Understanding the building-up process of three dimensional open-framework metal phosphates: Acid degradation of the 3D structures to lower dimensional structuresElectronic supplementary information (ESI) available: typical experimental parameters. See http://www.rsc.org/suppdata/cc/b2/b210037c/

2003 ◽  
pp. 366-367 ◽  
Author(s):  
Amitava Choudhury ◽  
C. N. R. Rao
Keyword(s):  
Three Dimensional ◽  
Supplementary Information ◽  
3D Structures ◽  
Metal Phosphates ◽  
Open Framework ◽  
Acid Degradation ◽  
Experimental Parameters ◽  
Lower Dimensional

scholarly journals iScore: a novel graph kernel-based function for scoring protein–protein docking models

2019 ◽  
Vol 36 (1) ◽  
pp. 112-121 ◽  
Author(s):  
Cunliang Geng ◽  
Yong Jung ◽  
Nicolas Renaud ◽  
Vasant Honavar ◽  
Alexandre M J J Bonvin ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Three Dimensional ◽  
Protein Docking ◽  
Graph Representation ◽  
Supplementary Information ◽  
Scoring Functions ◽  
Computational Docking ◽  
3D Structures ◽  
Novel Approach ◽  
Protein Interfaces

Abstract Motivation Protein complexes play critical roles in many aspects of biological functions. Three-dimensional (3D) structures of protein complexes are critical for gaining insights into structural bases of interactions and their roles in the biomolecular pathways that orchestrate key cellular processes. Because of the expense and effort associated with experimental determinations of 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D structures of biomolecular complexes. Despite recent progress, reliably distinguishing near-native docking conformations from a large number of candidate conformations, the so-called scoring problem, remains a major challenge. Results Here we present iScore, a novel approach to scoring docked conformations that combines HADDOCK energy terms with a score obtained using a graph representation of the protein–protein interfaces and a measure of evolutionary conservation. It achieves a scoring performance competitive with, or superior to, that of state-of-the-art scoring functions on two independent datasets: (i) Docking software-specific models and (ii) the CAPRI score set generated by a wide variety of docking approaches (i.e. docking software-non-specific). iScore ranks among the top scoring approaches on the CAPRI score set (13 targets) when compared with the 37 scoring groups in CAPRI. The results demonstrate the utility of combining evolutionary, topological and energetic information for scoring docked conformations. This work represents the first successful demonstration of graph kernels to protein interfaces for effective discrimination of near-native and non-native conformations of protein complexes. Availability and implementation The iScore code is freely available from Github: https://github.com/DeepRank/iScore (DOI: 10.5281/zenodo.2630567). And the docking models used are available from SBGrid: https://data.sbgrid.org/dataset/684). Supplementary information Supplementary data are available at Bioinformatics online.

Synthons and design in metal phosphates and oxalates with open architectures

2001 ◽  
Vol 57 (1) ◽  
pp. 1-12 ◽  
Author(s):  
C. N. R. Rao ◽  
Srinivasan Natarajan ◽  
Amitava Choudhury ◽  
S. Neeraj ◽  
R. Vaidhyanathan
Keyword(s):  
Linear Chain ◽  
Three Dimensional ◽  
Two Dimensional ◽  
Ladder Structure ◽  
One Dimensional ◽  
Metal Phosphates ◽  
Open Framework ◽  
Framework Materials ◽  
Layer Structures ◽  
The One

We briefly describe the structures of open-framework metal phosphates with different dimensionalities, such as the one-dimensional linear-chain and ladder structures, two-dimensional layer structures and three-dimensional structures with channels. We demonstrate the role of the zero-dimensional four-membered ring monomer and of the one-dimensional ladder structure as the starting building units or synthons involved in the formation of the complex architectures. Thus, we show how the one-dimensional ladder structure transforms to two- and three-dimensional structures under mild conditions. The two-dimensional layer structures also transform to three-dimensional structures, while the zero-dimensional monomer transforms to layered and three-dimensional structures under ordinary reaction conditions. These transformations provide an insight into the possible pathways involved in the building up of the complex structures of metal phosphates. The isolation of amine phosphates during the hydrothermal synthesis of metal phosphates and also the facile reactions between amine phosphates and metal ions to yield a variety of open-framework materials have thrown light on the mechanism of formation and design of these structures. The existence of a hierarchy of open-framework metal oxalates and their ready formation by employing amine oxalates as intermediates provides additional support to the observations made earlier with regard to the phosphates.

From Levinthal’s Paradox to the Effects of Cell Environmental Perturbation on Protein Folding

2020 ◽  
Vol 26 (42) ◽  
pp. 7537-7554 ◽  
Author(s):  
Juan Zeng ◽  
Zunnan Huang
Keyword(s):  
Protein Folding ◽  
Posttranslational Modifications ◽  
Three Dimensional ◽  
Rational Drug Design ◽  
Basic Knowledge ◽  
Sequence Evolution ◽  
3D Structures ◽  
Folding Mechanism ◽  
Cellular Environment ◽  
Environment Temperature

Background: The rapidly increasing number of known protein sequences calls for more efficient methods to predict the Three-Dimensional (3D) structures of proteins, thus providing basic knowledge for rational drug design. Understanding the folding mechanism of proteins is valuable for predicting their 3D structures and for designing proteins with new functions and medicinal applications. Levinthal’s paradox is that although the astronomical number of conformations possible even for proteins as small as 100 residues cannot be fully sampled, proteins in nature normally fold into the native state within timescales ranging from microseconds to hours. These conflicting results reveal that there are factors in organisms that can assist in protein folding. Methods: In this paper, we selected a crowded cell-like environment and temperature, and the top three Posttranslational Modifications (PTMs) as examples to show that Levinthal’s paradox does not reflect the folding mechanism of proteins. We then revealed the effects of these factors on protein folding. Results: The results summarized in this review indicate that a crowded cell-like environment, temperature, and the top three PTMs reshape the Free Energy Landscapes (FELs) of proteins, thereby regulating the folding process. The balance between entropy and enthalpy is the key to understanding the effect of the crowded cell-like environment and PTMs on protein folding. In addition, the stability/flexibility of proteins is regulated by temperature. Conclusion: This paper concludes that the cellular environment could directly intervene in protein folding. The long-term interactions of the cellular environment and sequence evolution may enable proteins to fold efficiently. Therefore, to correctly understand the folding mechanism of proteins, the effect of the cellular environment on protein folding should be considered.

scholarly journals An investigation of polyhedral deformation in two mixed-metal diarsenates: SrZnAs2O7and BaCuAs2O7

2015 ◽  
Vol 71 (4) ◽  
pp. 330-337 ◽  
Author(s):  
Sabina Kovač ◽  
Ljiljana Karanović ◽  
Tamara Đorđević
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
General Formula ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Open Framework ◽  
Geometrical Characteristics ◽  
Barium Copper

Two isostructural diarsenates, SrZnAs2O7(strontium zinc diarsenate), (I), and BaCuAs2O7[barium copper(II) diarsenate], (II), have been synthesized under hydrothermal conditions and characterized by single-crystal X-ray diffraction. The three-dimensional open-framework crystal structure consists of corner-sharingM2O5(M2 = Zn or Cu) square pyramids and diarsenate (As2O7) groups. Each As2O7group shares its five corners with five differentM2O5square pyramids. The resulting framework delimits two types of tunnels aligned parallel to the [010] and [100] directions where the large divalent nine-coordinatedM1 (M1 = Sr or Ba) cations are located. The geometrical characteristics of theM1O9,M2O5and As2O7groups of known isostructural diarsenates, adopting the general formulaM1IIM2IIAs2O7(M1II= Sr, Ba, Pb;M2II= Mg, Co, Cu, Zn) and crystallizing in the space groupP21/n, are presented and discussed.

A water-stable open-framework zirconium(IV) phosphate and its water-assisted high proton conduct

CrystEngComm ◽  
2021 ◽  
Author(s):  
Jing-Wei Yu ◽  
Hai-Jiao Yu ◽  
Zhi-Yuan Yao ◽  
Zi-Han Li ◽  
Qiu Ren ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Conducting Material ◽  
Proton Conducting ◽  
Open Framework ◽  
High Proton ◽  
3D Framework

A water stable proton-conducting material (NH4)5[Zr3(OH)3F6(PO4)2(HPO4) (ZrP) was hydrothermally synthesized. The three-dimensional (3D) framework of ZrP is composed of ZrF2O4 octahedra and HxPO4 phosphate units and forming 18-ring channels through...

scholarly journals MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX

2020 ◽  
Author(s):  
Arthur Ecoffet ◽  
Frédéric Poitevin ◽  
Khanh Dao Duc
Keyword(s):  
Optimal Transport ◽  
Three Dimensional ◽  
Linear Interpolation ◽  
The Other ◽  
Supplementary Information ◽  
Conformational Heterogeneity ◽  
Supplementary Data ◽  
Image Dataset ◽  
Standard Linear ◽  
Unique Potential

Abstract Motivation Cryogenic electron microscopy (cryo-EM) offers the unique potential to capture conformational heterogeneity, by solving multiple three-dimensional classes that co-exist within a single cryo-EM image dataset. To investigate the extent and implications of such heterogeneity, we propose to use an optimal-transport-based metric to interpolate barycenters between EM maps and produce morphing trajectories. Results While standard linear interpolation mostly fails to produce realistic transitions, our method yields continuous trajectories that displace densities to morph one map into the other, instead of blending them. Availability and implementation Our method is implemented as a plug-in for ChimeraX called MorphOT, which allows the use of both CPU or GPU resources. The code is publicly available on GitHub (https://github.com/kdd-ubc/MorphOT.git), with documentation containing tutorial and datasets. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Analysis of Te Inclusion Striations in (Cd,Zn)Te Crystals Grown by Traveling Heater Method

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 649
Author(s):  
Jiaona Zou ◽  
Alex Fauler ◽  
Alexander S. Senchenkov ◽  
Nikolai N. Kolesnikov ◽  
Michael Fiederle
Keyword(s):  
Growth Parameters ◽  
Three Dimensional ◽  
Three Dimensional Mapping ◽  
Zn Content ◽  
Experimental Parameters ◽  
Te Inclusions ◽  
Rich Solution ◽  
Traveling Heater Method ◽  
Periodic Temperature ◽  
Dimensional Mapping

The growth of (Cd,Zn)Te (CZT) crystals and the improvement of the crystal quality are part of a research project towards experiments under microgravity using the Traveling Heater Method (THM). In order to determine the experimental parameters, we performed a detailed ground-based program. Three CZT crystals with a nominal Zn content of 10% were grown using THM from a Te-rich solution. The size and distribution of the Te inclusions were evaluated by transmission infrared microscopy (IR). From the three-dimensional mapping of the inclusions, we observed striation-like patterns in all of the crystals. The correlation between the growth parameters and the formation of these striations was explored and discussed. We found that the inclusion striations are related to periodic temperature variations.

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