scholarly journals Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions

2021 ◽  
Author(s):  
Julita Gumna ◽  
Maciej Antczak ◽  
Ryszard Walenty Adamiak ◽  
Janusz Marek Bujnicki ◽  
Shi-Jie Chen ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Untranslated Regions ◽  
Dimensional Structure ◽  
Consensus Structure ◽  
Computational Tools ◽  
Functional Regions

The outbreak of the COVID-19 pandemic has led to intensive studies of both the structure and replication mechanism of SARS-CoV-2. In spite of some secondary structure experiments being carried out, the 3D structure of the key functional regions of the viral RNA has not yet been well understood. At the beginning of COVID-19 breakout, the RNA-Puzzles community attempted to envisage the three-dimensional structure of 5′- and 3′-Un-Translated Regions (UTRs) of the SARS-CoV-2 genome. Here, we report the results of this prediction challenge, presenting the methodologies developed by six participating groups and discussing 100 RNA 3D models (60 models of 5′-UTR and 40 of 3′-UTR) predicted through applying both human experts and automated server approaches. We describe the original protocol for the reference-free comparative analysis of RNA 3D structures designed especially for this challenge. We elaborate on the deduced consensus structure and the reliability of the predicted structural motifs. All the computationally simulated models, as well as the development and the testing of computational tools dedicated to 3D structure analysis, are available for further study.

scholarly journals Molecular Cloning, Modeling, and Characterization of Type 2 Metallothionein from Plantago ovata Forsk

Sequencing ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Amitava Moulick ◽  
Debashis Mukhopadhyay ◽  
Shonima Talapatra ◽  
Nirmalya Ghoshal ◽  
Sarmistha Sen Raychaudhuri
Keyword(s):  
Molecular Cloning ◽  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Transcript Level ◽  
Copper Stress ◽  
Dimensional Structure ◽  
Functional Study ◽  
Plantago Ovata

Plantago ovata Forsk is a medicinally important plant. Metallothioneins are cysteine rich proteins involved in the detoxification of heavy metals. Molecular cloning and modeling of MT from P. ovata is not reported yet. The present investigation will describe the isolation, structure prediction, characterization, and expression under copper stress of type 2 metallothionein (MT2) from this species. The gene of the protein comprises three exons and two introns. The deduced protein sequence contains 81 amino acids with a calculated molecular weight of about 8.1 kDa and a theoretical pI value of 4.77. The transcript level of this protein was increased in response to copper stress. Homology modeling was used to construct a three-dimensional structure of P. ovata MT2. The 3D structure model of P. ovata MT2 will provide a significant clue for further structural and functional study of this protein.

scholarly journals REALDIST: Real-valued protein distance prediction

2020 ◽  
Author(s):  
Badri Adhikari
Keyword(s):  
Structure Prediction ◽  
3D Structure ◽  
Three Dimensional ◽  
Prediction Method ◽  
3D Models ◽  
Classification Problem ◽  
Intermediate Step ◽  
Protein Distance ◽  
Multi Class Classification ◽  
Distance Prediction

AbstractProtein structure prediction continues to stand as an unsolved problem in bioinformatics and biomedicine. Deep learning algorithms and the availability of metagenomic sequences have led to the development of new approaches to predict inter-residue distances—the key intermediate step. Different from the recently successful methods which frame the problem as a multi-class classification problem, this article introduces a real-valued distance prediction method REALDIST. Using a representative set of 43 thousand protein chains, a variant of deep ResNet is trained to predict real-valued distance maps. The contacts derived from the real-valued distance maps predicted by this method, on the most difficult CASP13 free-modeling protein datasets, demonstrate a long-range top-L precision of 52%, which is 17% higher than the top CASP13 predictor Raptor-X and slightly higher than the more recent trRosetta method. Similar improvements are observed on the CAMEO ‘hard’ and ‘very hard’ datasets. Three-dimensional (3D) structure prediction guided by real-valued distances reveals that for short proteins the mean accuracy of the 3D models is slightly higher than the top human predictor AlphaFold and server predictor Quark in the CASP13 competition.

scholarly journals Identification and “in silico” Structural Analysis of the Glutamine-rich Protein Qrp (YheA) in Staphylococcus Aureus

2019 ◽  
Vol 12 (1) ◽  
pp. 18-29
Author(s):  
Javier Escobar-Perez ◽  
Katterine Ospina-Garcia ◽  
Zayda Lorena Corredor Rozo ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Jaime E Castellanos ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Structural Analysis ◽  
Protein Function ◽  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Models ◽  
Protein Domain ◽  
Dimensional Structure ◽  
Biofilm Growth

Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.

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 RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

RNA ◽  
2012 ◽  
Vol 18 (4) ◽  
pp. 610-625 ◽  
Author(s):  
J. A. Cruz ◽  
M.-F. Blanchet ◽  
M. Boniecki ◽  
J. M. Bujnicki ◽  
S.-J. Chen ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure

scholarly journals Analysis of structural similarities between brain Thy-1 antigen and immunoglobulin domains. Evidence for an evolutionary relationship and a hypothesis for its functional significance

1981 ◽  
Vol 195 (1) ◽  
pp. 31-40 ◽  
Author(s):  
F E Cohen ◽  
J Novotný ◽  
M J E Sternberg ◽  
D G Campbell ◽  
A F Williams
Keyword(s):  
Functional Significance ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Evolutionary Relationship ◽  
Dimensional Structure ◽  
Sequence Homologies ◽  
Beta Structure ◽  
Beta 2 Microglobulin

The Thy-1 membrane glycoprotein from rat brain is shown to have structural and sequence homologies with immunoglobulin (Ig) domains on the basis of the following evidence. 1. The two disulphide bonds of Thy-1 are both consistent with the Ig-fold. 2. The molecule contains extensive beta-structure as shown by the c.d. spectrum. 3. Secondary structure prediction locates beta-strands along the sequence in a manner consistent with the Ig-fold. 4. On the basis of rules derived from known beta-sheet structures, a three-dimensional structure with the Ig-fold is predicted as favourable for Thy-1. 5. Sequences in the proposed beta-strands of Thy-1 and known beta-strands of Ig domains show significant sequence homology. This homology is statistically more significant than for the comparison of proposed beta-strand sequences of beta 2-microglobulin with Ig domains. An hypothesis is presented for the possible functional significance of an evolutionary relationship between Thy-1 and Ig. It is suggested that both Thy-1 and Ig evolved from primitive molecules, with an Ig fold, which mediated cell--cell interactions. The present-day role of Thy-1 may be similar to that of the primitive domain.

3D Structure of Striations in the North Pacific

2021 ◽  
Author(s):  
YU ZHANG ◽  
YU PING GUAN ◽  
RUI XIN HUANG
Keyword(s):  
North Pacific ◽  
3D Structure ◽  
Three Dimensional ◽  
Vertical Plane ◽  
Dimensional Structure ◽  
The North ◽  
Layer Analysis ◽  
Fluid Potential ◽  
The North Pacific

AbstractOcean striations are composed of alternating quasi-zonal band-like flows; this kind of organized structure of currents be found in all world’s oceans and seas. Previous studies have mainly been focused on the mechanisms of their generation and propagation. This study uses the spatial high-pass filtering to obtain the three-dimensional structure of ocean striations in the North Pacific in both the z-coordinate and σ-coordinate based on 10-yr averaged SODA3 data. First, we identify an ideal-fluid potential density domain where the striations are undisturbed by the surface forcing and boundary effects. Second, using the isopycnal layer analysis, we show that on isopycnal surfaces the orientations of striations nearly follow the potential vorticity (PV) contours, while in the meridional-vertical plane the central positions of striations are generally aligned with the latitude of zero gradient of the relative PV. Our analysis provides a simple dynamical interpretation and better understanding for the role of ocean striations.

Prediction of Structural and Functional Aspects of Protein

2014 ◽  
pp. 317-333
Author(s):  
Arun G. Ingale
Keyword(s):  
Protein Structure ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Sequence Information ◽  
Predict Protein Structure ◽  
Basic Ideas

To predict the structure of protein from a primary amino acid sequence is computationally difficult. An investigation of the methods and algorithms used to predict protein structure and a thorough knowledge of the function and structure of proteins are critical for the advancement of biology and the life sciences as well as the development of better drugs, higher-yield crops, and even synthetic bio-fuels. To that end, this chapter sheds light on the methods used for protein structure prediction. This chapter covers the applications of modeled protein structures and unravels the relationship between pure sequence information and three-dimensional structure, which continues to be one of the greatest challenges in molecular biology. With this resource, it presents an all-encompassing examination of the problems, methods, tools, servers, databases, and applications of protein structure prediction, giving unique insight into the future applications of the modeled protein structures. In this chapter, current protein structure prediction methods are reviewed for a milieu on structure prediction, the prediction of structural fundamentals, tertiary structure prediction, and functional imminent. The basic ideas and advances of these directions are discussed in detail.

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