ASSESSING THE QUALITY OF THE HOMOLOGY-MODELED 3D STRUCTURES FROM ELECTROSTATIC STANDPOINT: TEST ON BACTERIAL NUCLEOSIDE MONOPHOSPHATE KINASE FAMILIES

2007 ◽  
Vol 05 (03) ◽  
pp. 693-715 ◽  
Author(s):  
PETRAS KUNDROTAS ◽  
PAULINA GEORGIEVA ◽  
ALEXANDRA SHOSHEVA ◽  
PETYA CHRISTOVA ◽  
EMIL ALEXOV
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Structural Defects ◽  
Large Protein ◽  
Homologous Proteins ◽  
X Ray ◽  
3D Structures ◽  
Large Sets

In this study, we address the issue of performing meaningful pKa calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pKa values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pKa calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pKa values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pKa calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pKa fluctuations among the models or have pKa values shifted by several pH units with respect to the pKa calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pKa calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pKa values for highly conserved titratable residues within large sets of homologous proteins.

scholarly journals Wavefront Modulation and Beam Shaping into Arbitrary Three-Dimensional Intensity Distributions

Photonics ◽  
2021 ◽  
Vol 8 (6) ◽  
pp. 179
Author(s):  
Tatiana Latychevskaia
Keyword(s):  
Three Dimensional ◽  
Beam Shaping ◽  
Intensity Modulation ◽  
Particle Trapping ◽  
X Ray ◽  
3D Structures ◽  
Spherical Waves

In this study the methods of three-dimensional (3D) wavefront intensity modulation by employing contrast-inverted holography, previously introduced as Gabor inverted holography, are further investigated. The present study provides the recipes for creating 3D wavefront intensity modulations using phase-only and amplitude-only modulators and compares the results. The 3D wavefront modulation using spherical waves is also demonstrated, and the miniaturization of 3D intensity beams is discussed; it is shown that both the resolution and the size of the created 3D structures are ultimately given by the wavelength of the employed radiation. The manuscript also addresses the quality of the formed 3D intensity curves and determines the parameters that provide the best smooth appearance of the 3D curves. The presented methods of 3D intensity wavefront modulation can be realized for all kinds of waves: light, X-ray, electron, etc, provided the modulator can be manufactured for the corresponding wavelength. The methods of 3D intensity wavefront modulation can be applied in various techniques: lithography, micro-robotics, particle trapping, etc.

scholarly journals Novel approach to computer modeling of seven-helical transmembrane proteins: current progress in the test case of bacteriorhodopsin.

2001 ◽  
Vol 48 (1) ◽  
pp. 53-64 ◽  
Author(s):  
G V Nikiforovich ◽  
S Galaktionov ◽  
J Balodis ◽  
G R Marshall
Keyword(s):  
Computer Modeling ◽  
Structure Prediction ◽  
3D Structure ◽  
3D Models ◽  
Great Accuracy ◽  
Test Case ◽  
X Ray ◽  
3D Structures ◽  
Helical Bundles ◽  
Novel Approach

G-protein coupled receptors (GPCRs) are thought to be proteins with 7-membered transmembrane helical bundles (7TM proteins). Recently, the X-ray structures have been solved for two such proteins, namely for bacteriorhodopsin (BR) and rhodopsin (Rh), the latter being a GPCR. Despite similarities, the structures are different enough to suggest that 3D models for different GPCRs cannot be obtained directly employing 3D structures of BR or Rh as a unique template. The approach to computer modeling of 7TM proteins developed in this work was capable of reproducing the experimental X-ray structure of BR with great accuracy. A combination of helical packing and low-energy conformers for loops most close to the X-ray structure possesses the r.m.s.d. value of 3.13 A. Such a level of accuracy for the 3D-structure prediction for a 216-residue protein has not been achieved, so far, by any available ab initio procedure of protein folding. The approach may produce also other energetically consistent combinations of helical bundles and loop conformers, creating a variety of possible templates for 3D structures of 7TM proteins, including GPCRs. These templates may provide experimentalists with various plausible options for 3D structure of a given GPCR; in our view, only experiments will determine the final choice of the most reasonable 3D template.

scholarly journals Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

RNA ◽  
2021 ◽  
pp. rna.078685.121
Author(s):  
Francisco Carrascoza ◽  
Maciej Antczak ◽  
Zhichao Miao ◽  
Eric Westhof ◽  
Marta Szachniuk
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Data Bank ◽  
3D Models ◽  
Its Sequence ◽  
In Silico Prediction ◽  
General Shape ◽  
Stereochemical Quality ◽  
Three Dimensional Models

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of RNA stereochemistry that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure modelling approaches.

Study the precision of creating 3D structure modeling form terrestrial laser scanner observations

2018 ◽  
Vol 12 (4) ◽  
pp. 303-309
Author(s):  
Zaki M. Zeidan ◽  
Ashraf A. Beshr ◽  
Ashraf G. Shehata
Keyword(s):  
Structural Model ◽  
3D Structure ◽  
Three Dimensional ◽  
Laser Scanner ◽  
Field Tests ◽  
3D Models ◽  
Terrestrial Laser Scanner ◽  
Analysis Of Results ◽  
3D Structure Modeling

Abstract Laser scanner has become widely used nowadays for several applications in civil engineering. An advantage of laser scanner as compared to other geodetic instruments is its capability of collecting hundreds or even thousands of point per second. Terrestrial laser scanner allows acquiring easy and fast complex geometric data from building, machines, objects, etc. Several experimental and field tests are required to investigate the quality and accuracy of scanner points cloud and the 3D geometric models derived from laser scanner. So this paper investigates the precision of creation three dimensional structural model resulted from terrestrial laser scanner observations. The paper also presented the ability to create 3D model by structural faces depending on the plane equation for each face resulted from coordinates of several observed points cover this face using reflector less total station observations. Precision comparison for the quality of 3D models created from laser scanner observations and structure faces is also presented.The results of the practical measurements, calculations and analysis of results are presented.

scholarly journals Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions

2021 ◽  
Author(s):  
Francisco Carrascoza ◽  
Maciej Antczak ◽  
Zhichao Miao ◽  
Eric Westhof ◽  
Marta Szachniuk
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Data Bank ◽  
3D Models ◽  
In Silico Prediction ◽  
General Shape ◽  
Stereochemical Quality ◽  
Three Dimensional Models

In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports on the stereochemical quality of the RNA three-dimensional models predicted using dedicated computer programs. The stereochemistry of 1,052 RNA 3D structures, including 1,030 models predicted by fully automated and human-guided approaches within 22 RNA-Puzzles challenges and reference structures, is analysed. The evaluation is based on standards of stereochemistry, established for RNA, that the Protein Data Bank requires from deposited experimental structures. Deviations from standard bond lengths and angles, planarity or chirality are quantified. A reduction in the number of such deviations should help in the improvement of RNA 3D structure prediction accuracy.

scholarly journals Synthesis of Three-Dimensional Fe3O4/Graphene Aerogels for the Removal of Arsenic Ions from Water

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Yan Ye ◽  
Da Yin ◽  
Bin Wang ◽  
Qingwen Zhang
Keyword(s):  
Electron Microscopy ◽  
Photoelectron Spectroscopy ◽  
3D Structure ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Graphene Aerogels ◽  
Transmission Electron ◽  
Potential Applications ◽  
Removal Of Arsenic

We report the synthesis of three-dimensional Fe3O4/graphene aerogels (GAs) and their application for the removal of arsenic (As) ions from water. The morphology and properties of Fe3O4/GAs have been characterized by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, X-ray photoelectron spectroscopy, and superconducting quantum inference device. The 3D nanostructure shows that iron oxide nanoparticles are decorated on graphene with an interconnected network structure. It is found that Fe3O4/GAs own a capacity of As(V) ions adsorption up to 40.048 mg/g due to their remarkable 3D structure and existence of magnetic Fe3O4nanoparticles for separation. The adsorption isotherm matches well with the Langmuir model and kinetic analysis suggests that the adsorption process is pseudo-second-ordered. In addition to the excellent adsorption capability, Fe3O4/GAs can be easily and effectively separated from water, indicating potential applications in water treatment.

Online quality evaluation of tissue paper structure on new generation tissue machines

2018 ◽  
Vol 33 (1) ◽  
pp. 133-141 ◽  
Author(s):  
Jukka-Pekka Raunio ◽  
Tommi Löyttyniemi ◽  
Risto Ritala
Keyword(s):  
3D Structure ◽  
Three Dimensional ◽  
Surface Profile ◽  
Absorption Capacity ◽  
Tissue Paper ◽  
Paper Manufacturing ◽  
Residual Variation ◽  
Residual Variances ◽  
New Generation

Abstract At present, the tissue paper manufacturing is mostly based on the dry crepe technology. During the last decade, the manufacturers have introduced new tissue machines concepts that increase the softness, bulk, and absorption capacity. Such machines produce a strong regular three-dimensional (3D) structure to the sheet before the Yankee cylinder. At present, the quality of the 3D structure is not evaluated, or it is evaluated only subjectively at the mill. This is mostly because of the difficulties to separate reliably the regular 3D pattern from other variations. This paper introduces a frequency analysis based method which separates the surface profile variances in tissue paper to the creping, to the regular 3D pattern and to the residual variation. The 3D surface profiles and their variances were determined online with the photometric stereo method. We show that the introduced analysis method evaluates the variance portions reliably and the results are consistent with the visual perception of the 3D surfaces. In one particular product, the regular 3D pattern explains 74 % of total surface variance; the creping explains 10 % and residual variations 16 %. Furthermore, the creping and residual variances are quite stable over time whereas the variance of the regular 3D pattern fluctuates significantly.

scholarly journals Three-dimensional propagation in near-field tomographic X-ray phase retrieval

2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt
Keyword(s):  
Phase Retrieval ◽  
Near Field ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Current Phase ◽  
Computationally Efficient ◽  
X Ray ◽  
Reconstruction Quality ◽  
Consistency Constraints

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

Solving the 3D structure of metal nanoparticles

2007 ◽  
Vol 222 (11/2007) ◽  
Author(s):  
Anatoly Frenkel
Keyword(s):  
Metal Nanoparticles ◽  
Short Range ◽  
Short Range Order ◽  
3D Structure ◽  
Three Dimensional ◽  
X Ray ◽  
Particle Distributions ◽  
Structure Of Metal ◽  
X Ray Absorption

We discuss methods of Extended X-ray Absorption Fine-Structure (EXAFS) analysis that provide three-dimensional structural characterization of metal nanoparticles, both mono- and bi-metallic. For the bimetallic alloys, we use short range order measurements to discriminate between random and non-random inter-particle distributions of atoms. We also discuss the application of EXAFS to heterogeneous nanoparticle systems.

A modified discrete tomography for improving the reconstruction of unknown multi-gray-level material in the `missing wedge' situation

2018 ◽  
Vol 25 (6) ◽  
pp. 1847-1859 ◽  
Author(s):  
Jianhong Liu ◽  
Zhiting Liang ◽  
Yong Guan ◽  
Wenbin Wei ◽  
Haobo Bai ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Iteration Process ◽  
Reconstruction Technique ◽  
Morphological Operations ◽  
Algebraic Reconstruction Technique ◽  
Discrete Tomography ◽  
Boundary Extraction ◽  
X Ray ◽  
Dimensional Reconstruction

Full angular rotational projections cannot always be acquired in tomographic reconstructions because of the limited space in the experimental setup, leading to the `missing wedge' situation. In this paper, a recovering `missing wedge' discrete algebraic reconstruction technique algorithm (rmwDART) has been proposed to solve the `missing wedge' problem and improve the quality of the three-dimensional reconstruction without prior knowledge of the material component's number or the material's values. By using oversegmentation, boundary extraction and mathematical morphological operations, `missing wedge' artifact areas can be located. Then, in the iteration process, by updating the located areas and regions, high-quality reconstructions can be obtained from the simulations, and the reconstructed images based on the rmwDART algorithm can be obtained from soft X-ray nano-computed tomography experiments. The results showed that there is the potential for discrete tomography.

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