Molecular modelling and simulation of retroviral proteins and nanobiocomposites

Doctoral Thesis / Dissertation from the year 2011 in the subject Biology - Micro- and Molecular Biology, grade: 1 (magna cum laude), University of Würzburg (Theodor-Boveri-Insitut für Biowissenschaften), course: computer science, virology, biophysics, language: English, abstract: HIV-1 integrase has nuclear localization signals (NLS) which play a crucial role in nuclear import of viral preintegration complex (PIC). However, the detailed mechanisms of PIC formation and its nuclear transport are not known. I investigated the interaction of this viral protein HIV-1 integrase with proteins of the nuclear pore complex such as transportin-SR2 (Shityakov et al., 2010). I showed that the transportin-SR2 in nuclear import is required due to its interaction with the HIV-1 integrase. I analyzed key domain interaction, and hydrogen bond formation in transportin-SR2.
In this thesis, I compared the transduction frequencies of PPT modified FV vectors with lentiviral vectors in nondividing and dividing alveolar basal epithelial cells from human adenocarcinoma (A549) by using molecular cloning, transfection and transduction techniques and several other methods. In contrast to lentiviral vectors, FV vectors were not able to efficiently transduce nondividing cell (Shityakov and Rethwilm, unpublished data). Despite the findings, which support the use of FV vectors as a safe and efficient alternative to lentiviral vectors, major limitation in terms of foamy-based retroviral vector gene transfer in quiescent cells still remains.
In computational drug design I used molecular modelling methods such as lead expansion algorithm (Tripos) to create a virtual library of compounds with different binding affinities to protease binding site. Further computational analyses revealed one unique compound with different protease binding ability from the initial hit and its role for possible new class of protease inhibitors is discussed (Shityakov and Dandekar, 2009).
The phenomenon of an intercalated single-wall carbon nanotube in the centre of lipid membrane was extensively studied and analyzed. The root mean square deviation and root mean square fluctuation functions were calculated in order to measure stability of lipid membranes.
The results indicated that an intercalated carbon nanotube restrains the conformational freedom of adjacent lipids and hence has an impact on the membrane stabilization dynamics (Shityakov and Dandekar, 2011). The results derived from this thesis will help to develop stable nanobiocomposites for construction of novel biomaterials and delivery of various biomolecules for medicine and biology.