Jiri Mares

Docent, Ph.D.

Postdoctoral Researcher

tel: (+358-8)-553 1306
office: KE316
email: firstname.lastname@oulu.fi

Topics of experience

Structural biology

Even though this chapter returns to my PhD studies with Prof. Oliver Zerbe at the University of Zurich, one successful example can be mentioned - elucidation of molecular interaction between a lipopolysaccharide (LPS) of a bacterial membrane and the antibiotics polymyxin B. Here I developped the purification protocol for LPS, obtained intermolecular NOE signals by NMR in membrane mimetics and finally created a model using molecular modeling using restrains derived from the NMR measurements [10.1074/jbc.M806587200].

Paramagnetic NMR

A long period with Prof. Juha Vaara, accumulating a lot of knowledge in computational chemistry and theory of NMR, especially paramagnetic NMR (pNMR) shielding. A notable results culminated in presenting the point-dipole approximation within pNMR theory [10.1039/C8CP04123G, 10.1002/anie.201608829] .

Forcefield development

A practical sidetrack when needing a molecular dynamics simulations has been to optimize the required forcefield parameters. Twice in projects with Prof. Vaara (a single particle parameters for polarizable forcefield)[10.1016/j.chemphys.2014.09.008, 10.1038/s41598-018-25418-4], and recently a larger-scale optimization of parameters for joined NMR and molecular dynamics study of solution of surfactant molecules in project with Prof. Ville-Veikko Telkki.

NMR relaxation and spin dynamics

NMR relaxation has been topic in several studies together with pNMR effects [10.1039/C3CP55522D] and molecular-dynamics driven spin dynamics simulation [10.1063/1.4885050], where spin-dynamics was not my task yet. I have programmed my own spin-dynamics code for recent project dealing with chemical exchange of OH protons of glucose, a project started with Asoc. Prof. Timo Liimatainen [Manuscript under evaluation in PCCP]. The code is under development for more recent projects with Prof. Ville-Veikko Telkki.

Other

In different project I played a minor role in taskts like sampling of conformational space [10.1038/s41467-022-29249-w], specra fitting [10.1016/j.xcrp.2023.101281] or tailored in silico molecular manipulations in several projects.