RNA Systems Molecular Dynamics Simulations

It is well understood that RNA plays a wide variety of roles in the cell and is involved in all cellular processing of genetic information, from splicing to translation to modification, and particularly regulation, via RNA interference in eukaryotes and riboswitches in bacteria. As a world-class provider of biotechnology, Creative Biolabs provides omnidirectional technologies to meet the diverse needs of our customers. With our professional experience and advanced protein engineering platform, we can provide molecular dynamics simulations of RNA systems to meet the diverse needs of our customers.

Molecular Dynamics Simulation of RNA Systems

Understanding how RNA molecules carry out their biological functions will necessarily involve understanding RNA structure and dynamics at the atomistic level, a challenge that can be addressed using a combination of experimental studies and molecular dynamics (MD) simulations. The goal of MD simulations is to mimic the real-time dynamics of single solvated biomolecules in order to elucidate atomic-resolution details of their structural dynamics and eventually estimate the free energies of specific conformations. Simulated RNA molecules are immersed in a sufficiently large box of water molecules and ions that is periodically extended in all directions. The molecules are described by simple pair additive atomistic potentials that treat atoms as van der Waals spheres with partial, constant, point charges localized at the individual atomic centers, linked by harmonic springs mimicking the covalent structure and supplemented by simple torsion profiles.

In MD simulations, a "possible" time evolution of the chosen system starting from an initial set of coordinates and velocities is calculated by integrating Newton’s classical equations of motion over a predefined timeframe. The force fields for simulating RNA were refined and stable simulation protocols for polyanionic RNA molecules have been introduced, primarily the Particle-Mesh Ewald (PME) treatment of the strong, long-range electrostatic forces. A broad set of RNA applications were tested using the AMBER code and associated force field. This method matches quantum chemical data for stacking and base pairing and has provided long stable simulations of numerous complex RNA molecules.

Fig.1 Four stages of the tRNA movement in MD simulation.

Services

MD simulations of RNA have reached a point where they can be used in a wide variety of systems to complement experiments and verify or explain experimental results. The timescales of experiment and simulation are getting closer, with experiments able to access faster and faster dynamics and with more computational power leading to longer simulations. The key to MD simulations of RNA is the adjustment of the force fields, the development of better methods to estimate free energies, and integration of molecular mechanics with quantum mechanical treatments. We can provide molecular dynamics simulation services of RNA systems to meet customers' specific requirements.

Creative Biolabs has been involved in the field of protein engineering for many years and we are fully committed to working with you to facilitate the successful completion of the projects. We have accumulated a wealth of experience from the accomplished projects and are very proud of our high-quality platforms to meet diverse needs from our clients. If you are interested in our services, please contact us for more details.

All listed services and products are For Research Use Only. Do Not use in any diagnostic or therapeutic applications.

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