scholarly journals Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

2021 ◽  
Author(s):  
Miquel Huix-Rotllant ◽  
Karno Schwinn ◽  
Nicolas Ferré
Keyword(s):  
Arabidopsis Thaliana ◽  
Infrared Spectroscopy ◽  
Ir Spectra ◽  
Normal Mode ◽  
Infrared Spectra ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
Electrostatic Embedding

Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.

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 Deciphering conformational transitions of proteins by small angle X-ray scattering and normal mode analysis

2016 ◽  
Vol 18 (8) ◽  
pp. 5707-5719 ◽  
Author(s):  
Alejandro Panjkovich ◽  
Dmitri I. Svergun
Keyword(s):  
Normal Mode ◽  
Small Angle ◽  
Normal Mode Analysis ◽  
Conformational Transitions ◽  
Scattering Data ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Scattering ◽  
Insight Into

SREFLEX employs normal mode analysis for the flexible refinement of atomic models of biological macromolecules against solution scattering data, providing insight into conformational transitions.

Modeling the heme vibrational spectrum: Normal-mode analysis of nickel (II) etioporphyrin-I from resonance raman, ft-raman, and infrared spectra of multiple isotopomers

1995 ◽  
Vol 1 (6) ◽  
pp. 395-412 ◽  
Author(s):  
Songzhou Hu ◽  
Arka Mukherjee ◽  
Christine Piffat ◽  
Ronald S. W. Mak ◽  
Xiao-Yuan Li ◽  
...  
Keyword(s):  
Vibrational Spectrum ◽  
Normal Mode ◽  
Infrared Spectra ◽  
Normal Mode Analysis ◽  
Resonance Raman ◽  
Mode Analysis ◽  
Ft Raman
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