Real-time monitoring of conformational transitions of single-molecule histone deacetylase 8 with nanocircuits

Abstract

Using single-molecule approaches, we directly observed the dynamic interaction between HDAC8 and various ligands as well as conformational interconversions during the catalytic reaction. Statistical analysis identified key kinetic parameters, demonstrating that the enzymatic activity is highly sensitive to both minor variations in the ligand structures and small synthetic molecules.

Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8

“…According to the results of the MD simulation and clustering analysis, it is shown that the holoenzyme form of HDAC8 is flexible, as shown in Figures and . Previous studies have demonstrated the flexibility of the HDAC8 and showed that it exists in “in” and “out” conformations at the active site especially amino acids 83–108, where these amino acids contain the binding rail Tyr100 and Asp101 . , Our results are in accordance with these studies, where we showed that HDAC8 is flexible at the active site and periphery. Figure A shows the Tyr100 phi angle for each frame of the MD, where it shows that most of the time HDAC8 holoenzyme exists in “out” conformation ( Tyr100 Φ < −60°) .…”

The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations

“…Taken together, these experimental results strongly suggest that the conductance kinetics of the carbon nanotube bioFET depends directly on the electrostatic potential generated by the biomolecule as it performs its function or as it folds. Following studies based on similar constructs also support this view: on the interaction between the immunoglobulin E antibody and an aptamer-modified carbon nanotube, 26 on DNA hybridization 20,21 and folding 16 as well as on the function of the several enzymes such as the Klenow fragment of DNA polymerase I, 23,27 the b-lactamase, 28 the Histone deacetylase 8, 29 the protein kinase A, 24 and the lysozyme. 25,30,31 Similar observations were also made using a silicon nanowire-based field-effect transistor (SiNW-FET).…”

Real-time tracking of single-molecule collagenase on native collagen and partially structured collagen-mimic substrates

“…We performed atomic force microscopy (AFM) measurements and electronic-based single-molecule nanocircuit measurements. 16–18 Our measurements compare MMP1’s catalytic ability, efficiency, processivity, and rate-limiting factors for the native collagen and lipopeptides substrates at a single-molecule level. The results provide detailed information about enzyme-ligand interaction at single-molecule resolution, providing new insights into designing effective drug carriers for enzyme-triggered contents-release.…”

“…S1), in which the Cu 2+ ion binds to N-terminal His-tag of MMP1 and the pyrene moiety binds to the sidewall of the SWNT through π-π interaction. 16, 18 Thus, MMP1 can freely interact with substrates and form the MMP1-substrate complex. When MMP1 or the complex undergoes conformational changes to bind, unwind, hydrolyze, and release the products, motions of charge residues associated with the conformational transition induce current fluctuations ( ΔI ( t )) underlying the SWNT-FET through a charge gating effect that has been proven by our previous work.…”