Application of a Fluorescent Biosensor in Determining the Binding of 5-HT to Calmodulin

Here, we show the utility of the fluorescent biosensor hCaM-M124C-mBBr in detecting and determining the affinity of serotonin (5-HT). We obtained a Kd of 5-HT (0.71 μm) for the first time, the same order of magnitude as most anti-CaM drugs. This data can contribute to understanding the direct and indirect modulation of CaM on its binding proteins when the 5-HT concentration varies in different tissues or explain some of the side effects of anti-CaM drugs. On the other hand, molecular modeling tools help the rational design of biosensors and adequately complement the experimental results. For example, the docking study indicates that 5-HT binds at the same site as chlorpromazine (site 1) with a theoretical Ki of 2.84 μM; while the molecular dynamics simulations indicate a stability of the CaM–5-HT complex with a theoretical ΔG of −4.85 kcal mol−1, where the enthalpy contribution is greater. Thus, the combination of biotechnology and bioinformatics helps in the design and construction of more robust biosensors.

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MOLECULAR DYNAMICS SIMULATIONS OF LIQUID CRYSTAL ANCHORING AT AN AMORPHOUS POLYMER SURFACE

International Journal of Modern Physics C ◽

10.1142/s0129183199000310 ◽

1999 ◽

Vol 10 (02n03) ◽

pp. 415-429 ◽

Cited By ~ 8

Author(s):

T. P. DOERR ◽

P. L. TAYLOR

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Amorphous Polymer ◽

Polymer Surface ◽

The Other ◽

Substantial Fraction ◽

Dynamics Simulations ◽

First Time

Atomistic molecular dynamics simulations have been used, apparently for the first time, to investigate the anchoring behavior of a liquid crystal at the interface with an amorphous polymer. The simulations studied a system consisting of the nematogen 5CB at the surface of amorphous polyethylene, and used the simple Dreiding II force field. The simulations indicate a preference for nonplanar anchoring. Two distinct microscopic paths have been identified by which the liquid crystal changes orientation at the surface. In one case, only one or a few of the 5CB molecules are rotating at any particular time. In the other case, a substantial fraction of the molecules rotate simultaneously.

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Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

ASME/JSME 2011 8th Thermal Engineering Joint Conference ◽

10.1115/ajtec2011-44457 ◽

2011 ◽

Author(s):

Toshihiro Kaneko ◽

Kenji Yasuoka ◽

Ayori Mitsutake ◽

Xiao Cheng Zeng

Keyword(s):

Molecular Dynamics ◽

Heat Capacity ◽

Transition Temperature ◽

Peak Position ◽

Temperature Curve ◽

Dynamics Simulation ◽

Lennard Jones ◽

Dynamics Simulations ◽

First Time ◽

Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

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The role of side chains in the interaction of new antitumor pyrimidoacridinetriones with DNA: molecular dynamics simulations.

Acta Biochimica Polonica ◽

10.18388/abp.2000_4061 ◽

2000 ◽

Vol 47 (1) ◽

pp. 47-57 ◽

Cited By ~ 3

Author(s):

J Mazerski ◽

I Antonini ◽

S Martelli

Keyword(s):

Molecular Dynamics ◽

Rational Design ◽

Md Simulations ◽

Ring System ◽

Side Chain ◽

Side Chains ◽

Intercalation Complex ◽

Highly Active ◽

Simulation Techniques ◽

Dynamics Simulations

Pyrimidoacridinetriones (PATs) are a new group of highly active antitumor compounds. It seems reasonable to assume that, like for some other acridine derivatives, intercalation into DNA is a necessary, however not a sufficient condition for antitumor activity of these compounds. Rational design of new compounds of this chemotype requires knowledge about the structure of the intercalation complex, as well as about interactions responsible for its stability. Computer simulation techniques such as molecular dynamics (MD) may provide valuable information about these problems. The results of MD simulations performed for three rationally selected PATs are presented in this paper. The compounds differ in the number and position of side chains. Each of the compounds was simulated in two systems: i) in water, and ii) in the intercalation complex with the dodecamer duplex d(GCGCGCGCGCGC)2. The orientation of the side chain in relation to the ring system is determined by the position of its attachment. Orientation of the ring system inside the intercalation cavity depends on the number and position of side chain(s). The conformations of the side chain(s) of all PATs studied in the intercalation complex were found to be very similar to those observed in water.

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HT-SuMD: Making Molecular Dynamics Simulations Suitable for Fragment-Based Screening. a Comparative Study with NMR

10.26434/chemrxiv.12582662.v1 ◽

2020 ◽

Cited By ~ 1

Author(s):

Francesca Ferrari ◽

Maicol Bissaro ◽

Simone Fabbian ◽

Jessica de Almeida Roger ◽

Stefano Mammi ◽

...

Keyword(s):

Molecular Dynamics ◽

Solution Nmr ◽

Protein Recognition ◽

Fragment Screening ◽

Fragment Library ◽

Dynamics Simulations ◽

A Prospective Study ◽

First Time ◽

Established Technique ◽

State Of Art

<p>In this manuscript, for the first time, we presented a fragment library and we validated its performance by comparison with a well-established technique for fragment screening as solution NMR. We were able to screen 400 different fragments producing a total of 1200 independent fragment-protein recognition pathways. As far as we know, this represents the largest screening based on Molecular dynamics ever reported. Our simulations successfully detected the true binders in the library in a prospective study, showing a notable agreement with a state-of-art screening we performed by NMR on the same dataset.</p>

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Absorption of Mechanical Energy via Formation of Ice Nanotubes in Zeolite

Physical Chemistry Chemical Physics ◽

10.1039/d1cp01482j ◽

2021 ◽

Author(s):

Kenji Mochizuki

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Heterogeneous System ◽

Mechanical Energy ◽

Bulk Water ◽

Pure Silica ◽

Dynamics Simulations ◽

First Time

Abstract Molecular dynamics simulations are carried out for a heterogeneous system composed of bulk water and pure-silica zeolites of the AFI type. Our simulations show, for the first time, the...

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Study of the Lamellar and Micellar Phases of Pluronic F127: A Molecular Dynamics Approach

Processes ◽

10.3390/pr7090606 ◽

2019 ◽

Vol 7 (9) ◽

pp. 606 ◽

Cited By ~ 1

Author(s):

Juan Albano ◽

Damian Grillo ◽

Julio Facelli ◽

Marta Ferraro ◽

Mónica Pickholz

Keyword(s):

Molecular Dynamics ◽

Amorphous Structure ◽

Pluronic F127 ◽

Coarse Grain ◽

Lamellar Thickness ◽

Initial Polymer ◽

Lamellar Phases ◽

New Information ◽

Order Of Magnitude ◽

Dynamics Simulations

In this work, we analyzed the behavior of Pluronic F127 through molecular dynamics simulations at the coarse-grain level, focusing on the micellar and lamellar phases. To this aim, two initial polymer conformations were considered, S-shape and U-shape, for both simulated phases. Through the simulations, we were able to examine the structural and mechanical properties that are difficult to access through experiments. Since no transition between S and U shapes was observed in our simulations, we inferred that all single co-polymers had memory of their initial configuration. Nevertheless, most copolymers had a more complex amorphous structure, where hydrophilic beads were part of the lamellar-like core. Finally, an overall comparison of the micellar a lamellar phases showed that the lamellar thickness was in the same order of magnitude as the micelle diameter (approx. 30 nm). Therefore, high micelle concentration could lead to lamellar formation. With this new information, we could understand lamellae as orderly packed micelles.

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Oxygen Anion Diffusion in Doped Ceria MxCe1-xO2-0.5x (M=Gd, Sm and Pr): A Molecular Dynamics Simulation Study

MRS Advances ◽

10.1557/adv.2019.165 ◽

2019 ◽

Vol 4 (13) ◽

pp. 783-792 ◽

Cited By ~ 1

Author(s):

Neetu Kumari ◽

Uzma Anjum ◽

M. Ali Haider ◽

Suddhastawa Basu

Keyword(s):

Molecular Dynamics ◽

Dopant Concentration ◽

Optimum Concentration ◽

Dynamics Simulation ◽

Doped Ceria ◽

Oxygen Anion ◽

Anion Diffusion ◽

Order Of Magnitude ◽

Pure Ceria ◽

Dynamics Simulations

ABSTRACTMolecular dynamics simulations were utilized to determine the oxygen anion diffusivity in pure ceria (CeO2) and doped ceria MxCe1-xO2-0.5x(M=Gd, Sm and Pr) with varying level of dopant concentration from 5-30% (x = 0.05-0.3). Doping with Gd showed an improvement in oxygen anion diffusivity value by two order of magnitude (D = 4.67x10-8cm2/s at 1173 K) as compared to the undoped ceria (D = 1.33x10-10cm2/s at 1173 K). 10% of doping level was estimated as the optimum concentration of all the dopants at which all of the doped ceria materials showed maximum diffusivity of oxygen anion. Among the three dopants studied, Pr was observed to show maximum diffusivity of oxygen anion in the temperature range of 773-1173 K of simulations.

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