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 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.

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

Fluorophore environments in membrane-bound probes: A red edge excitation shift study

Biochemistry ◽  
1993 ◽  
Vol 32 (14) ◽  
pp. 3804-3811 ◽  
Author(s):  
Amitabha Chattopadhyay ◽  
Sushmita Mukherjee
Keyword(s):  
Red Edge ◽  
Red Edge Excitation Shift ◽  
Membrane Bound ◽  
Shift Study

scholarly journals Environment-Sensitive Fluorescence of 7-Nitrobenz-2-oxa-1,3-Diazol-4-yl (NBD)-Labeled Ligands for Serotonin Receptors

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3848
Author(s):  
Parijat Sarkar ◽  
Kaleeckal G. Harikumar ◽  
Satinder S. Rawat ◽  
Sanjib Das ◽  
Tushar K. Chakraborty ◽  
...  
Keyword(s):  
Cell Surface ◽  
Serotonin Receptors ◽  
Multiple Roles ◽  
Synthesis And Characterization ◽  
Future Studies ◽  
Serotonin1a Receptor ◽  
Red Edge ◽  
Red Edge Excitation Shift ◽  
Fluorescent Ligands

Serotonin is a neurotransmitter that plays a crucial role in the regulation of several behavioral and cognitive functions by binding to a number of different serotonin receptors present on the cell surface. We report here the synthesis and characterization of several novel fluorescent analogs of serotonin in which the fluorescent NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl) group is covalently attached to serotonin. The fluorescent ligands compete with the serotonin1A receptor specific radiolabeled agonist for binding to the receptor. Interestingly, these fluorescent ligands display a high environmental sensitivity of their fluorescence. Importantly, the human serotonin1A receptor stably expressed in CHO-K1 cells could be specifically labeled with one of the fluorescent ligands with minimal nonspecific labeling. Interestingly, we show by spectral imaging that the NBD-labeled ligand exhibits a red edge excitation shift (REES) of 29 nm when bound to the receptor, implying that it is localized in a restricted microenvironment. Taken together, our results show that NBD-labeled serotonin analogs offer an attractive fluorescent approach for elucidating the molecular environment of the serotonin binding site in serotonin receptors. In view of the multiple roles played by the serotonergic systems in the central and peripheral nervous systems, these fluorescent ligands would be useful in future studies involving serotonin receptors.

scholarly journals Red-Edge Excitation Shift Spectroscopy (REES): Application to Hidden Bound States of Ligands in Protein–Ligand Complexes

2021 ◽  
Vol 22 (5) ◽  
pp. 2582
Author(s):  
Md Lutful Kabir ◽  
Feng Wang ◽  
Andrew H. A. Clayton
Keyword(s):  
Thermodynamic Parameters ◽  
Bound States ◽  
Bound State ◽  
Spectroscopic Technique ◽  
Physical Parameters ◽  
Red Edge ◽  
Molecule Inhibitor ◽  
Red Edge Excitation Shift ◽  
Statistical Mechanical Model ◽  
Fluorescent Ligand

Ligand-protein binding is responsible for the vast majority of bio-molecular functions. Most experimental techniques examine the most populated ligand-bound state. The determination of less populated, intermediate, and transient bound states is experimentally challenging. However, hidden bound states are also important because these can strongly influence ligand binding and unbinding processes. Here, we explored the use of a classical optical spectroscopic technique, red-edge excitation shift spectroscopy (REES) to determine the number, population, and energetics associated with ligand-bound states in protein–ligand complexes. We describe a statistical mechanical model of a two-level fluorescent ligand located amongst a finite number of discrete protein microstates. We relate the progressive emission red shift with red-edge excitation to thermodynamic parameters underlying the protein–ligand free energy landscape and to photo-physical parameters relating to the fluorescent ligand. We applied the theoretical model to published red-edge excitation shift data from small molecule inhibitor–kinase complexes. The derived thermodynamic parameters allowed dissection of the energetic contribution of intermediate bound states to inhibitor–kinase interactions.

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