5 research outputs found
The Use of Chlorobenzene as a Probe Molecule in Molecular Dynamics Simulations
We map ligand binding sites on protein
surfaces in molecular dynamics
simulations using chlorobenzene as a probe molecule. The method was
validated on four proteins. Two types of affinity maps that identified
halogen and hydrophobic binding sites on proteins were obtained. Our
method could prove useful for the discovery and development of halogenated
inhibitors
The Application of Ligand-Mapping Molecular Dynamics Simulations to the Rational Design of Peptidic Modulators of Protein–Protein Interactions
A computational
ligand-mapping approach to detect protein surface
pockets that interact with hydrophobic moieties is presented. In this
method, we incorporated benzene molecules into explicit solvent molecular
dynamics simulations of various protein targets. The benzene molecules
successfully identified the binding locations of hydrophobic hot-spot
residues and all-hydrocarbon cross-links from known peptidic ligands.
They also unveiled cryptic binding sites that are occluded by side
chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein–protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules
Supplementary material for 'Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion'
Nucleic acid aptamers as antibody alternatives bind specifically to target molecules. These aptamers are generated by isolating candidates from libraries with random sequence fragments, through an evolutionary engineering system. We recently reported a high-affinity DNA aptamer generation method that introduces unnatural bases (UBs) as a fifth letter into the library, by genetic alphabet expansion. By incorporating hydrophobic UBs, the affinities of DNA aptamers to target proteins are increased over 100-fold, as compared to those of conventional aptamers with only the natural four letters. However, there is still plenty of room for improvement of the methods for routinely generating high-affinity UB-containing DNA (UB-DNA) aptamers. The success probabilities of the high-affinity aptamer generation depend on the existence of the aptamer candidate sequences in the initial library. We estimated the success probabilities by analysing several UB-DNA aptamers that we generated, as examples. In addition, we investigated the possible improvement of conventional aptamer affinities by introducing one UB at specific positions. Our data revealed that UB-DNA aptamers adopt specific tertiary structures, in which many bases including UBs interact with target proteins for high affinity, suggesting the importance of the UB-DNA library design.This article is part of the theme issue ‘Reactivity and mechanism in chemical and synthetic biology’
Ultra-High Signal Detection of Human Embryonic Stem Cells Driven by Two-Dimensional Materials
We
observed a unique bioelectric signal of human embryonic stem
cells using direct current–voltage measurements facilitated
by few-layered 2D-MoS<sub>2</sub> sheets. A 1.828 mA cell signal was
achieved (2 orders of magnitude higher than previous electrical-based
detection methods) as well as multiple cell reading cycles demonstrating <i>I</i> ∼ 1.9 mA. Native stem cell proliferation, viability,
and pluripotency were preserved. Molecular dynamics simulations elucidated
the origin of the 2D-MoS<sub>2</sub> sheet-assisted increase in current
flow. This paves the way for the development of a broadly applicable,
fast, and damage-free stem cell detection method capable of identifying
pluripotency with virtually any complementary-metal-oxide-semiconductor
circuits
Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design
Protein
flexibility poses a major challenge in binding site identification.
Several computational pocket detection methods that utilize small-molecule
probes in molecular dynamics (MD) simulations have been developed
to address this issue. Although they have proven hugely successful
at reproducing experimental structural data, their ability to predict
new binding sites that are yet to be identified and characterized
has not been demonstrated. Here, we report the use of benzenes as
probe molecules in ligand-mapping MD (LMMD) simulations to predict
the existence of two novel binding sites on the surface of the oncoprotein
MDM2. One of them was serendipitously confirmed by biophysical assays
and X-ray crystallography to be important for the binding of a new
family of hydrocarbon stapled peptides that were specifically designed
to target the other putative site. These results highlight the predictive
power of LMMD and suggest that predictions derived from LMMD simulations
can serve as a reliable basis for the identification of novel ligand
binding sites in structure-based drug design