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Molecular dynamics simulations of the muscarinic receptor
 Cajzl, Radim ; Barvík, Ivan (advisor) ; Pospíšil, Miroslav (referee)
Title: Molecular dynamics simulations of the muscarinic receptor Author: Radim Cajzl Department: Institute of Physics of Charles University Supervisor: RNDr. Ivan Barvík, Ph.D., Division of Biomolecular Physics Abstract: This thesis is devoted to molecular dynamics simulations of the mus- carinic M2 receptor placed in a phospholipidic membrane. Basic algorithms of molecular dynamics are described and applied on a simple model of rare gases. Relations for calculation of binding free energies are derived. Several tricks for sa- ving up computational time are presented. Next part contains a brief description of proteins and cellular membranes, structure and biological relevance of musca- rinic receptors and known crystal structures of the muscarinic M2 receptor. The chapter with results contains detailed description of calculations of bin- ding free energy differences for several ligands bound to the muscarinic M2 recep- tor. Obtained values match the experimental ones. Dynamics of the muscarinic M2 receptor was also studied yielding a direction for future studies of the acti- vation mechanism. Short discussion on application of obtained results in rational drug design can be found in the Conclusion chapter. Keywords: molecular dynamics, membrane proteins, free energy perturbation, muscarinic receptor,...
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