Hello, A new project on the LCRC cluster has been requested. Please forward the information on to the LCRC Allocation sub-committee. Applicant's name: Bachir Aoun Applicant's institution: ANL Applicant's division: XSD Project Name: MD_for_riboA Project title: Molecular Dynamics Simulation of the unbounded Adenine Riboswitch RNA Associated funding: BES/DOE Other Systems: No Science: The main objective of this proposal is to use computer simulations to characterize molecular processes in riboswitch ribonucleic acid (RNA), make direct connections to solution x-ray scattering results, and better understand the structural and dynamic properties key to its biological function. For a long time, all RNAs but tRNA, mRNA, and rRNA that involve protein synthesis had been considered junk material in biological organisms. However, in the past two decades, these non-coding RNAs have been discovered to play pivotal biological roles, such as catalysis and gene regulation, many of which had been thought only capable of being performed by its counterpart, protein. Despite their biological importance, knowledge of three dimensional structural details of RNAs is very limited due to the characterization difficulties in RNA structure determination . This project uses the molecular dynamics (MD) simulation method to model solution state structures of the unbounded aptamer domain of adenine riboswitch RNA molecule. Riboswitch RNAs are gene-regulatory, non-coding RNA elements found in bacteria, fungi and plants and are likely candidates for drug-targets. Adenine riboswitch RNA was found in the add gene of Bacillus subtilis. The aptamer domain of adenine riboswitch RNA has 71 nucleotides (riobA71), and the structure and dynamics of the unbounded riboA71 is closely connected to the RNA’s function. However, in general, the inherit flexibility of the unbounded RNA states makes it difficult to extract atomistically detailed information from most standard characterization tools. Solution x-ray scattering is a powerful structural characterization tool capable of measuring spatial information from all atoms within large molecules; however, its resolution is relatively low due to the isotropic nature of solution phase samples. MD simulations, on the other hand, can provide detailed molecular-level information and probe dynamical processes. The results from the herein proposed MD simulations will be coupled with x-ray scattering measurements to generate a unifying picture of this complex system and help elucidate the structure and dynamics of riboA71. We have already measured riboA71 under various conditions using solution x-ray scattering and obtained low-resolution envelopes for the RNA. We expect this combined simulation and experimental characterization study will generate a strong feedback loop between theory and experiment to obtain an atomic level delineation on the riboswitch RNA’s structure and dynamics (e.g. identification of base pairs key to open/close mechanism, structure and accessibility of binding sites, structural evolution in different salt environments) and ultimately provide structural insights into RNA structure-function relationships. Project description: In this project, adenine riboswitch RNA will be investigated using the molecular dynamics simulation method. Adenine riboswitch RNA consists of an aptamer domain and an expression platform domain which partially overlap each other in sequence. The aptamer domain binds to an adenine ligand and leaves the translation promoter, the Shine-Dalgarno sequence, in the expression platform domain accessible to the translation apparatus starting the translation process. The crystal structural adenine-bounded aptamer domain has been solved in 2005 and many mutagenesis studies have been performed on the bounded structures since then. The extensive studies on the bounded aptamer domain make it a model system for an RNA structural study. However, unbound states, which are important for understanding the RNA function, have been less studied due to technical difficulties discussed above. Recently, we have employed solution x-ray scattering technique to study the apta mer domain of riboA71 under various conditions, including with and without adenine, MgCl2, and urea, and successfully obtained the low-resolution molecular envelope of riboA from the scattering data . In this project, we plan to perform the molecular dynamics simulation on riboA71 under the same experimental conditions. The purpose of this project is three folds: (1) providing a atomistic structural picture of the unbounded riboA71 and insights into the RNA function; (2) trying to find the governing principles for the structure and dynamics key to RNA folding; (3) providing a solid foundation for near-future projects focused on the adenine ligand capture process for the aptamer domain and the full length RNA. Currently, we have done some short time simulations on a small cluster and observed encouraging agreement with x-ray scattering measurements. For example, the RNA structure was successfully reproduced for the case of no adenine and Mg2+ within a 10 nanosecond (ns) simulation, but it is imperative to run a longer (80-100 ns) simulation to check convergence of equilibrium properties, such as structure stability, and sample long-time dynamical modes of the system. We are currently in the position to immediately begin running simulations at the start of the award period for these important simulations. The MD simulations in this project will calculated using the NAMD code, which has been ported to several high-performance computing architectures and is efficiently parallelized for large-scale computations. In total, 10 systems of varying salt concentrations and ligands will be simulated to make a direct comparison to the experimental characterization results. Each simulation requires 100 ns to obtain statistically converged results. The parallel efficiency of the NAMD code using the riobA71 system currently being examined (47,582 particles) was determined to be 85.2% and 58.2% on 256 and 512 Intel Sandy Bridge cores, respectively. On 512 cores, with a productivity of 29.16 ns/day each 100 ns trajectory would require 42,140 core-hours. Thus, the total allocation request encompassing all ten planned simulations brings the total allocation request to 421,400 core-hours with a nearly linear burn-rate over the course of the award period. The herein planned simulations will be managed by Bachir Aoun (XSD) and Chris Knight (LCF), both of whom have extensive experience with running molecular simulations. Xiaobing Zuo (XSD) has performed the x-ray scattering measurements and will be involved in all discussions regarding the comparisons between simulated and experimental characterizations of these riboA71 systems. Project URL: Requested allocation: 421400 Q1: 105350 Q2: 105350 Q3: 105350 Q4: 105350 Justification: The requester has used undetermined amount hours of their initial startup project. In addition to approving an initial amount, please specify a Category and Subcategory for this project. For a list of the current selection of approved categories, please see: https://wiki.lcrc.anl.gov/wiki/Processes/Categories Once the Allocation committee has approved the project, please go to the Project Management page to create it: https://accounts.lcrc.anl.gov/projects.php Thank You, The LCRC Accounts System