In Silico Characterization of Calcineurin from Pathogenic Obligate Intracellular Trypanosomatids: Potential New Biological Roles

Calcineurin (CaN) is present in all eukaryotic cells, including intracellular trypanosomatid parasites such as Trypanosoma cruzi (Tc) and Leishmania spp. (Lspp). In this study, we performed an in silico analysis of the CaN subunits, comparing them with the human (Hs) and looking their structure, post-translational mechanisms, subcellular distribution, interactors, and secretion potential. The differences in the structure of the domains suggest the existence of regulatory mechanisms and differential activity between these protozoa. Regulatory subunits are partially conserved, showing differences in their Ca2+-binding domains and myristoylation potential compared with human CaN. The subcellular distribution reveals that the catalytic subunits TcCaNA1, TcCaNA2, LsppCaNA1, LsppCaNA1_var, and LsppCaNA2 associate preferentially with the plasma membrane compared with the cytoplasmic location of HsCaNAα. For regulatory subunits, HsCaNB-1 and LsppCaNB associate preferentially with the nucleus and cytoplasm, and TcCaNB with chloroplast and cytoplasm. Calpain cleavage sites on CaNA suggest differential processing. CaNA and CaNB of these trypanosomatids have the potential to be secreted and could play a role in remote communication. Therefore, this background can be used to develop new drugs for protozoan pathogens that cause neglected disease.

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In-Vitro and In-Silico Characterization of Xylose Reductase from Emericella nidulans

Current Chemical Biology ◽

10.2174/2212796812666180622103906 ◽

2019 ◽

Vol 13 (2) ◽

pp. 159-170 ◽

Cited By ~ 1

Author(s):

Vishal Ahuja ◽

Aashima Sharma ◽

Ranju Kumari Rathour ◽

Vaishali Sharma ◽

Nidhi Rana ◽

...

Keyword(s):

Production Process ◽

In Silico ◽

Xylose Reductase ◽

In Silico Analysis ◽

Emericella Nidulans ◽

Higher Temperature ◽

In Silico Characterization ◽

Silico Analysis

Background: Lignocellulosic residues generated by various anthropogenic activities can be a potential raw material for many commercial products such as biofuels, organic acids and nutraceuticals including xylitol. Xylitol is a low-calorie nutritive sweetener for diabetic patients. Microbial production of xylitol can be helpful in overcoming the drawbacks of traditional chemical production process and lowring cost of production. Objective: Designing efficient production process needs the characterization of required enzyme/s. Hence current work was focused on in-vitro and in-silico characterization of xylose reductase from Emericella nidulans. Methods: Xylose reductase from one of the hyper-producer isolates, Emericella nidulans Xlt-11 was used for in-vitro characterization. For in-silico characterization, XR sequence (Accession No: Q5BGA7) was used. Results: Xylose reductase from various microorganisms has been studied but the quest for better enzymes, their stability at higher temperature and pH still continues. Xylose reductase from Emericella nidulans Xlt-11 was found NADH dependent and utilizes xylose as its sole substrate for xylitol production. In comparison to whole cells, enzyme exhibited higher enzyme activity at lower cofactor concentration and could tolerate higher substrate concentration. Thermal deactivation profile showed that whole cell catalysts were more stable than enzyme at higher temperature. In-silico analysis of XR sequence from Emericella nidulans (Accession No: Q5BGA7) suggested that the structure was dominated by random coiling. Enzyme sequences have conserved active site with net negative charge and PI value in acidic pH range. Conclusion: Current investigation supported the enzyme’s specific application i.e. bioconversion of xylose to xylitol due to its higher selectivity. In-silico analysis may provide significant structural and physiological information for modifications and improved stability.

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In Silico Characterization and Screening for Inhibitors of Sdia: A Protein Involved in Quorom Sensing in Escherichia Coli

International Journal of Engineering and Advanced Technology - Regular Issue ◽

10.35940/ijeat.a1147.1291s419 ◽

2019 ◽

Vol 9 (1S4) ◽

pp. 797-802

Keyword(s):

Quorum Sensing ◽

In Silico ◽

Response Regulator ◽

In Silico Analysis ◽

Structural Level ◽

E Coli ◽

Functional Aspects ◽

Regulator Protein ◽

In Silico Characterization ◽

Response Regulator Protein

Bacteria use quorum sensing as a way of inter and intra- species communication. Quorum sensing was found to be important for bacteria for various processes including establishing an infection through virulence and biofilm formation. This is mediated autoinducers, which are usually produced by one group of bacteria and recognized by another group through a response regulator protein. LuxR is a response regulator protein first discovered in Vibreo fischeri and it recognizes autoinducers produced by the same species of bacteria. E. coli also has a response regulator called SdiA which is a homolog of LuxR, originally found to be involved in transcription and cell division. SdiA was later reported to regulate quorum sensing by binding to autoinducers called Acyl Homoserine Lactones (AHLs). SdiA is also reported to be involved in enhancing the multidrug resistance and virulence in pathogenic E. coli. Though many studies elaborate the functional aspects of SdiA, sequence and structural level analysis of this protein is missing in the literature. The current work aims at the in silico analysis and targeting of SdiA with structural analogs of AHLs. 7 compounds were found to be promising molecules to inhibit quorum sensing in E. coli.

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In Silico Characterization of Ageratum Enation Virus, Ageratum Leaf Curl Betasatellite and Marigold Leaf Curl Alphasatellite Infecting an Important Ornamental Plant Marigold (Tagetes Patula) in Indian Subcontinent.

JOURNAL OF ADVANCES IN BIOTECHNOLOGY ◽

10.24297/jbt.v1i1.1781 ◽

2014 ◽

Vol 1 (1) ◽

pp. 8-21 ◽

Cited By ~ 1

Author(s):

Avinash Marwal ◽

Rajneesh Prajapat ◽

R K Gaur

Keyword(s):

In Silico ◽

Indian Subcontinent ◽

Ornamental Plants ◽

In Silico Analysis ◽

Ornamental Plant ◽

Tagetes Patula ◽

Alternate Host ◽

Depth Study ◽

In Silico Characterization ◽

Leaf Curl

Ornamental plants act as an alternate host of begomoviruses and its associated satellite molecules in the absence of main crop. Marigold (Tagetes patula) an important ornamental plant, widely cultivated in India were found infected with three begomovirus components i.e. Ageratum enation virus (AEV: KC589699), Ageratum leaf curl betasatellite (ALCB: KC589700) and Marigold leaf curl alphasatellite (MLCuA: KC206078). This study supported evidence that virus associated with Marigold was studied through In Silico analysis for in depth study. The phylogenetic studies revealed closeness to other virus prominent in other neighbouring countries and can be replicated by other begomovirus species which increases the possibility of recombination and reassortment events.

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A systematic review with in silico analysis on transcriptomic profile of gallbladder carcinoma

Seminars in Oncology ◽

10.1053/j.seminoncol.2020.02.012 ◽

2020 ◽

Vol 47 (6) ◽

pp. 398-408

Author(s):

Sonam Tulsyan ◽

Showket Hussain ◽

Balraj Mittal ◽

Sundeep Singh Saluja ◽

Pranay Tanwar ◽

...

Keyword(s):

Systematic Review ◽

Gallbladder Carcinoma ◽

In Silico ◽

In Silico Analysis ◽

Transcriptomic Profile ◽

Silico Analysis

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In Silico Analysis of Single Nucleotide Polymorphism in Human Prothrombin Gene

10.1055/s-0039-1680245 ◽

2019 ◽

Author(s):

I. Farah ◽

A. El-Mubark ◽

M. Osman ◽

A. Soliman ◽

F. Ali ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

In Silico ◽

In Silico Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Prothrombin Gene ◽

Silico Analysis

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THERMOCHEMICAL ENERGY STORAGE: FROM IN-SILICO CHARACTERIZATION TO FULL-SCALE EXPERIMENTATION

10.1615/ihtc16.kn.000024 ◽

2018 ◽

Author(s):

E. Iype ◽

Huaichen Zhang ◽

A.D. Pathak ◽

Shuiquan Lan ◽

C. Ferchaud ◽

...

Keyword(s):

Energy Storage ◽

In Silico ◽

Full Scale ◽

In Silico Characterization

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IN VITRO/IN SILICO CHARACTERIZATION OF ACTIVE AND PASSIVE STRESSES IN CARDIAC MUSCLE

International Journal for Multiscale Computational Engineering ◽

10.1615/intjmultcompeng.2011002352 ◽

2012 ◽

Vol 10 (2) ◽

pp. 171-188 ◽

Cited By ~ 7

Author(s):

Markus Boel ◽

Oscar J. Abilez ◽

Ahmed N Assar ◽

Christopher K. Zarins ◽

Ellen Kuhl

Keyword(s):

Cardiac Muscle ◽

In Silico ◽

In Silico Characterization

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Enalos Suite of Tools: Enhancing Cheminformatics and Nanoinfor - matics through KNIME

Current Medicinal Chemistry ◽

10.2174/0929867327666200727114410 ◽

2020 ◽

Vol 27 (38) ◽

pp. 6523-6535 ◽

Cited By ~ 3

Author(s):

Antreas Afantitis ◽

Andreas Tsoumanis ◽

Georgia Melagraki

Keyword(s):

Data Analysis ◽

Virtual Screening ◽

In Silico ◽

Model Development ◽

In Silico Analysis ◽

Material Design ◽

Efficient Solutions ◽

Biological Data ◽

Cost Efficient ◽

Silico Analysis

Drug discovery as well as (nano)material design projects demand the in silico analysis of large datasets of compounds with their corresponding properties/activities, as well as the retrieval and virtual screening of more structures in an effort to identify new potent hits. This is a demanding procedure for which various tools must be combined with different input and output formats. To automate the data analysis required we have developed the necessary tools to facilitate a variety of important tasks to construct workflows that will simplify the handling, processing and modeling of cheminformatics data and will provide time and cost efficient solutions, reproducible and easier to maintain. We therefore develop and present a toolbox of >25 processing modules, Enalos+ nodes, that provide very useful operations within KNIME platform for users interested in the nanoinformatics and cheminformatics analysis of chemical and biological data. With a user-friendly interface, Enalos+ Nodes provide a broad range of important functionalities including data mining and retrieval from large available databases and tools for robust and predictive model development and validation. Enalos+ Nodes are available through KNIME as add-ins and offer valuable tools for extracting useful information and analyzing experimental and virtual screening results in a chem- or nano- informatics framework. On top of that, in an effort to: (i) allow big data analysis through Enalos+ KNIME nodes, (ii) accelerate time demanding computations performed within Enalos+ KNIME nodes and (iii) propose new time and cost efficient nodes integrated within Enalos+ toolbox we have investigated and verified the advantage of GPU calculations within the Enalos+ nodes. Demonstration data sets, tutorial and educational videos allow the user to easily apprehend the functions of the nodes that can be applied for in silico analysis of data.

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In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

Current Proteomics ◽

10.2174/1570164616666190401204009 ◽

2020 ◽

Vol 17 (1) ◽

pp. 40-50

Author(s):

Farzane Kargar ◽

Amir Savardashtaki ◽

Mojtaba Mortazavi ◽

Masoud Torkzadeh Mahani ◽

Ali Mohammad Amani ◽

...

Keyword(s):

Phylogenetic Tree ◽

In Silico ◽

Alpha Helix ◽

In Silico Analysis ◽

Glycogen Storage ◽

Docking Studies ◽

Random Coil ◽

Special Topic ◽

Industrial Biotechnology ◽

In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

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