Biomolecular simulations, from RNA to protein : thermodynamic and dynamic aspects

The process of transforming the information stored in the DNA of genes into functional RNA molecules and proteins via transcription and translation is the most fundamental process of all known life. Even though these processes involve large macromolecules and dynamics on long time scales they all ultimately rely on atomic level interactions between nucleic acids or amino acids. Only a few experimental techniques are available that can study the large systems involved in atomic detail. Computer simulations, modeling biological macromolecules, are therefore an important tool in investigating fundamental biological processes. In this thesis, Molecular Dynamics (MD) simulations have been used to study the translation of mRNA by tRNA and the function of the regulatory riboswitches. The thesis also covers the improvement of methodology by the development of a new representation of the important Mg ions and an improvement of the understanding of the connection between MD and experimental NMR data. In Paper I, the effect of post transcriptional modifications of the tRNA anti codon on the decoding of mRNA in the ribosome is studied. All atom MD simulations have been performed of the ribosomal A site with and without modifications present, including extensive free energy calculations. The results show two mechanism by which the decoding is affected: The further reach provided by the modifications allows an alternative outer conformation to be formed for the non cognate base pairs, and the modifications results in increased “catalytic” contacts between tRNA, mRNA and the ribosome. In Paper II, the folding mechanism of the add A riboswitch is studied under different ionic conditions and with and without the ligand bound. In addition to standard simulations, we simulated the unfolding by umbrella sampling of distance between the L2 and L3 loops. In the results, no significant effect of Mg or Na ion environments or ligand presence can be seen. But a consistent mechanism with the P3 stem being more flexible than P2 is observed. More data might however be needed to draw general conclusions. In Paper III, the parameters describe Mg ions in MD simulations are improved by optimizing to kinetic data of the H2O exchange. Data from NMR relaxation experiments was used as optimization goal. The newly developed parameters do not only display better kinetic properties, but also better agreement with experimental structural data. In Paper IV, the dynamical data, obtained from NMR relaxation experiment of a protein is related to dynamics seen in an MD simulation. The analysis provides important information for the interpretation of experimental data and the development of simulation methods. The results show, among other things, that significant parts of the entropy are not seen by NMR due to a limited time window and inability to account for correlation of motions. LIST OF PUBLICATIONS I. OLOF ALLNÉR and Lennart Nilsson. Nucleotide modifications and tRNA anticodon mRNA codon interactions on the ribosome, 2011, RNA, 17(12):2177-2188 II. OLOF ALLNÉR, Lennart Nilsson, Alessandra Villa. Effects of Ion Environment and Ligand on the Kissing Loops in the add Adenine-Riboswitch, 2012, manuscript III. OLOF ALLNÉR, Lennart Nilsson, Alessandra Villa. Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations, 2012, Journal of Chemical Theory and Computation, 8(4):1493-1502 IV. OLOF ALLNÉR and Lennart Nilsson. Motions and Entropies in Proteins as Seen in NMR Relaxation and Molecular Dynamics Simulations, 2012, manuscript