scholarly journals The first one hundred nanometers inside the pre-synaptic terminal where calcium diffusion triggers vesicular release

2018 ◽  
Author(s):  
C. Guerrier ◽  
D. Holcman
Keyword(s):  
Time Scale ◽  
Calcium Binding ◽  
Coarse Grained ◽  
Synaptic Terminal ◽  
Calcium Buffer ◽  
Calcium Sensors ◽  
Vesicular Release ◽  
Calcium Diffusion ◽  
Asynchronous Release ◽  
Coarse Grained Simulations

AbstractCalcium diffusion in the thin one hundred nanometers layer located between the plasma membrane and docked vesicles in the pre-synaptic terminal of neuronal cells mediates vesicular fusion and synaptic transmission. Accounting for the narrow-cusp geometry located underneath the vesicle is a key ingredient that defines the probability and the time scale of calcium diffusion to bind calcium sensors for the initiation of vesicular release. We study here the time scale, the calcium binding dynamics and the consequences for asynchronous versus synchronous release. To conclude, threedimensional modeling approaches and the associated coarse-grained simulations can now account efficiently for the precise co-organization of vesicles and Voltage-Gated-Calcium-Channel (VGCC). This co-organization is a key determinant of short-term plasticity and it shapes asynchronous release. Moreover, changing the location of VGCC from few nanometers underneath the vesicle modifies significantly the release probability. Finally, by modifying the calcium buffer concentration, a single synapse can switch from facilitation to depression.

Grand-Reaction Method for Simulations of Ionization Equilibria and Ion Partitioning in a Broad Range of pH and Ionic Strength

2019 ◽  
Author(s):  
Jonas Landsgesell ◽  
Oleg Rud ◽  
Pascal Hebbeker ◽  
Raju Lunkad ◽  
Peter Košovan ◽  
...  
Keyword(s):  
Mean Field ◽  
Coarse Grained ◽  
Reactive System ◽  
Acid Base ◽  
Buffer Solution ◽  
Reaction Method ◽  
Ionization Equilibria ◽  
Coarse Grained Simulations ◽  
Ph Range ◽  
Weak Polyelectrolytes

We introduce the grand-reaction method for coarse-grained simulations of acid-base equilibria in a system coupled to a reservoir at a given pH and concentration of added salt. It can be viewed as an extension of the constant-pH method and the reaction ensemble, combining explicit simulations of reactions within the system, and grand-canonical exchange of particles with the reservoir. Unlike the previously introduced methods, the grand-reaction method is applicable to acid-base equilibria in the whole pH range because it avoids known artifacts. However, the method is more general, and can be used for simulations of any reactive system coupled to a reservoir of a known composition. To demonstrate the advantages of the grand-reaction method, we simulated a model system: A solution of weak polyelectrolytes in equilibrium with a buffer solution. By carefully accounting for the exchange of all constituents, the method ensures that all chemical potentials are equal in the system and in the multi-component reservoir. Thus, the grand-reaction method is able to predict non-monotonic swelling of weak polyelectrolytes as a function of pH, that has been known from mean-field predictions and from experiments but has never been observed in coarse-grained simulations. Finally, we outline possible extensions and further generalizations of the method, and provide a set of guidelines to enable safe usage of the method by a broad community of users.<br><br>

scholarly journals Changes in the Population Size of Calbindin D-28k-Immunoreactive Enteric Neurons in the Porcine Caecum under the Influence of Bisphenol A: A Preliminary Study

Toxics ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. 1
Author(s):  
Ignacy Gonkowski ◽  
Slawomir Gonkowski ◽  
Ewa Dzika ◽  
Joanna Wojtkiewicz
Keyword(s):  
Bisphenol A ◽  
Calcium Binding ◽  
Neuronal Cells ◽  
Enteric Neurons ◽  
Toxic Activity ◽  
Protective Properties ◽  
Calcium Buffer ◽  
Preliminary Study ◽  
Living Organisms ◽  
Calbindin D

Calbindin D-28k (CB) is a calcium-binding protein widely distributed in living organisms that may act as a calcium buffer and sensory protein. CB is present in the enteric nervous system (ENS) situated in the gastrointestinal tract, which controls the majority of activities of the stomach and intestine. The influence of various doses of bisphenol A (BPA)—a chemical compound widely used in plastics production—on the number and distribution of CB-positive enteric neuronal cells in the porcine caecum was investigated with an immunofluorescence technique. The obtained results showed that low dosages of BPA resulted in an increase in the number of CB-positive neuronal cells in the myenteric (MP) and inner submucous (ISP) plexuses, whereas it did not alter the number of such neuronal cells in the outer submucous plexus (OSP). High dosages of BPA caused the increase in the amount of CB-positive perikarya in all the above-mentioned kinds of the caecal neuronal plexuses. These observations strongly suggest that CB in the ENS participates in the processes connected with the toxic activity of BPA. Most likely, the changes noted in this experiment result from the adaptive and protective properties of CB.

scholarly journals Prediction and validation of protein intermediate states from structurally rich ensembles and coarse-grained simulations

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Laura Orellana ◽  
Ozge Yoluk ◽  
Oliver Carrillo ◽  
Modesto Orozco ◽  
Erik Lindahl
Keyword(s):  
Coarse Grained ◽  
Intermediate States ◽  
Coarse Grained Simulations

Effect of oligonucleic acid (ONA) backbone features on assembly of ONA–star polymer conjugates: a coarse-grained molecular simulation study

Soft Matter ◽  
2017 ◽  
Vol 13 (38) ◽  
pp. 6770-6783 ◽  
Author(s):  
Joshua E. Condon ◽  
Arthi Jayaraman
Keyword(s):  
Molecular Simulation ◽  
Simulation Study ◽  
Coarse Grained ◽  
Star Polymer ◽  
Backbone Flexibility ◽  
Polymer Architecture ◽  
Polymer Conjugates ◽  
Coarse Grained Simulations

Using coarse-grained simulations, we study the effect of varying oligonucleic acid (ONA) backbone flexibility, ONA charge and star polymer architecture on structure and thermodynamics of ONA–star polymer conjugates assembly.

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