An assessment of water placement algorithms in quantum mechanics/molecular mechanics modeling: the case of rhodopsins’ first spectral absorption band maxima

2020 ◽  
Vol 22 (32) ◽  
pp. 18114-18123
Author(s):  
Dmitrii M. Nikolaev ◽  
Andrey A. Shtyrov ◽  
Andrey S. Mereshchenko ◽  
Maxim S. Panov ◽  
Yuri S. Tveryanovich ◽  
...  
Keyword(s):  
Quantum Mechanics ◽  
Absorption Band ◽  
Molecular Mechanics ◽  
Accurate Prediction ◽  
Water Molecules ◽  
Spectral Absorption ◽  
High Quality ◽  
Placement Algorithms

Accurate prediction of water molecules in protein cavities is an important factor for obtaining high-quality rhodopsin QM/MM models.

Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data

BIOPHYSICS ◽  
2013 ◽  
Vol 58 (5) ◽  
pp. 583-591 ◽  
Author(s):  
E. González ◽  
J. Lino ◽  
A. Deriabina ◽  
J. N. F. Herrera ◽  
V. I. Poltev
Keyword(s):  
Experimental Data ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Dna Bases ◽  
Water Molecules

scholarly journals Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

2019 ◽  
Author(s):  
Igor Polyakov ◽  
Bella Grigorenko ◽  
Alexander Nemukhin
Keyword(s):  
Quantum Mechanics ◽  
Absorption Band ◽  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Absorption Spectra ◽  
Fluorescent Protein ◽  
Deinococcus Radiodurans ◽  
Binding Domain ◽  
Excitation Energies

<p>We report the results of quantum mechanics/molecular mechanics (QM/MM) simulations of structures and absorption spectra of the fluorescent protein IFP1.4 engineered from the chromophore-binding domain of <i>Deinococcus radiodurans</i> (<i>Dr</i>CBD). In this work, we focus on different protonation states of the biliverdin chromophore in the red-absorbing form of the protein. To this goal, the protein with the all-protonated chromophore as well as the structures obtained by removal of protons from the biliverdin pyrrole rings to a suitable acceptor within the system are considered. Several quantum chemistry methods to compute the S<sub>0</sub>→S<sub>1</sub> excitation energies are used in the QM part to estimate shifts in the absorption band maxima upon chromophore deprotonation. </p>

scholarly journals Modeling Structure and Absorption Spectra of the Bacteriophytochrome-Based Fluorescent Protein IFP1.4

2019 ◽  
Author(s):  
Igor Polyakov ◽  
Bella Grigorenko ◽  
Alexander Nemukhin
Keyword(s):  
Quantum Mechanics ◽  
Absorption Band ◽  
Quantum Chemistry ◽  
Molecular Mechanics ◽  
Absorption Spectra ◽  
Fluorescent Protein ◽  
Deinococcus Radiodurans ◽  
Binding Domain ◽  
Excitation Energies

<p>We report the results of quantum mechanics/molecular mechanics (QM/MM) simulations of structures and absorption spectra of the fluorescent protein IFP1.4 engineered from the chromophore-binding domain of <i>Deinococcus radiodurans</i> (<i>Dr</i>CBD). In this work, we focus on different protonation states of the biliverdin chromophore in the red-absorbing form of the protein. To this goal, the protein with the all-protonated chromophore as well as the structures obtained by removal of protons from the biliverdin pyrrole rings to a suitable acceptor within the system are considered. Several quantum chemistry methods to compute the S<sub>0</sub>→S<sub>1</sub> excitation energies are used in the QM part to estimate shifts in the absorption band maxima upon chromophore deprotonation. </p>

On-the-Fly Determination of Active Region Centers in Adaptive-Partitioning QM/MM

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Quantum Mechanics ◽  
Active Region ◽  
Molecular Mechanics ◽  
Active Regions ◽  
Available Energy ◽  
Adaptive Partitioning ◽  
Different Levels

Quantum mechanics/molecular mechanics (QM/MM) methods partition the system into active and environmental regions and treat them with different levels of theory, achieving accuracy and efficiency at the same time. Adaptive-partitioning (AP) QM/MM methods allow on-the-fly changes to the QM/MM partitioning of the system. Many of the available energy-based AP-QM/MM methods partition the system according to distances to pre-chosen centers of active regions. For such AP-QM/MM methods, I develop an adaptive-center (AC) method that allows on-the-fly determination of the centers of active regions according to general geometrical or potential-related criteria, extending the range of application of energy-based AP-QM/MM methods to systems where active regions may occur or vanish during the simulation.

A Conserved Asparagine in a Ubiquitin Conjugating Enzyme Positions the Substrate for Nucleophilic Attack

2018 ◽  
Author(s):  
Walker M. Jones ◽  
Aaron G. Davis ◽  
R. Hunter Wilson ◽  
Katherine L. Elliott ◽  
Isaiah Sumner
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Reaction Rates ◽  
Nucleophilic Attack ◽  
Classical Molecular Dynamics ◽  
Ubiquitin Conjugating Enzyme ◽  
Conjugating Enzyme

We present classical molecular dynamics (MD), Born-Oppenheimer molecular dynamics (BOMD), and hybrid quantum mechanics/molecular mechanics (QM/MM) data. MD was performed using the GPU accelerated pmemd module of the AMBER14MD package. BOMD was performed using CP2K version 2.6. The reaction rates in BOMD were accelerated using the Metadynamics method. QM/MM was performed using ONIOM in the Gaussian09 suite of programs. Relevant input files for BOMD and QM/MM are available.

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching

2007 ◽  
Vol 3 (2) ◽  
pp. 628-639 ◽  
Author(s):  
Patrick Maurer ◽  
Alessandro Laio ◽  
Håkan W. Hugosson ◽  
Maria Carola Colombo ◽  
Ursula Rothlisberger
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Force Fields ◽  
Force Matching
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