Molecular mechanism related to the binding of fluorophores to Mango-II revealed by multiple-replica molecular dynamics simulations

Abstract

Recently, the RNA aptamers activating small-molecule fluorophores have been successfully applied to tag and track RNAs in vivo. It is of significance to investigate the molecular mechanism of the fluorophore-RNA...

Deciphering the binding mechanism of inhibitors of the SARS-CoV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes

“…With the continuous enhancement of computer processing power and the widespread application of theoretical simulation methods, molecular dynamics simulations [38][39][40][41][42][43][44][45] and binding free energy calculations [46][47][48][49][50][51][52] have been powerful tools for understanding ligand-target binding mechanisms and conformational changes of targets. [53][54][55][56][57][58] However, conventional molecular dynamics (cMD) simulations may cause the sampled conformation to be trapped in a local minimum space for some time, resulting in insufficient sampling in the protein conformational space.…”

Decoding the Identification Mechanism of an SAM-III Riboswitch on Ligands through Multiple Independent Gaussian-Accelerated Molecular Dynamics Simulations

“…The PC analysis plays an important role in obtaining insight into the conformational changes of receptors induced by ligand binding. Structurally, the carbon atom C1′ connects the adenine group of a nucleotide to the phosphate group; thus, a covariance matrix constructed using the coordinates of the carbon atoms C1′ can rationally reflect the conformational change of nucleotides, which is verified by our previous studies. , The PC analysis was executed by diagonalizing a covariance matrix constructed using the coordinates of the atoms C1′ from SAM-III recorded in the SMT. The eigenvalues from the PC analysis are depicted in Figure S5 in the decreasing order versus the corresponding eigenvector indices of four simulated systems.…”

“…In the previous computational studies related to insights into the RNA function, different RNA force fields were used to model systems. For example, in our study with regard to effect of mutations on binding of ligands to the guanine riboswitch, the force field ff 99SB was adopted to construct the simulation systems, but in another work on exploration of the binding mechanism of fluorophores to Mango-II, the force field ff 99OL3 was utilized to model systems . Bao et al.…”