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Molecular Modelling

 

There have been studies which have hypothesized a possible interaction mechanism between RF and various protein or DNA activities in living organisms. This project seeks to apply a published and patented molecular modelling theory based on digital signal processing to test the feasibility of such mechanisms for the heat shock protein families. The Resonant Recognition Model (RRM) will be used to investigate the time scale of protein interactions, influence of water as a medium for electromagnetic radiation, and the impact of available chemical energy supply for molecular activation. Importantly, it is proposed that the resulting predictions be tested empirically with in vitro and in vivo techniques to corroborate those results.

 

Current Projects

 

Molecular Modelling of RF/HSP interaction

Project Leader:  Prof. Irena Cosic, Dr Elena Pirogova (NHMRC funded Research Fellow)

 

NHMRC funded staff: Vuk Vojisavljevic, PhD candidate

 

Aims: To discover the mechanisms that are underlying the process of protein activation and the selectivity of protein interactions. To investigate the changes in bioactivity of selected protein groups exposed to electromagnetic fields (EMF). Particularly, two protein groups, dehydrogenases and HSPs, are irradiated with a theoretically predicted specific frequency of electromagnetic radiation, and their protein activity is measured before and after the exposures.

 

Methods:

 

Computational analysis of protein sequences using the Resonant Recognition Model

 

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Application of the RRM in the structure-function analysis of dehydrogenase and HSP protein sequences aiming to identify the characteristic frequencies that correspond to the biological behaviour of the analysed protein groups.

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Based on this characteristic frequency identified for each analysed protein we will then calculate the wavelength of EMF to be applied to the analysed protein samples to modify their bioactivity (stages are completed).

 

Wavelength of light irradiation determination

To test the feasibility of our protocol, initial work is commenced at optical wavelengths to replicate known results.  It is inferred that approximate wavelengths in real frequency space can be calculated from the RRM characteristic frequencies for each biologically related group of sequences. These calculations are used to predict the wavelength of light irradiation which might affect the biological activity of proteins exposed (work completed).

 

3-D structure prediction

Using Discovery Studio (DS) Modelling Software, Accelrys Inc. we analyse and predict the 3-D structures of the newly designed peptide analogs based on the characteristic frequency determined by RRM. Also we perform a comparative analysis of 3-D structures of these peptides and their parent proteins, dehydrogenase and HSP sequences (work completed).

 

Experimental study (work in progress)

The experimental procedure has been established. The study consists of the series of experiments that can confirm predictions by RRM that protein activity can be influenced by external electromagnetic radiation. Preliminary studies with L-Lactate Dehydrogenase has been completed with the results presented at the IEEE EMBS International Conference in Shanghai, China.

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Based on the characteristic frequency identified for each analysed enzyme we will then calculate the wavelength of the applied electromagnetic radiation, λ=201/fRRM

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Irradiate protein samples with external EMF of predicted wavelength

 

Monochromator SPEX 270M (1200g/mm grating , focal length - 270 mm, resolution - 0.1nm on 500nm, dispersion - 3.1 nm/mm) with a lamp Olympus 68v5A TP1 is used as a source of visible/near IR radiation. According to preliminary results, the time of illumination should be at least for 10min. Also, a chopper frequency in the range from 1Hz to 1500Hz is used.

 

The experimental procedure for monitoring changes in the kinetics of the selected enzyme samples before and after the exposures is provided below.

 

L-Lactate Dehydrogenase (EC 1.1.1.27)

The proposed experimental study consists of the series of experiments to monitor the change of enzyme kinetics before and after exposure to an external source of EMF radiation.  L-Lactate dehydrogenase (LDH) catalyses the following reaction:

                                             LDH

             Pyruvate + NADH ------> Lactate + NAD+ + H+

 

The suitability of LDH enzyme for our experiments is attributed to the absorption characteristics of NADH (Nicotinamide Adenine Dinucleotide, Reduced form). NADH is able to absorb the light at 340nm in contradiction to the NAD (Nicotinamide Adenine Dinucleotide Nicotinamide Adenine Dinucleotide, Oxidized form), which is inactive at this frequency. Due to the different absorption characteristics of NADH and NAD we are able to optically observe if the reaction Pyruvate ® Lactate in the presence of LDH as an accelerator has occurred and then determine the amount of the reactants. The reaction rate depends on the concentration of enzyme and substrate.

 

Future work will include the experiments with heat shock proteins (HSP)

 

Results: Expected in 2008

 

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