Protonation structure of the photosynthetic water oxidizing complex in the S0 state as revealed by normal mode analysis using quantum mechanics/molecular mechanics calculations

2020 ◽  
Vol 22 (42) ◽  
pp. 24213-24225
Author(s):  
Masao Yamamoto ◽  
Shin Nakamura ◽  
Takumi Noguchi
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Vibrations ◽  
Molecular Mechanics Calculations ◽  
Water Oxidizing Complex

Protonation structure of the first intermediate of the water oxidizing complex was determined by QM/MM calculations of molecular vibrations.

scholarly journals A force field for virtual atom molecular mechanics of proteins

2009 ◽  
Vol 106 (37) ◽  
pp. 15667-15672 ◽  
Author(s):  
Anil Korkut ◽  
Wayne A. Hendrickson
Keyword(s):  
Force Field ◽  
Molecular Mechanics ◽  
Normal Mode ◽  
Conformational Changes ◽  
Normal Mode Analysis ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
Molecular Mechanics Calculations ◽  
Low Degrees

Activities of many biological macromolecules involve large conformational transitions for which crystallography can specify atomic details of alternative end states, but the course of transitions is often beyond the reach of computations based on full-atomic potential functions. We have developed a coarse-grained force field for molecular mechanics calculations based on the virtual interactions of Cα atoms in protein molecules. This force field is parameterized based on the statistical distribution of the energy terms extracted from crystallographic data, and it is formulated to capture features dependent on secondary structure and on residue-specific contact information. The resulting force field is applied to energy minimization and normal mode analysis of several proteins. We find robust convergence in minimizations to low energies and energy gradients with low degrees of structural distortion, and atomic fluctuations calculated from the normal mode analyses correlate well with the experimental B-factors obtained from high-resolution crystal structures. These findings suggest that the virtual atom force field is a suitable tool for various molecular mechanics applications on large macromolecular systems undergoing large conformational changes.

scholarly journals Quantum mechanics/molecular mechanics simulation of the ligand vibrations of the water-oxidizing Mn4CaO5 cluster in photosystem II

2016 ◽  
Vol 113 (45) ◽  
pp. 12727-12732 ◽  
Author(s):  
Shin Nakamura ◽  
Takumi Noguchi
Keyword(s):  
Quantum Mechanics ◽  
Photosystem Ii ◽  
Molecular Mechanics ◽  
Water Oxidation ◽  
Structural Changes ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Difference Spectra ◽  
Carboxylate Groups ◽  
Water Ligands

During photosynthesis, the light-driven oxidation of water performed by photosystem II (PSII) provides electrons necessary to fix CO2, in turn supporting life on Earth by liberating molecular oxygen. Recent high-resolution X-ray images of PSII show that the water-oxidizing center (WOC) is composed of an Mn4CaO5 cluster with six carboxylate, one imidazole, and four water ligands. FTIR difference spectroscopy has shown significant structural changes of the WOC during the S-state cycle of water oxidation, especially within carboxylate groups. However, the roles that these carboxylate groups play in water oxidation as well as how they should be properly assigned in spectra are unresolved. In this study, we performed a normal mode analysis of the WOC using the quantum mechanics/molecular mechanics (QM/MM) method to simulate FTIR difference spectra on the S1 to S2 transition in the carboxylate stretching region. By evaluating WOC models with different oxidation and protonation states, we determined that models of high-oxidation states, Mn(III)2Mn(IV)2, satisfactorily reproduced experimental spectra from intact and Ca-depleted PSII compared with low-oxidation models. It is further suggested that the carboxylate groups bridging Ca and Mn ions within this center tune the reactivity of water ligands bound to Ca by shifting charge via their π conjugation.

PIDOTIMOD, a new immunostimulating dipeptide, studied by molecular mechanics, normal mode analysis and dynamics calculations

1993 ◽  
Vol 298 ◽  
pp. 177-190 ◽  
Author(s):  
Vincenzo Villani ◽  
Rachele Pucciariello ◽  
Tiziano Crimella ◽  
Riccardo Stradi
Keyword(s):  
Molecular Mechanics ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis
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