Enhanced sampling strategies for molecular simulation of DNA

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2024, Volume and Issue: 14(2)

Published: March 1, 2024

Abstract Molecular dynamics (MD) simulations can provide detailed insights into complex molecular systems, such as DNA, at high resolution in space and time. Using current computer architectures, time scales of tens microseconds are feasible with contemporary all‐atom force fields. However, these timescales insufficient to accurately characterize large conformational transitions DNA compare calculations experimental data. This review discusses the advantages drawbacks two simulation approaches overcome timescale challenge. The first approach is based on adding biasing potentials system drive transitions. Umbrella sampling, steered MD, metadynamics examples methods. A key challenge methods necessity selecting one or a few efficient coordinates, commonly referred collective variables (CVs), along which apply potential. path‐metadynamics methodology addresses this issue by finding optimal route(s) between states multi‐dimensional CV space. second strategy path focuses MD assumption that even though rare, they generally fast. Stopping soon reach stable state significantly increase efficiency. We introduce two‐dimensional Müller–Brown applications featured for different processes: Watson–Crick–Franklin Hoogsteen transition adenine–thymine base pairs binding DNA‐binding protein domain DNA. article categorized under: Statistical Mechanics Dynamics Monte‐Carlo Methods Free Energy Software Simulation

Language: Английский

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Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

ABSTRACT The study of natural enzyme catalytic processes at a molecular level can provide essential information for rational design new enzymes, to be applied in more efficient and environmentally friendly industrial processes. use computational tools, combined with experimental techniques, is providing outstanding milestones the last decades. However, apart from complexity associated nature these large flexible biomolecular machines, full catalyzed process involves different physical chemical steps. Consequently, point view, deep understanding every single step requires selection proper technique get reliable, robust useful results. In this article, we summarize techniques their process, including conformational diversity, allostery those steps, as well enzymes. Because impact artificial intelligence all aspects science during years, special attention has been methods based on foundations some selected recent applications.

Language: Английский

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A dual-lock toehold-exchange-based aptamer switch for detecting tetracyclines in foods using non-G-quadruplex/hemin DNAzyme

Sensors and Actuators B Chemical, Journal Year: 2025, Volume and Issue: unknown, P. 137528 - 137528

Published: Feb. 1, 2025

Language: Английский

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Reaction Mechanism Path Sampling Based on Parallel Cascade Selection QM/MM Molecular Dynamics Simulation: PaCS-Q

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 28, 2025

Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations are essential for elucidating complex biochemical reaction mechanisms. However, conventional enhanced sampling methods, such as umbrella and metadynamics, often face limitations in computational cost, completeness, reliance on predefined coordinates. To address these challenges, we developed Parallel Cascade Selection QM/MM MD (PaCS-Q) simulation, a novel strategy that efficiently explores pathways by iteratively identifying high-potential structures configurational transitions without biases or external constraints. PaCS-Q directly tracks changes bond distances over time, enabling the identification of transition states intermediates. Validation Claisen rearrangement chorismate mutase peptidyl aldehyde Zika virus NS2B/NS3 serine protease demonstrated accurate pathway capture, reduced costs, efficient sampling. With its user-friendly workflow, broadens accessibility experimental researchers, offering robust tool studying enzymatic mechanisms with high accuracy efficiency.

Language: Английский

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Graphene Derivatives as Efficient Transducing Materials for Covalent Immobilization of Biocomponents in Electrochemical Biosensors

ChemElectroChem, Journal Year: 2025, Volume and Issue: unknown

Published: April 17, 2025

This review highlights the role of graphene derivatives in advancing electrochemical biosensors for applications diagnostics, environmental monitoring, and industrial sensing. Graphene derivatives, including oxide (GO), reduced GO, wide range graphenes prepared via fluorographene chemistry, represent a prominent class transducing materials biosensor development. Their ability to support covalent immobilization biocomponents ensures stability, specificity, long‐term performance, addressing limitations noncovalent methods. Advances fabrication, such as laser‐assisted reduction, enable scalable cost‐effective production conductive graphene‐based electrodes. Covalent functionalization techniques, like carbodiimide coupling click facilitate integration with bioreceptors, leading highly selective biosensors. Emerging approaches, inkjet printing inks onto eco‐friendly substrates, promise sustainable portable diagnostic devices. These advances aligned modern technologies. Future efforts must focus on production, improved multiplexing, sustainability fully harness potential

Language: Английский

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