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DFT Applications in Molecular Biology and Biophysics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 January 2024) | Viewed by 1829

Special Issue Editor

Special Issue Information

Dear Colleagues,

Density functional theory (DFT), in its various forms, is a computational quantum method that has become an invaluable tool for many researchers across a range of disciplines. DFT methods have emerged during the past several decades as a powerful methodology for the simulation of chemical systems, and they have become an important research tool for chemists, physicists and molecular biologists. DFT methods provide the best combination of accuracy and efficiency, and they are extensively used today in the prediction of the biomolecular structure and electronic properties of many systems, in computer-aided drug design, in catalysis and chemical reactivity, in surfaces and periodic solids, in transport, optical and magnetic properties, etc. The combination of DFT calculations with molecular dynamics promises to provide an efficient way to study structures and reactions in molecules and extended systems. They are less computationally demanding than other computational methods, and have a similar accuracy.

This Special Issue aims to collect papers related to any aspect of DFT Applications in Molecular Biology and Biophysics, including molecular simulations, structure predictions, and inter-molecular interactions, in computer-aided drug design and in all biomolecules more generally.

Dr. Mauricio Alcolea Palafox
Guest Editor

Manuscript Submission Information

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Keywords

  • biophysics
  • molecular biology
  • molecular systems and processes
  • biomolecular interactions
  • docking calculations
  • DFT applications

Published Papers (1 paper)

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Research

18 pages, 1760 KiB  
Article
Quantum Mechanical Study of Oxygen Ligands Protonation for the Stable States of the Laccase Active Site
by Sergei Gavryushov, Nikolay N. Kuzmich and Konstantin M. Polyakov
Int. J. Mol. Sci. 2023, 24(3), 2990; https://doi.org/10.3390/ijms24032990 - 3 Feb 2023
Cited by 1 | Viewed by 1374
Abstract
Laccases are enzymes catalyzing the oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Recently, oxygen reduction by laccases has been studied by single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution. There [...] Read more.
Laccases are enzymes catalyzing the oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Recently, oxygen reduction by laccases has been studied by single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution. There were two determined structures corresponding to the reduced and oxidized stable states of the laccase active site. However, the protonation of the oxygen ligands involved cannot be determined even at subatomic resolution. In the present work, the protonation of oxygen ligands in the active site of laccase for the two stable states determined in the X-ray study was explored using quantum mechanical and continuum-electrostatics calculations. This is important for understanding the reaction of the oxygen reduction mechanism in laccases. The high precision of X-ray data at subatomic resolutions allowed us to optimize the quantum mechanical calculations. Full article
(This article belongs to the Special Issue DFT Applications in Molecular Biology and Biophysics)
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