Related papers: RNA Folding Pathways in Stop Motion
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
Accurate prediction of RNA three-dimensional (3D) structure remains an unsolved challenge. Determining RNA 3D structures is crucial for understanding their functions and informing RNA-targeting drug development and synthetic biology design.…
This work presents the use of graph learning for the prediction of multi-step experimental outcomes for applications across experimental research, including material science, chemistry, and biology. The viability of geometric learning for…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
We report the folding thermodynamics of ccUUCGgg and ccGAGAgg RNA tetraloops using atomistic molecular dynamics simulations. We obtain a previously unreported estimation of the folding free energy using parallel tempering in combination…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of…
Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states.…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
Infrared and Raman spectroscopy are widely used for the characterization of gases, liquids, and solids, as the spectra contain a wealth of information concerning in particular the dynamics of these systems. Atomic scale simulations can be…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…