Coarse-grained calculations on electronic polarization effects in proteins 

Thesis event information

Date and time of the thesis defence

Place of the thesis defence

Leena Palotie auditorium 101A Kontinkangas campus

Topic of the dissertation

Coarse-grained calculations on electronic polarization effects in proteins 

Doctoral candidate

Master of Science Outi Lampela

Faculty and unit

University of Oulu Graduate School, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, Biocomputing

Subject of study

Biochemistry

Opponent

professor Mikko Karttunen, The University of Western Ontario, London, Ontario, Canada 

Custos

Doctor André Juffer, Biocenter Oulu, University of Oulu

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Coarse-grained calculations on electronic polarization effects in proteins 

Computational models enable simulation of complex systems and testing of theories, especially at the molecular level, nano scale, where experimental methods are restricted. 

Electrostatic interactions are crucial for the functioning of biomolecules such as proteins. Examples of proteins include the enzymes that catalyse chemical reactions in cells or collagen of connective tissues. Part of the electrostatic interaction is electronic polarization, where negatively charged electrons within an atom redistribute as a response to an applied electric field, forming induced dipoles with the positively charged protons of the atomic nucleus. Polarizability is important in predicting the optical properties and modelling electrostatic interactions. Understaning electronic polarization effects can improve the methods used to detect protein interactions and can aid in designing better interactions for example in drug design. 

The atomistic computational models that include electronic polarization are heavy. There is a need to model bigger systems in protein research, thus it is of interest to study the inclusion of electronic polarization to the less detailed,  coarse-grained, molecular models of proteins.  

This work studied how one of the atomistic models of electronic polarization, the point dipole model, would work at coarse-grained computations. The work examined computation of the electronic polarizability of proteins and the interaction energies with the coarse-grained model.   

Based on the results, the point dipole approximation model used is applicable to coarse-grained calculation in the analysis of molecular interactions and optical properties. The results also highlight the need to focus in the future on specifying the impact of the electric field produced by electronic polarization in the coarse-grained calculation. 
Last updated: 8.12.2022