scholarly journals Homology modeling and functional characterization of multidrug effluxor Mta protein from Bacillus Atrophaeus: An explanatory insilico approach

2020 ◽  
Author(s):  
Mohammad Rejaur Rahman ◽  
Ishtiak Malique Chowdhury ◽  
Anik Banik ◽  
Emran Hossain Sajib
Keyword(s):  
Function Analysis ◽  
Functional Characterization ◽  
Bacillus Atrophaeus ◽  
Uncharacterized Protein ◽  
Protein Protein Interaction ◽  
Functional Aspects ◽  
Resistance Function ◽  
Spore Forming Bacteria ◽  
Protein Pocket

AbstractPhenotypically similar to B. subtilis, Bacillus atrophaeus is a Gram-positive, aerobic, spore-forming bacteria. It is a black-pigmented bacterial genus. Therefore, it is of interest to study the uncharacterized proteins in the genome. For a detailed computational sequence-structure-function analysis using available data and resources, an uncharacterized protein Mta (AKL87074.1) in the genome was selected. In this study, attempts were made to study the physicochemical properties, predict secondary structure, modeling the 3-D protein, pocket identification, protein-protein interaction and phylogenetic analysis of Mta protein. The predicted active site using CASTp is analyzed for understanding their multidrug resistance function. Because Mta is a MerR family member, these investigations on these functional aspects could lead us for better understanding of antibiotic resistance phenomenon.

scholarly journals Functional characterization of human Kindlin-2 core promoter identifies a key role of SP1 in Kindlin-2 transcriptional regulation

2011 ◽  
Vol 16 (4) ◽  
Author(s):  
Ammad Khan ◽  
Takashi Shimokawa ◽  
Staffan Strömblad ◽  
Hongquan Zhang
Keyword(s):  
Transcriptional Regulation ◽  
Core Promoter ◽  
Functional Characterization ◽  
Ph Domain ◽  
Interacting Protein ◽  
Normal Tissues ◽  
Functional Aspects

AbstractKindlin-2 is a recently identified FERM and PH domain containing integrin interacting protein. Kindlin-2 is ubiquitously expressed in normal tissues. So far, much effort has been spent exploring the functional aspects of Kindlin-2. However, the transcriptional regulation of Kindlin-2 has not yet been investigated. In this study we identified and functionally characterized the promoter of the human Kindlin-2 gene. We show that the core promoter of Kindlin-2 is a 39 base pair long GC rich fragment located −122/-83 upstream of the Kindlin-2 transcription start site. Functional characterization of this core promoter region by both in silico as well as in vitro/in vivo analysis shows that the transcription factor SP1 plays an important role in regulation of Kindlin-2 expression.

scholarly journals Protein-protein interaction analysis for functional characterization of helicases

Methods ◽  
2016 ◽  
Vol 108 ◽  
pp. 56-64 ◽  
Author(s):  
Boris L. Zybailov ◽  
Alicia K. Byrd ◽  
Galina V. Glazko ◽  
Yasir Rahmatallah ◽  
Kevin D. Raney
Keyword(s):  
Protein Interaction ◽  
Interaction Analysis ◽  
Functional Characterization ◽  
Protein Protein Interaction

scholarly journals Structural and Functional Characterization of the Interdomain Interaction in the Mineralocorticoid Receptor

2009 ◽  
Vol 23 (9) ◽  
pp. 1360-1370 ◽  
Author(s):  
Jyotsna B. Pippal ◽  
Yizhou Yao ◽  
Fraser M. Rogerson ◽  
Peter J. Fuller
Keyword(s):  
Mineralocorticoid Receptor ◽  
Functional Characterization ◽  
Glutathione S Transferase ◽  
Protein Protein Interaction ◽  
Functional Differences ◽  
Electrolyte Homeostasis ◽  
Interdomain Interaction ◽  
Two Hybrid

Abstract The mineralocorticoid receptor (MR) plays a central role in electrolyte homeostasis and in cardiovascular disease. We have previously reported a ligand-dependent N/C-interaction in the MR. In the present study we sought to fully characterize the MR N/C-interaction. By using a range of natural and synthetic MR ligands in a mammalian two-hybrid assay we demonstrate that in contrast to aldosterone, which strongly induces the interaction, the physiological ligands deoxycorticosterone and cortisol weakly promote the interaction but predominantly inhibit the aldosterone-mediated N/C-interaction. Similarly, progesterone and dexamethasone antagonize the interaction. In contrast, the synthetic agonist 9α-fludrocortisol robustly induces the interaction. The ability of the N/C interaction to discriminate between MR agonists suggests a subtle conformational difference in the ligand-binding domain induced by these agonists. We also demonstrate that the N/C interaction is not cell specific, consistent with the evidence from a glutathione-S-transferase pull-down assay, of a direct protein-protein interaction between the N- and C-terminal domains of the MR. Examination of a panel of deletions in the N terminus suggests that several regions may be critical to the N/C-interaction. These studies have identified functional differences between physiological MR ligands, which suggest that the ligand-specific dependence of the N/C-interaction may contribute to the differential activation of the MR that has been reported in vivo.

scholarly journals Predicting Protein Functions from Protein Interaction Networks

2012 ◽  
Vol 3 (4) ◽  
pp. 50-70 ◽  
Author(s):  
Hon Nian Chua ◽  
Limsoon Wong
Keyword(s):  
Protein Interaction ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Functional Characterization ◽  
Function Prediction ◽  
Functional Annotations ◽  
Protein Protein Interaction ◽  
Protein Functions ◽  
High Throughput Manner

Functional characterization of genes and their protein products is essential to biological and clinical research. Yet, there is still no reliable way of assigning functional annotations to proteins in a high-throughput manner. In this article, the authors provide an introduction to the task of automated protein function prediction. They discuss about the motivation for automated protein function prediction, the challenges faced in this task, as well as some approaches that are currently available. In particular, they take a closer look at methods that use protein-protein interaction for protein function prediction, elaborating on their underlying techniques and assumptions, as well as their strengths and limitations.

scholarly journals Predicting Protein Functions from Protein Interaction Networks

2009 ◽  
pp. 203-222 ◽  
Author(s):  
Hon Nian Chua ◽  
Limsoon Wong
Keyword(s):  
Protein Interaction ◽  
Protein Function ◽  
Protein Function Prediction ◽  
Functional Characterization ◽  
Function Prediction ◽  
Functional Annotations ◽  
Protein Protein Interaction ◽  
Protein Functions ◽  
High Throughput Manner

Functional characterization of genes and their protein products is essential to biological and clinical research. Yet, there is still no reliable way of assigning functional annotations to proteins in a high-throughput manner. In this chapter, the authors provide an introduction to the task of automated protein function prediction. They discuss about the motivation for automated protein function prediction, the challenges faced in this task, as well as some approaches that are currently available. In particular, they take a closer look at methods that use protein-protein interaction for protein function prediction, elaborating on their underlying techniques and assumptions, as well as their strengths and limitations.

Functional characterization of human brown adipose tissue metabolism

2020 ◽  
Vol 477 (7) ◽  
pp. 1261-1286 ◽  
Author(s):  
Marie Anne Richard ◽  
Hannah Pallubinsky ◽  
Denis P. Blondin
Keyword(s):  
Adipose Tissue ◽  
Brown Adipose Tissue ◽  
Functional Characterization ◽  
Human Infants ◽  
Positron Emission ◽  
Brown Adipose ◽  
Treatment Of Obesity ◽  
And Function

Brown adipose tissue (BAT) has long been described according to its histological features as a multilocular, lipid-containing tissue, light brown in color, that is also responsive to the cold and found especially in hibernating mammals and human infants. Its presence in both hibernators and human infants, combined with its function as a heat-generating organ, raised many questions about its role in humans. Early characterizations of the tissue in humans focused on its progressive atrophy with age and its apparent importance for cold-exposed workers. However, the use of positron emission tomography (PET) with the glucose tracer [18F]fluorodeoxyglucose ([18F]FDG) made it possible to begin characterizing the possible function of BAT in adult humans, and whether it could play a role in the prevention or treatment of obesity and type 2 diabetes (T2D). This review focuses on the in vivo functional characterization of human BAT, the methodological approaches applied to examine these features and addresses critical gaps that remain in moving the field forward. Specifically, we describe the anatomical and biomolecular features of human BAT, the modalities and applications of non-invasive tools such as PET and magnetic resonance imaging coupled with spectroscopy (MRI/MRS) to study BAT morphology and function in vivo, and finally describe the functional characteristics of human BAT that have only been possible through the development and application of such tools.

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