scholarly journals What Does Time-Dependent Fluorescence Shift (TDFS) in Biomembranes (and Proteins) Report on?

2021 ◽  
Vol 9 ◽  
Author(s):  
Federica Scollo ◽  
Hüseyin Evci ◽  
Mariana Amaro ◽  
Piotr Jurkiewicz ◽  
Jan Sykora ◽  
...  

The organization of biomolecules and bioassemblies is highly governed by the nature and extent of their interactions with water. These interactions are of high intricacy and a broad range of methods based on various principles have been introduced to characterize them. As these methods view the hydration phenomena differently (e.g., in terms of time and length scales), a detailed insight in each particular technique is to promote the overall understanding of the stunning “hydration world.” In this prospective mini-review we therefore critically examine time-dependent fluorescence shift (TDFS)—an experimental method with a high potential for studying the hydration in the biological systems. We demonstrate that TDFS is very useful especially for phospholipid bilayers for mapping the interfacial region formed by the hydrated lipid headgroups. TDFS, when properly applied, reports on the degree of hydration and mobility of the hydrated phospholipid segments in the close vicinity of the fluorophore embedded in the bilayer. Here, the interpretation of the recorded TDFS parameters are thoroughly discussed, also in the context of the findings obtained by other experimental techniques addressing the hydration phenomena (e.g., molecular dynamics simulations, NMR spectroscopy, scattering techniques, etc.). The differences in the interpretations of TDFS outputs between phospholipid biomembranes and proteins are also addressed. Additionally, prerequisites for the successful TDFS application are presented (i.e., the proper choice of fluorescence dye for TDFS studies, and TDFS instrumentation). Finally, the effects of ions and oxidized phospholipids on the bilayer organization and headgroup packing viewed from TDFS perspective are presented as application examples.

Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...


1998 ◽  
Vol 543 ◽  
Author(s):  
Edmund B. Webb ◽  
Gary S. Grest

AbstractThe interface between liquid hexadecane and the (010) surface of silicalite was studied by molecular dynamics. The structure of molecules in the interfacial region is influenced by the presence of pore mouths on the silicalite surface. For this surface, whose pores are the entrances to straight channels, the concentration profile for partially absorbed molecules is peaked around 10 monomers inside the zeolite. No preference to enter or exit the zeolite based on absorption length is observed except for very small or very large absorption lengths. We also found no preferential conformation of the unabsorbed tails for partially absorbed molecules.


2011 ◽  
Vol 115 (21) ◽  
pp. 7109-7121 ◽  
Author(s):  
Elin Säwén ◽  
Baltzar Stevensson ◽  
Jennie Östervall ◽  
Arnold Maliniak ◽  
Göran Widmalm

2014 ◽  
Vol 25 (5) ◽  
pp. 1443-1455 ◽  
Author(s):  
Pabla A. Barra ◽  
Luis F. Barraza ◽  
Verónica A. Jiménez ◽  
José A. Gavin ◽  
Joel B. Alderete

RSC Advances ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 3902-3915 ◽  
Author(s):  
Inna Ermilova ◽  
Alexander P. Lyubartsev

Molecular dynamics simulations of Aβ(25–35) peptides in phospholipid bilayers are carried out to investigate the effect of polyunsaturated lipids and cholesterol on aggregation of the peptides.


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