Molecular dynamics simulations of the rotary motor F(0) under external electric fields across the membrane

Influences of electric fields on the operation of Aqy1 aquaporin channels: a molecular dynamics study

The dynamics of water molecules inside an Aquaporin channel, embedded within a stochastically fluctuating membrane, was modeled by means of the application of the molecular dynamics (MD) simulation method. We considered the effect of the existence and nonexistence of an external electric field, either constant or oscillating, on the stability of the channel. It was observed that the permeation of water molecules through the channel was increased when the channel was exposed to a constant electric field of strength -0.2 mV nm-1. Moreover, oscillating electric fields of 5 and 10 GHz frequencies, which is the range of field frequency generally present in our daily life, were applied to the channel, showing not significant effects on the stability of the channel and its important parts. In addition, we investigated the influence of the application of electric fields on the water molecule ordinations in the channels, and the results showed that the water molecule orientations were changed in response to the applied field.

Multi scale modeling of 2450MHz electric field effects on microtubule mechanical properties

Microtubule (MT) rigidity and response to 2450MHz electric fields were investigated, via multi scale modeling approach. For this purpose, six systems were designed and simulated to consider all types of feasible interactions between α and β monomers in MT, by using all atom molecular dynamics method. Subsequently, coarse grain modeling was used to design different lengths of MT. Investigation of effects of external 2450MHz electric field on MT showed MT less rigidity in the presence of such field, which may perturb its functions. Moreover, an additional computational setup was designed to study effects of 2450MHz field on MT response to AFM tip. It was found, more tip velocity led to MT faster transformation and less time was required to change MT elastic response to plastic one, applying constant radius. Moreover it was observed smaller tip caused to increase required time to change MT elastic response to plastic one, considering constant velocity. Furthermore, exposing MT to 2450MHz field led to no significant changes in MT response to AFM tip, but quick change in MT elastic response to plastic one.

The effects of external electric fields of 900 MHz and 2450 MHz frequencies onαβ-tubulin dimer stabilized by paclitaxel: Molecular dynamics approach

Using molecular dynamics simulation method, the effects of external electric fields of 900[Formula: see text]MHz and 2450 frequencies on [Formula: see text]-tubulin dimer stabilized by paclitaxel, have been modeled. Due to this purpose, two systems, (A) [Formula: see text]-tubulin dimer and (B) [Formula: see text]-tubulin dimer stabilized by paclitaxel, were exposed to an external electric field of 0.01[Formula: see text]V/nm with frequency values of 900[Formula: see text]MHz and 2450[Formula: see text]MHz. It was found that application of these fields, which are in the range of cell phone and microwave frequencies, increased the flexibility of each system. Since paclitaxel, as chemotherapy drug, is used to increase the rigidity of dimer, application of such fields may disturb the effect of paclitaxel on the dimer. Consequently, negative side effects on the chemotherapy process may be observed.

Water molecules response to an external GHz electric field in KcsA potassium channel: A molecular modeling approach

KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K + and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel.

Influence of GHz electric fields on the mechanical properties of a microtubule

The effects of external GHz electric fields on the mechanical properties of a microtubule (MT) have been modeled through the application of a molecular dynamics simulation method. To explore the properties of the MT, two different systems each consisting of a pair of dimers were exposed to an 0.03 V/nm electric field with a frequency ranging between 1 to 10 GHz. It was found that the Young's modulus of each system, which is related to the flexibility of the MT, was lower at some frequencies and higher at others in comparison with normal biological conditions. Hence, the application of such an electric field with a frequency in this range may affect MT function, which could have positive or negative effects on cell health. Positive effects include its potential use in cancer treatment, where the application of such a field could lead to a decrease in MT rigidity, similar to the effect of Taxol on MTs. Negative effects include unwanted changes to the mechanical properties of MTs (e.g., disturbing the cell division process and in turn increasing the risk of cancer) upon the application of such a field.

External electric field effects on the mechanical properties of the αβ-tubulin dimer of microtubules: a molecular dynamics study

The mechanical properties of the αβ-tubulin dimer of microtubules was modeled by using the molecular dynamics (MD) simulation method. The effect on the mechanical properties of the dimer of the existence and nonexistence of an applied electric field, either constant or periodic, was studied. Since there are charged or polar groups in the dimer structure, the electric field can interact with the dimer. The elastic constant and Young's modulus of the dimer were decreased when the dimer was exposed to a constant electric field of 0.03 V/nm. Furthermore, applying an oscillating electric field in the 1 GHz range to the dimer increased the elastic constant and Young's modulus of the dimer. These parameters were related to dimer rigidity and, consequently, in this frequency range, the application of electric fields may affect the function of microtubules.

Constant electric field simulations of the membrane potential illustrated with simple systems

Advances in modern computational methods and technology make it possible to carry out extensive molecular dynamics simulations of complex membrane proteins based on detailed atomic models. The ultimate goal of such detailed simulations is to produce trajectories in which the behavior of the system is as realistic as possible. A critical aspect that requires consideration in the case of biological membrane systems is the existence of a net electric potential difference across the membrane. For meaningful computations, it is important to have well validated methodologies for incorporating the latter in molecular dynamics simulations. A widely used treatment of the membrane potential in molecular dynamics consists of applying an external uniform electric field E perpendicular to the membrane. The field acts on all charged particles throughout the simulated system, and the resulting applied membrane potential V is equal to the applied electric field times the length of the periodic cell in the direction perpendicular to the membrane. A series of test simulations based on simple membrane-slab models are carried out to clarify the consequences of the applied field. These illustrative tests demonstrate that the constant-field method is a simple and valid approach for accounting for the membrane potential in molecular dynamics studies of biomolecular systems. This article is part of a Special Issue entitled: Membrane protein structure and function.