Congratulations: Daniel Jaroň has got MSc
Congratulations to our student Daniel Jaroň who has got this MSc with thesis “Calculations of free energy of interaction of amphiphilic peptides”. We wish him a lot of success and all the best in his future career.
Coiled-coil (CC) is a structural motif very abundant among proteins and is one of the main structural components of self-assembly structures. The simplest type of CC is a dimer formed from two parallel α helices, which are bound together via hydrophobic interaction. Typical characteristics of such helices are specific pattern of seven amino acids noted A-G. The goal of the thesis was to investigate the interaction of three groups of CC dimers. The first group is related with biologically important MYC protein, which is Transcription factor, often related with cancer. In the second group we studied synthetically created peptide, whose self-assembled structures and impact of specific amino acids was well-investigated. In the third group we systematically changed sequence and investigated impact of salt bridges on dissociation energy of CC. Using MD simulations and umbrella sampling method, we computed dissociation free energy of all studied systems. Results from the first group showed that the part of MYC (which participate in CC motif) binds OmoMYC and MYC weakly, however MAX and MAD are bound strongly. By analysis of the second group, we show that B, C, and F positions have no impact of dissociation energy. And the results from third group did not show any connection between number of SB and dissociation free energy, which led us to understanding the importance of proper reaching free energy minima and its connection to the protocol. This thesis results contribute to understanding of interaction of CC and impact of specific amino acids. Understanding all aspects of the CC interaction might lead to the development of possible inhibitors of important binding sites, and to the design of peptides, that self-assemble to predefined structures.