The Secret Lives of Fluorescent Membrane Probes as Revealed by Molecular Dynamics Simulations

Filipe, Hugo A. L.; Moreno, Maria João; Loura, Luís M. S.

doi:10.3390/molecules25153424

Cited by 23 publications

(17 citation statements)

References 166 publications

(224 reference statements)

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“…Since the value of a bilayer viscosity is characteristic of the membrane it should be independent of inclusion size, and it should not be affected by the addition of a fluorescent probe. The later has been corroborated by molecular dynamics simulations [42,43], which show that the addition of a probe has a minimal effect on bilayer viscosity. An identical value should be derived for a bilayer viscosity regardless of the size of a diffusing inclusion embedded into this bilayer.…”

Section: Resultsmentioning

confidence: 79%

How to best estimate the viscosity of lipid bilayers

Adrien

Rayan

Astafyeva

et al. 2022

Biophysical Chemistry

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Section: Resultsmentioning

confidence: 79%

How to best estimate the viscosity of lipid bilayers

Adrien

Rayan

Astafyeva

et al. 2022

Biophysical Chemistry

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“…Fluorescent labels [514][515][516][517][518][519][520][521][522][523][524][525][526][527][528][529] Fragrance Musk xylene [132] 2-aminoethoxydiphenyl borate (inhibitor of IP 3 receptors and TRP channels) [530] Organic solvents…”

Section: Application Xenobioticmentioning

confidence: 99%

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

2021

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We review the use of molecular dynamics (MD) simulation as a drug design tool in the context of the role that the lipid membrane can play in drug action, i.e., the interaction between candidate drug molecules and lipid membranes. In the standard “lock and key” paradigm, only the interaction between the drug and a specific active site of a specific protein is considered; the environment in which the drug acts is, from a biophysical perspective, far more complex than this. The possible mechanisms though which a drug can be designed to tinker with physiological processes are significantly broader than merely fitting to a single active site of a single protein. In this paper, we focus on the role of the lipid membrane, arguably the most important element outside the proteins themselves, as a case study. We discuss work that has been carried out, using MD simulation, concerning the transfection of drugs through membranes that act as biological barriers in the path of the drugs, the behavior of drug molecules within membranes, how their collective behavior can affect the structure and properties of the membrane and, finally, the role lipid membranes, to which the vast majority of drug target proteins are associated, can play in mediating the interaction between drug and target protein. This review paper is the second in a two-part series covering MD simulation as a tool in pharmaceutical research; both are designed as pedagogical review papers aimed at both pharmaceutical scientists interested in exploring how the tool of MD simulation can be applied to their research and computational scientists interested in exploring the possibility of a pharmaceutical context for their research.

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“…The relevant time and length scales governing the thermodynamics and dynamics of long-chain polyzwitterions in solution, their adsorption or chemical grafting onto solid surfaces, and their antifouling action exceed by far the range of microseconds and tens of nanometers that can be addressed by atomistic simulations on readily available computational platforms; 26,27 judicious coarse-graining is thus necessary.…”

Section: Introductionmentioning

confidence: 99%