Molecular Simulation Studies of Dynamics and Interactions in Nucleic Acids

In my thesis work, I conducted molecular simulation studies to explore dynamics and interactions in nucleic acids. I began my work by applying conventional molecular dynamics (MD) simulations to study the local and global dynamics of the transactivation response (TAR) element from the type-1 human immunodeficiency virus (HIV-1) and the effect of binding of ligands on the dynamics of TAR RNA. I determined that the TAR RNA structure was stabilized on binding of ligands due to the decreased flexibility in helices that comprise TAR RNA. This rigidity of the TAR RNA structure was coupled with the decreased flipping of bulge nucleotides. I also observed that different initial conformations of TAR RNA converged to similar conformations in the course of MD simulations. Finally, I observed the formation of binding pockets in unliganded TAR structures that could accommodate ligands of various sizes. After comprehensively exploring the dynamics of TAR RNA with and without ligands, I conducted more specific studies on the interactions that were formed or broken during the (un)binding process of two ligands, a small molecule inhibitor and a helical peptide, from the viral RNA molecules using non-equilibrium simulations. Firstly, I observed that the dissociation of a small molecule is coupled with a base flipping event which I described using physical variables and thermodynamic properties. Secondly, I observed that the dissociation process of a helical peptide is facilitated by a network of hydrogen bonding and salt bridging interactions which are formed across four distinct dissociation pathways. I also resolved the free-energy profiles for each pathway which revealed metastable states and dissociation barriers. Based on the free-energy profiles, I proposed a preferred dissociation pathway and identified one arginine amino acid that plays an important role in the recognition of the peptide by the viral RNA. Next, I focused on studying a more complex reaction coordinate (RC) that could describe a base flipping mechanism in a double-stranded RNA (dsRNA) molecule using transition path sampling (TPS) methods. Additionally, I used the likelihood maximization method to determine a refined RC based on an ensemble of 1000 transition trajectories created by the path sampling algorithm. The refined RC consisted of two collective variables (CVs), a distance and a dihedral angle between the neighboring nucleotides and the flipping base. I also projected a free-energy profile along the refined RC which revealed three free-energy minima. I proposed that one of the free-energy minima represented a wobbled conformation of the flipping nucleobase. I also analyzed the reactive trajectories which showed that the base flipping is coupled with global conformational changes in a stem-loop of dsRNA. Outside of studies involving RNA, I conducted conventional MD simulations to study the dynamics of a porphyrin/DNA nanoassembly which revealed the overall left-handed orientation of the nanoassembly. I characterized the resulting porphyrin/DNA system using various physical variables. Overall, my thesis revealed the local and global dynamics of RNA as well as DNA systems, and perturbations to dynamics originating in binding of ligands of various sizes

Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides

Interactions between RNA molecules and proteins are critical to many cellular processes and are implicated in various diseases. The RNA-peptide complexes are good model systems to probe the recognition mechanism of RNA by proteins. In this work, we report studies on the binding-unbinding process of a helical peptide from a viral RNA element using nonequilibrium molecular dynamics simulations. We explored the existence of various dissociation pathways with distinct free-energy profiles that reveal metastable states and distinct barriers to peptide dissociation. We also report the free-energy differences for each of the four pathways to be 96.47 ± 12.63, 96.1 ± 10.95, 91.83 ± 9.81, and 92 ± 11.32 kcal/mol. Based on the free-energy analysis, we further propose the preferred pathway and the mechanism of peptide dissociation. The preferred pathway is characterized by the formation of sequential hydrogen-bonding and salt-bridging interactions between several key arginine amino acids and the viral RNA nucleotides. Specifically, we identified one arginine amino acid (R8) of the peptide to play a significant role in the recognition mechanism of the peptide by the viral RNA molecule

Role of conformational heterogeneity in ligand recognition by viral RNA molecules

Ribonucleic acid (RNA) molecules are known to undergo conformational changes in response to various environmental stimuli including temperature, pH, and ligands. In particular, viral RNA molecules are a key example of conformationally adapting molecules that have evolved to switch between many functional conformations. The transactivation response element (TAR) RNA from the type-1 human immunodeficiency virus (HIV-1) is a viral RNA molecule that is being increasingly explored as a potential therapeutic target due to its role in the viral replication process. In this work, we have studied the dynamics in TAR RNA in apo and liganded states by performing explicit-solvent molecular dynamics (MD) simulations initiated with 27 distinct structures. We determined that the TAR RNA structure is significantly stabilized on ligand binding with especially decreased fluctuations in its two helices. This rigidity is further coupled with the decreased flipping of bulge nucleotides, which were observed to flip more frequently in the absence of ligands. We found that initially-distinct structures of TAR RNA converged to similar conformations on removing ligands. We also report that conformational dynamics in unliganded TAR structures leads to the formation of binding pockets capable of accommodating ligands of various sizes

Местные и региональные элиты

The article reviews the history of the notion of elite, its mission and functions, and, first of all, how it forms the reasons for existence. It also features the role of the elite in the relations between the state and the society. Organization of the power is newly characterized as a meritocracy, or a merit-based power system. In the conclusion of the article there are proposals for inclusion of regional and local elites in the processes of regional development and planning.В статье реконструируется история формирования понятия «элита», предназначение и функции элиты, прежде всего формирование ею смыслов существования. Показано место элиты в отношениях между государством и обществом. Дана новая характеристика организации власти как меритократии, власти по заслугам. Статья заканчивается предложениями по включению региональных и местных элит в процессы регионального развития и проектирования

Reaction Coordinate and Thermodynamics of Base Flipping in RNA

Base flipping is a key biophysical event involved in recognition of various ligands by ribonucleic acid (RNA) molecules. However, the mechanism of base flipping in RNA remains poorly understood, in part due to the lack of atomistic details on complex rearrangements in neighboring bases. In this work, we applied transition path sampling (TPS) methods to study base flipping in a double-stranded RNA (dsRNA) molecule that is known to interact with RNA-editing enzymes through this mechanism. We obtained an ensemble of 1000 transition trajectories to describe the base-flipping process. We used the likelihood maximization method to determine the refined reaction coordinate (RC) consisting of two collective variables (CVs), a distance and a dihedral angle between nucleotides that form stacking interactions with the flipping base. The free energy profile projected along the refined RC revealed three minima, two corresponding to the initial and final states and one for a metastable state. We suggest that the metastable state likely represents a wobbled conformation of nucleobases observed in NMR studies that is often characterized as the flipped state. The analyses of reactive trajectories further revealed that the base flipping is coupled to a global conformational change in a stem-loop of dsRNA

Heavily loaded joints for assembling aerobrake support trusses

The major emphasis was to develop erectable joints for large aerobrake support trusses. The truss joints must be able to withstand the large forces experienced by the truss during the aero-pass, as well as be easily assembled and disassembled on orbit by astronauts or robots. Other important design considerations include; strength, stiffness, and allowable error in strut length. Six mechanical joint designs, as well as a seventh joint design, where a high strength epoxy is injected to make the connection rigid, are presented

Axiology and Teleology of Theoretical Work (on the Occasion of the Seventieth Birthday of Boris Rodoman)

The article discusses the most important principles of theoretical work, the etymology of the origin of the concept “theory”, examines the relevance of theoretical and historical approaches, presents the main constructs of theoretical work: model, concept, method. Theory can act as a hermeneutical tool. It is argued that if a theory does not cause an ontological shock, then it is insufficient. The reflexivity of any theoretical work is emphasized