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RNA is involved in the processing of all cellular genetic information, from splicing, translation to modification, and is particularly regulated by RNA interference in eukaryotes and riboswitches in bacteria. With the support of our advanced protein engineering platform established for many years, Creative BioMart discovers how RNA molecules perform their biological functions by combining experimental studies and molecular dynamics (MD) simulations to study structure and dynamics at the atomic level. Our scientists provide you with a comprehensive customized molecular dynamics simulation of RNA systems service to study the structural and thermodynamic properties of RNA molecules, facilitating the use of MD simulations as a tool to study biologically meaningful RNA molecules and protein-RNA complexes.
Ribonucleic acid (RNA) with catalytic and genetic functions is probably the most pluripotent chemical in molecular biology, and its function is closely related to its structure and dynamics. Molecular dynamics (MD) simulations have emerged as a powerful tool for detailing the conformational changes that proteins undergo at the atomic level. Furthermore, MD simulations allow the study of the structural dynamics of RNA molecular systems with unprecedented temporal and spatial resolution. The main goals of atomic MD simulations are (a) to simulate the structural dynamics of RNA molecules explicitly and in real time to support the interpretation and planning of experimental measurements of such dynamics; (b) to provide reliable and experimentally testable predictions; and (c) to furnish insights that are not obtainable by current experimental methods but which help explain RNA's multitudinous functional roles. MD simulations related to RNA systems have become very important, and more than 30 different simulations of RNA, RNA protein, and RNA ligand systems have been reported.
Fig 1. Scheme of some methods of MD simulation. (Šponer J, et al., 2018)
The physical models ("force fields") used in RNA simulations are widely considered to be generally less accurate than those used in protein simulations, so improving the accuracy of RNA force fields would greatly facilitate the use of MD simulations to study biologically meaningful functional dynamics of RNA molecules. Creative BioMart has successfully used AMBER for force fields for MD simulations of RNA systems, which can be used in a variety of systems to complement experiments and validate or interpret experimental results. In addition, faster and faster dynamics can be obtained with greater computational power and longer simulation times. We start with simple oligonucleotides and investigate the application of MD mimics in RNA motifs, riboswitches, ribosomes, and RNA/protein complexes.
The most important limitation of MD simulations is that the time scales that can be simulated are limited by the available computing resources. Moreover, the time scales on which the conformational transitions of RNAs occur are very heterogeneous. Our scientists are committed to using the following methods to allow the use of relatively short simulations to study properties emerging on long time scales, resulting in true thermodynamic and kinetic properties of the processes studied.
In addition, we complemented MD simulations with quantum mechanical (QM) calculations, which can be used to assess the possibility of specific chemical reaction pathways involving RNases, thereby motivating new experimental tests or helping to interpret existing RNA catalysis experimental data. We are also working on the use of various coarse-grained methods to study larger-scale kinetic and conformational changes not available through conventional atomic MD simulations. Here, you will experience the most professional and comprehensive molecular dynamics simulation services for RNA systems to meet your specific requirements.
Creative BioMart is based on innovative, pragmatic and honest, adhering to the tenet of "Quality is our life, providing customers with the best quality service", providing customized services to customers around the world.
We will be glad to discuss details of intended interaction studies with you and develop experimental strategies/methods tailored to your requirement. Our customer service representatives are enthusiastic and trustworthy 24 hours a day, Monday to Friday. If you are interested in our services, please do not hesitate to contact us for more information or to discuss in detail.
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