scholarly journals Computational Study on Temperature Driven Structure–Function Relationship of Polysaccharide Producing Bacterial Glycosyl Transferase Enzyme

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1771
Author(s):  
Patricio González-Faune ◽  
Ignacio Sánchez-Arévalo ◽  
Shrabana Sarkar ◽  
Krishnendu Majhi ◽  
Rajib Bandopadhyay ◽  
...  
Keyword(s):  
Structural Integrity ◽  
Computational Study ◽  
In Silico Analysis ◽  
Temperature Dependent ◽  
Bacterial Exopolysaccharide ◽  
Function Relationship ◽  
Industrial Level ◽  
Relationship Of ◽  
Bacterial Sources ◽  
Silico Analysis

Glycosyltransferase (GTs) is a wide class of enzymes that transfer sugar moiety, playing a key role in the synthesis of bacterial exopolysaccharide (EPS) biopolymer. In recent years, increased demand for bacterial EPSs has been observed in pharmaceutical, food, and other industries. The application of the EPSs largely depends upon their thermal stability, as any industrial application is mainly reliant on slow thermal degradation. Keeping this in context, EPS producing GT enzymes from three different bacterial sources based on growth temperature (mesophile, thermophile, and hyperthermophile) are considered for in silico analysis of the structural–functional relationship. From the present study, it was observed that the structural integrity of GT increases significantly from mesophile to thermophile to hyperthermophile. In contrast, the structural plasticity runs in an opposite direction towards mesophile. This interesting temperature-dependent structural property has directed the GT–UDP-glucose interactions in a way that thermophile has finally demonstrated better binding affinity (−5.57 to −10.70) with an increased number of hydrogen bonds (355) and stabilizing amino acids (Phe, Ala, Glu, Tyr, and Ser). The results from this study may direct utilization of thermophile-origin GT as best for industrial-level bacterial polysaccharide production.

scholarly journals Structure-Function Relationship of Cytoplasmic and Nuclear IκB Proteins: An In Silico Analysis

PLoS ONE ◽  
2010 ◽  
Vol 5 (12) ◽  
pp. e15782 ◽  
Author(s):  
Balachandran Manavalan ◽  
Shaherin Basith ◽  
Yong-Min Choi ◽  
Gwang Lee ◽  
Sangdun Choi
Keyword(s):  
Structure Function ◽  
In Silico ◽  
In Silico Analysis ◽  
Structure Function Relationship ◽  
Function Relationship ◽  
Relationship Of ◽  
Silico Analysis

scholarly journals CriTER-A: A Novel Temperature-Dependent Noncoding RNA Switch in the Telomeric Transcriptome of Chironomus riparius

2021 ◽  
Vol 22 (19) ◽  
pp. 10310
Author(s):  
Cristina Romero-López ◽  
Alfredo Berzal-Herranz ◽  
José Luis Martínez-Guitarte ◽  
Mercedes de la Fuente
Keyword(s):  
Thermal Stress ◽  
Noncoding Rna ◽  
Relative Proportion ◽  
Chironomus Riparius ◽  
Temperature Dependent ◽  
Differential Behaviour ◽  
High Sequence Homology ◽  
Function Relationship ◽  
Relationship Of

The telomeric transcriptome of Chironomus riparius has been involved in thermal stress response. One of the telomeric transcripts, the so-called CriTER-A variant, is highly overexpressed upon heat shock. On the other hand, its homologous variant CriTER-B, which is the most frequently encoded noncoding RNA in the telomeres of C. riparius, is only slightly affected by thermal stress. Interestingly, both transcripts show high sequence homology, but less is known about their folding and how this could influence their differential behaviour. Our study suggests that CriTER-A folds as two different conformers, whose relative proportion is influenced by temperature conditions. Meanwhile, the CriTER-B variant shows only one dominant conformer. Thus, a temperature-dependent conformational equilibrium can be established for CriTER-A, suggesting a putative functional role of the telomeric transcriptome in relation to thermal stress that could rely on the structure–function relationship of the CriTER-A transcripts.

scholarly journals Microsecond simulation unravel the structural dynamics of SARS-CoV-2 Spike-C-terminal cytoplasmic tail (residues 1242-1273)

2021 ◽  
Author(s):  
Prateek Kumar ◽  
Taniya Bhardwaj ◽  
Neha Garg ◽  
Rajanish Giri
Keyword(s):  
Structural Dynamics ◽  
Viral Proteins ◽  
Spike Protein ◽  
Temperature Dependent ◽  
Replica Exchange Molecular Dynamics ◽  
Structural Conformation ◽  
Human Coronaviruses ◽  
Function Relationship ◽  
Dynamics Simulations ◽  
Relationship Of

AbstractSpike protein of human coronaviruses has been a vital drug and vaccine target. The multifunctionality of this protein including host receptor binding and apoptosis has been proved in several coronaviruses. It also interacts with other viral proteins such as membrane (M) protein through its C-terminal domain. The specific dibasic motif signal present in cytosolic region at C-terminal of spike protein helps it to localize within the endoplasmic reticulum (ER). However, the structural conformation of cytosolic region is not known in SARS-CoV-2 using which it interacts with other proteins and transporting vesicles. Therefore, we have demonstrated the conformation of cytosolic region and its dynamics through computer simulations up to microsecond timescale using OPLS and CHARMM forcefields. The simulations have revealed the unstructured conformation of cytosolic region (residues 1242-1273). Also, in temperature dependent replica-exchange molecular dynamics simulations it has shown to form secondary structures. We believe that our findings will surely help us understand the structure-function relationship of the spike protein’s cytosolic region.

scholarly journals In-silico analysis reveals druggable single nucleotide polymorphisms in angiotensin 1 converting enzyme involved in the onset of blood pressure

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Brenda Udosen ◽  
Opeyemi Soremekun ◽  
Chinwe Ekenna ◽  
Olaposi Idowu Omotuyi ◽  
Tinashe Chikowore ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Single Nucleotide Polymorphisms ◽  
Critical Role ◽  
Point Mutations ◽  
In Silico Analysis ◽  
Nucleotide Polymorphisms ◽  
Converting Enzyme ◽  
Single Nucleotide ◽  
Function Relationship ◽  
Relationship Of

Abstract Objective The Angiotensin 1 converting enzyme (ACE1) gene plays a critical role in regulating blood pressure and thus, it has become a major therapeutic target of antihypertensives. Single nucleotide polymorphisms (SNPs) occurring within a gene most especially at the functional segment of the genes alter the structure–function relationship of that gene. Results Our study revealed that five nsSNPs of the ACE1 gene were found to be potentially deleterious and damaging and they include rs2229839, rs14507892, rs12709442, and rs4977 at point mutations P351R, R953Q, I1018T, F1051V, and T1187M. The protein stability predictive tools revealed that all the nsSNPs decreased stability of the protein and the Consurf server which estimates the evolutionary conservation profile of a protein showed that three mutants were in the highly conserved region. In conclusion, this study predicted potential druggable deleterious mutants that can be further explored to understand the pathological basis of cardiovascular disease.

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

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

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

2020 ◽  
Vol 27 (38) ◽  
pp. 6523-6535 ◽  
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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