scholarly journals Configuration determination by residual dipolar couplings: accessing the full conformational space by molecular dynamics with tensorial constraints

2019 ◽  
Vol 10 (38) ◽  
pp. 8774-8791 ◽  
Author(s):  
Pavleta Tzvetkova ◽  
Ulrich Sternberg ◽  
Thomas Gloge ◽  
Armando Navarro-Vázquez ◽  
Burkhard Luy
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Structural Models ◽  
Dipolar Couplings ◽  
Conformational Space ◽  
Flexible Molecules ◽  
Dynamics Simulations

The use of tensorial orientational constraints for NMR-derived residual dipolar couplings (RDCs) in molecular dynamics simulations brings detailed structural models of flexible molecules in solution in reach.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations

2015 ◽  
Vol 53 (3) ◽  
pp. 213-217 ◽  
Author(s):  
Andreas O. Frank ◽  
J. Christoph Freudenberger ◽  
Alexey K. Shaytan ◽  
Horst Kessler ◽  
Burkhard Luy
Keyword(s):  
Molecular Dynamics ◽  
Small Molecules ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Dynamics Simulations

Limited Flexibility of Lactose Detected from Residual Dipolar Couplings Using Molecular Dynamics Simulations and Steric Alignment Methods

2005 ◽  
Vol 127 (10) ◽  
pp. 3589-3595 ◽  
Author(s):  
Manuel Martín-Pastor ◽  
Angeles Canales ◽  
Francisco Corzana ◽  
Juan L. Asensio ◽  
Jesús Jiménez-Barbero
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
Dynamics Simulations

The Possible Structural Models for Polyglutamine Aggregation: A Molecular Dynamics Simulations Study

2011 ◽  
Vol 28 (5) ◽  
pp. 743-758 ◽  
Author(s):  
Zheng-Li Zhou ◽  
Jian-Hua Zhao ◽  
Hsuan-Liang Liu ◽  
Josephine W. Wu ◽  
Kung-Tien Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Models ◽  
Dynamics Simulations ◽  
Polyglutamine Aggregation

scholarly journals Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
Thomas R. Caulfield ◽  
Batsal Devkota ◽  
Geoffrey C. Rollins
Keyword(s):  
Electron Microscopy ◽  
Molecular Dynamics ◽  
Range Of Motion ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
X Ray ◽  
Maxwell’S Demon ◽  
Density Maps ◽  
Maxwell's Demon ◽  
Dynamics Simulations

We examined tRNA flexibility using a combination of steered and unbiased molecular dynamics simulations. Using Maxwell's demon algorithm, molecular dynamics was used to steer X-ray structure data toward that from an alternative state obtained from cryogenic-electron microscopy density maps. Thus, we were able to fit X-ray structures of tRNA onto cryogenic-electron microscopy density maps for hybrid states of tRNA. Additionally, we employed both Maxwell's demon molecular dynamics simulations and unbiased simulation methods to identify possible ribosome-tRNA contact areas where the ribosome may discriminate tRNAs during translation. Herein, we collected >500 ns of simulation data to assess the global range of motion for tRNAs. Biased simulations can be used to steer between known conformational stop points, while unbiased simulations allow for a general testing of conformational space previously unexplored. The unbiased molecular dynamics data describes the global conformational changes of tRNA on a sub-microsecond time scale for comparison with steered data. Additionally, the unbiased molecular dynamics data was used to identify putative contacts between tRNA and the ribosome during the accommodation step of translation. We found that the primary contact regions were H71 and H92 of the 50S subunit and ribosomal proteins L14 and L16.

scholarly journals Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations

2016 ◽  
Vol 18 (8) ◽  
pp. 5743-5752 ◽  
Author(s):  
Witold Andrałojć ◽  
Enrico Ravera ◽  
Loïc Salmon ◽  
Giacomo Parigi ◽  
Hashim M. Al-Hashimi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Space ◽  
Nmr Data ◽  
Conformational Preferences ◽  
Tar Rna ◽  
Dynamics Simulations ◽  
Maximum Occurrence ◽  
Hiv 1

Molecular dynamics simulations and maximum occurrence distribution identify the same most likely sampled conformations over the available conformational space.

scholarly journals Conformational Analysis of Cinhonine and Cinhonidine by Tensor Decomposition of Molecular Dynamics Trajectories

2019 ◽  
Vol 92 (2) ◽  
pp. 259-267
Author(s):  
Karlo Sović ◽  
Tea Ostojić ◽  
Ines Primožič ◽  
Tomica Hrenar ◽  
Mirjana Skočibušić ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Conformational Analysis ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Principal Component ◽  
Conformational Space ◽  
Cartesian Coordinates ◽  
Dynamics Simulations ◽  
Quantum Chemical Molecular Dynamics

Full conformational space of cinchonine and cinchonidine has been investigated by means of statistical analysis of quantum chemical molecular dynamics simulations. Recently developed procedure comprising principal component analysis of molecular dynamics trajectories was applied on cinchonine and cinchonidine as well as on their protonated and methylated quaternary derivatives. The method for full conformational analysis includes Cartesian coordinates sampling through quantum chemical molecular dynamics simulations, reduction of dimensionality by principal component analysis, determination of probability distributions in a reduced space of Cartesian coordinates and search for all the strict extrema points in probability distribution functions. In order to gain crucial insight in the understanding of chirality induction of these alkaloids, comparison of the determined conformational spaces of pseudo-enantiomers has been made. It was shown that protonation of the quinuclidine nitrogen atom stabilizes the conformers with the intramolecular 1N–H∙∙∙9O hydrogen bond whereas methylation on the same position results in the reduction of the domain of internal coordinates responsible for the conformational space.

scholarly journals Changes of Conformation in Albumin with Temperature by Molecular Dynamics Simulations

Entropy ◽  
2020 ◽  
Vol 22 (4) ◽  
pp. 405
Author(s):  
Piotr Weber ◽  
Piotr Bełdowski ◽  
Krzysztof Domino ◽  
Damian Ledziński ◽  
Adam Gadomski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
Mean Square Displacement ◽  
Conformational Space ◽  
Global Dynamics ◽  
Mean Square ◽  
Conformational Entropy ◽  
The Mean ◽  
Dynamics Simulations

This work presents the analysis of the conformation of albumin in the temperature range of 300 K – 312 K , i.e., in the physiological range. Using molecular dynamics simulations, we calculate values of the backbone and dihedral angles for this molecule. We analyze the global dynamic properties of albumin treated as a chain. In this range of temperature, we study parameters of the molecule and the conformational entropy derived from two angles that reflect global dynamics in the conformational space. A thorough rationalization, based on the scaling theory, for the subdiffusion Flory–De Gennes type exponent of 0 . 4 unfolds in conjunction with picking up the most appreciable fluctuations of the corresponding statistical-test parameter. These fluctuations coincide adequately with entropy fluctuations, namely the oscillations out of thermodynamic equilibrium. Using Fisher’s test, we investigate the conformational entropy over time and suggest its oscillatory properties in the corresponding time domain. Using the Kruscal–Wallis test, we also analyze differences between the mean root mean square displacement of a molecule at various temperatures. Here we show that its values in the range of 306 K – 309 K are different than in another temperature. Using the Kullback–Leibler theory, we investigate differences between the distribution of the mean root mean square displacement for each temperature and time window.

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