Running title: Force field dependence of riboswitch dynamics Force field dependence of riboswitch dynamics
نویسندگان
چکیده
منابع مشابه
Iterative Force-Field Calculation and Molecular Dynamics of Cyclooctanone
Body's iterative force-field computer program has been used to calculate strain energies in cyclooctanone (I). 348 MHZ 1H NMR spectra of (I) have been investigated over the temperature range of 25° to -160°C. Two conformation processes affect the 1H NMR spectrum of (I). Iterative force-field calculations on the conformations and conformational interconversion paths of ...
متن کاملRole of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.
Riboswitches are RNA-based genetic control elements that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket. To facilitate an atomic detail interpretation of experimental investigations on the role of the adenine ligand on the conformational properties and kinetics of folding of the add adenine riboswitch, we performed molecular dynami...
متن کاملMolecular Dynamics Simulation of Al/NiO Thermite Reaction Using Reactive Force Field (ReaxFF)
In this work, the thermal reaction of aluminum (Al) and nickel oxide (NiO) was investigated by molecular dynamics simulations. Some effective features of reaction such as reaction temperature, the reaction mechanism, and diffusion rate of oxygen into aluminum structure were studied. ReaxFF force field was performed to study the Al/NiO thermite reaction behavior at five different temperatures (5...
متن کاملApproach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.
Riboswitches are noncoding mRNA segments that can regulate the gene expression via altering their structures in response to specific metabolite binding. We proposed a coarse-grained Gaussian network model (GNM) to examine the unfolding and folding dynamics of adenosine deaminase (add) A-riboswitch upon the adenine dissociation, in which the RNA is modeled by a nucleotide chain with interaction ...
متن کاملAtomistic details of the ligand discrimination mechanism of S(MK)/SAM-III riboswitch.
SAM-III riboswitch, involved in regulating sulfur metabolic pathways in lactic acid bacteria, is capable of differentiating S-adenosyl-l-methionine (SAM) from its structurally similar analogue S-adenosyl-l-homocysteine (SAH). Atomic level understanding of the ligand recognition mechanism of riboswitches is essential for understanding their structure-function relationships in general. In the pre...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2015