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Molecular study of transmembrane protein under nanosecond electric signals

STSM by Paolo Marracino, PhD Student

Period of mission: from 12/10/2014 to 25/10/2014

Home institution: Department of Information Engineering, Electronics and Telecommunications, Sapienza, University of Rome, Rome, Italy

Host institution: University College Dublin (UCD), Dublin, Ireland

The use of extremely short and intense electric pulses, allows the manipulation of intracellular membranes and to possibly interact with proteins, both intracellular or embedded in membranes. Full atomistic molecular dynamics simulations aim to shed light to the main mechanisms of interactions between the exogenous electric pulses and these kinds of targets. The present STSM had two major objectives: first of all to perform a feasibility study for the integration of “realistic electric signals” inside a simulation package (NAMD) which does not envisage using this feature; secondly to investigate the possibility to import the topology of a transmembrane protein, the aquaporin (already investigated by the STSM grantee via NAMD simulations), into a GROMACS compatible format. In particular for the first task, the TCL scripting language (Tool Command Language) has been adopted to create a series of scripts that tell NAMD to apply certain forces (for example the ones exerted by external electromagnetic fields) to certain atoms. Therefore specific scripts have been written, each for a particular electric signal (the magnetic components are usually omitted in classical molecular dynamics simulations), specifically a Gaussian pulse, a Bipolar pulse (the Gaussian derivative) and a square wave signal. The scripts were written with the underlying idea to give the user a complete control of signal characteristics in terms of duration, amplitude and frequency content. A series of very short simulations established the right implementation of the TCL script in NAMD. The second task has been tackled by means of some functions embedded in GROMACS package and via the VMD (Visual Molecular Dynamics) program. A series of conversion steps led to a complete topology fully compatible with the GROMACS format.

Oral presentation(s) originating from this mission

Event 1st World Congress on Electroporation and Pulsed Electric Fields in Biology, Medicine and Food & Environmental Technologies
Location Portorož/Slovenia
Period 06/09 - 10/09/2015
Authors Paolo Marracino, Micaela Liberti, Francesca Apollonio and Andrea Amadei
Title nsPEfs induce irreversible denaturation of sperm whale myoglobin: a thermodynamics analysis

Poster presentation(s) originating from this mission

Event 1st World Congress on Electroporation and Pulsed Electric Fields in Biology, Medicine and Food & Environmental Technologies
Location Portorož/Slovenia
Period

06/09 - 10/09/2015

Authors Paolo Marracino, Micaela Liberti, Francesca Apollonio and Andrea Amadei
Title nsPEfs induce irreversible denaturation of sperm whale myoglobin in water: a kinetics analysis

 


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