Computer modeling of biological nanostructures


prof. dr hab. Ewa Brocławik (ICSC) (mail)


Computer modeling of biological nanostructures

Foreign partner:

Prof. P.E.M. Siegbahn,Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden

Brief description:

Understanding mechanisms of metalloenzymes at the atomic scale is a prerequisite for rational design of bio- or biomimetic catalysts. The goal of this project is to contribute to that understanding by applying theoretical methods to reliable models of selected metalloenzymes. With the use of various theoretical methods, including molecular dynamics, QM/MM methods and pure quantum chemical modeling, a coherent description of enzymatic processes will be sought.

Students international exchange:

The student will stay in the group of the Swedish partner for two reporting periods (V-th and VI-th) performing quantum chemical studies.

The purpose of the student's visit at the Stockholm University is to master the scientific art of quantum chemical simulations for reactions catalyzed by metalloenzymes. Prof Per E.M. Siegbahn, who will supervise the student, was a pioneer of such studies, and nowadays he is renowned for his outstanding contribution to this field. The great expertise of Prof Siegbahn, documented by 118 publications since 2000, together with ample computer resources available at the Stockholm University, will enable the student to pursue the project efficiently.

During his/her stay at the Stockholm University the student will construct reliable models of the active site regions in the enzyme-substrate complexes and perform computational investigations of the reaction mechanisms, involving locating intermediates and transition states along reaction coordinate(s). The computational results will be confronted with available experimental data, and based on the quality of such comparison, the quantum chemical models and calculations may be refined. The actual identity of the studied system will be motivated by the state of the knowledge at the time soon before the commencement of the PhD study.

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