scholarly journals Novel insights in linking solvent relaxation dynamics and protein conformations utilizing red edge excitation shift approach

2021 ◽  
Author(s):  
Rupasree Brahma ◽  
H. Raghuraman
Keyword(s):  
The Novel ◽  
Relaxation Dynamics ◽  
Complex Biological System ◽  
Physiological Processes ◽  
Red Edge ◽  
Structural Ensembles ◽  
Red Edge Excitation Shift ◽  
Cellular Context ◽  
Energy Dependent ◽  
Protein Fluctuations

Protein hydration dynamics plays an important role in many physiological processes since protein fluctuations, slow solvation, and the dynamics of hydrating water are all intrinsically related. Red edge excitation shift (REES) is a unique and powerful wavelength-selective (i.e. excitation-energy dependent) fluorescence approach that can be used to directly monitor the environment-induced restriction and dynamics around a polar fluorophore in a complex biological system. This review is mainly focused on recent applications of REES and a novel analysis of REES data to monitor the structural dynamics, functionally relevant conformational transitions and to unmask the structural ensembles in proteins. In addition, the novel utility of REES in imaging protein aggregates in a cellular context is discussed. We believe that the enormous potential of REES approach showcased in this review will engage more researchers, particularly from life sciences.

scholarly journals The red edge excitation shift phenomenon can be used to unmask protein structural ensembles: implications for NEMO-ubiquitin interactions

FEBS Journal ◽  
2016 ◽  
Vol 283 (12) ◽  
pp. 2272-2284 ◽  
Author(s):  
Dragana A.M. Catici ◽  
Hope E. Amos ◽  
Yi Yang ◽  
Jean M.H. van den Elsen ◽  
Christopher R. Pudney
Keyword(s):  
Red Edge ◽  
Structural Ensembles ◽  
Red Edge Excitation Shift

scholarly journals Split NanoLuc technology allows quantitation of interactions between PII protein and its receptors with unprecedented sensitivity and reveals transient interactions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Rokhsareh Rozbeh ◽  
Karl Forchhammer
Keyword(s):  
The Novel ◽  
Multiple Target ◽  
Interacting Protein ◽  
Effector Molecule ◽  
Target Proteins ◽  
Pii Protein ◽  
Protein X ◽  
Cellular Context ◽  
Pii Proteins ◽  
Transient Interactions

AbstractPII proteins constitute a widespread signal transduction superfamily in the prokaryotic world. The canonical PII signal proteins sense metabolic state of the cells by binding the metabolite molecules ATP, ADP and 2-oxoglutarate. Depending on bound effector molecule, PII proteins interact with and modulate the activity of multiple target proteins. To investigate the complexity of interactions of PII with target proteins, analytical methods that do not disrupt the native cellular context are required. To this purpose, split luciferase proteins have been used to develop a novel complementation reporter called NanoLuc Binary Technology (NanoBiT). The luciferase NanoLuc is divided in two subunits: a 18 kDa polypeptide termed “Large BiT” and a 1.3 kDa peptide termed “Small BiT”, which only weakly associate. When fused to proteins of interest, they reconstitute an active luciferase when the proteins of interest interact. Therefore, we set out to develop a new NanoBiT sensor based on the interaction of PII protein from Synechocystis sp. PCC6803 with PII-interacting protein X (PipX) and N-acetyl-L-glutamate kinase (NAGK). The novel NanoBiT sensor showed unprecedented sensitivity, which made it possible to detect even weak and transient interactions between PII variants and their interacting partners, thereby shedding new light in PII signalling processes.

Tubulin Conformation and Dynamics:  A Red Edge Excitation Shift Study

Biochemistry ◽  
1996 ◽  
Vol 35 (41) ◽  
pp. 13426-13433 ◽  
Author(s):  
Suranjana Guha ◽  
Satinder S. Rawat ◽  
Amitabha Chattopadhyay ◽  
Bhabatarak Bhattacharyya
Keyword(s):  
Red Edge ◽  
Red Edge Excitation Shift ◽  
Shift Study

scholarly journals Cloning and characterization of a second member of the mouse mdr gene family.

1988 ◽  
Vol 8 (7) ◽  
pp. 2770-2778 ◽  
Author(s):  
P Gros ◽  
M Raymond ◽  
J Bell ◽  
D Housman
Keyword(s):  
Multidrug Resistance ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Amino Acid Sequence ◽  
Gene Family ◽  
Predicted Amino Acid Sequence ◽  
Coding Region ◽  
Physiological Processes ◽  
Strong Homology ◽  
Energy Dependent

The mammalian mdr gene family comprises a small number of closely related genes. Previously, we have shown that one member, mdr1, has the capacity to convey multidrug resistance to drug-sensitive recipient cells in a gene transfer protocol. However, the functional characteristics of other members of this gene family have not been examined. In this report, we characterize a second member of the mdr gene family which we designated mdr2. We determined the nucleotide sequence corresponding to the complete coding region of this mdr2 transcript. The predicted amino acid sequence of this protein (1,276 amino acids) showed that it is a membrane glycoprotein highly homologous to mdr1 (85%), strongly suggesting that both genes originate from a common ancestor. Regions of divergence between mdr1 and mdr2 proteins are concentrated in two discrete segments of the predicted polypeptides, each approximately 100 residues in length. The mdr2 protein appears to be formed by the duplication of a structural unit which encodes three putative transmembrane loops and a predicted nucleotide-binding fold and is highly homologous to bacterial transport proteins such as hlyB. This strong homology suggests that mdr2 also participates in an energy-dependent membrane transport process. However, the direct relationship, if any, of this new member of the mdr family to multidrug resistance remains to be established. Knowledge of the complete nucleotide sequence and predicted amino acid sequence of the mdr2 gene product will enable the preparation of gene-specific probes and antibodies necessary to study the functional role of this gene in multidrug resistance and normal physiological processes.

scholarly journals Characterization of the novel duplicated PRLR gene at the late-feathering K locus in Lohmann chickens

2013 ◽  
Vol 51 (2) ◽  
pp. 261-276 ◽  
Author(s):  
Guixian Bu ◽  
Guian Huang ◽  
Hao Fu ◽  
Juan Li ◽  
Simiao Huang ◽  
...  
Keyword(s):  
Receptor Gene ◽  
Tissue Expression ◽  
Luciferase Reporter ◽  
The Novel ◽  
Rt Pcr ◽  
Reporter System ◽  
Physiological Processes ◽  
Spatiotemporal Expression ◽  
Membrane Spanning

A partial duplication of the prolactin (PRL) receptor gene (designated asdPRLR) has been identified at the late-feathering (LF)Klocus on chromosome Z of some chicken strains recently, implying thatdPRLRis probably a candidate gene associated with LF development in chickens. However, little is known about the structure, functionality, and spatiotemporal expression of thedPRLRgene in chickens. In this study, using 3′-RACE and RT-PCR, the full-length cDNA of thedPRLRobtained from the kidneys of male Lohmann layer chickens carrying aKallele was cloned. The cloneddPRLRis predicted to encode a membrane-spanning receptor of 683 amino acids, which is nearly identical to the original PRLR, except for its lack of a 149-amino acid C-terminal tail. Using a 5× STAT5–Luciferase reporter system and western blot analysis, we demonstrated that dPRLR expressed in HepG2 cells could be potently activated by chicken PRL and functionally coupled to the intracellular STAT5 signaling pathway, suggesting that dPRLR may function as a novel receptor for PRL. RT-PCR assays revealed that similar to the originalPRLRgene,dPRLRmRNA is widely expressed in all embryonic and adult tissues examined including the skin of male Lohmann chickens with aKallele. These findings, together with the expression ofPRLmRNA detected in the skin of embryos at embryonic day 20 and 1-week-old chicks, suggest that skin-expressed dPRLR and PRLR, together with plasma and skin-derived PRL, may be involved in the control of the LF development of chicks at hatching. Moreover, the wide tissue expression ofdPRLRimplies that dPRLR may regulate other physiological processes of chickens carrying theKallele.

scholarly journals Validation of a radioimmunoassay-based fecal corticosteroid assay for Richardson’s ground squirrels Urocitellus richard-sonii and behavioural correlates of stress

2014 ◽  
Vol 60 (5) ◽  
pp. 591-601 ◽  
Author(s):  
James F. Hare ◽  
Calen P. Ryan ◽  
Chris Enright ◽  
Laura E. Gardiner ◽  
Lindsay J Skyner ◽  
...  
Keyword(s):  
Hpa Axis ◽  
Plasma Cortisol ◽  
Ground Squirrels ◽  
Antipredator Behaviour ◽  
The Novel ◽  
Free Living ◽  
Handling Stress ◽  
Non Invasive ◽  
Fecal Glucocorticoid Metabolites ◽  
Physiological Processes

Abstract We validated a radioimmunoassay-based method quantifying fecal glucocorticoid metabolites (FGMs) from captive male and female Richardson’s ground squirrels Urocitellus richardsonii. Blood samples were drawn to explore the correlation between plasma cortisol and FGM concentrations. We also injected groups of squirrels with normal saline (CTL; control), adre-nocorticotropic hormone (ACTH; stimulating adrenal activity), or dexamethasone (DEX; suppressing adrenal activity). Potential correlations between stress and behaviour were explored through quantification of fecal pellet production and the intervention necessary to elicit defecation, as well as the behaviour of subjects in the context of handling. Changes in plasma cortisol concentration between capture (baseline), and following handling (stress-induced) were also quantified for free-living squirrels. While glucocorticoid concentrations recovered from feces during our captive-animal study were not well correlated with plasma cortisol concentrations, and uncorrelated with defecation or behaviour, FGM concentrations did reflect the activation of the hypothalamic-pituitary-adrenal (HPA) axis. FGM concentrations increased significantly during initial captivity, but declined to baseline level as individuals acclimated to the novel environment. Injection of subjects with ACTH increased FGMs above baseline, confirming activation of the HPA axis. Plasma cortisol concentrations increased significantly with induced stress, indicating that capture and handling activated the glucocorticoid stress response even among previously handled, free-living subjects. Our findings validate a non-invasive tool that will afford new insight into the physiological processes underlying social, reproductive and antipredator behaviour of Richardson’s ground squirrels.

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