legobody approach thus overcomes the current size limitations of cryo-EM analysis.

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