Certification of Molecular Dynamics Trajectories with NMR Chemical Shifts

2009 ◽  
Vol 1 (1) ◽  
pp. 246-248 ◽  
Author(s):  
Da-Wei Li ◽  
Rafael Brüschweiler
Keyword(s):  
Molecular Dynamics ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts

Solvation chemical shifts of perylenic antenna molecules from molecular dynamics simulations

2014 ◽  
Vol 16 (40) ◽  
pp. 22309-22320 ◽  
Author(s):  
Nergiz Özcan ◽  
Jiří Mareš ◽  
Dage Sundholm ◽  
Juha Vaara
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Solvation Model ◽  
Nmr Chemical Shifts ◽  
Dynamics Simulations ◽  
Distinct Features

Solvent-induced carbon-13 NMR chemical shifts of nine candidate antenna molecules were analysed using a dynamic solvation model, revealing the distinct features of perimeter and inside nuclear sites.

ChemInform Abstract: Calculated and Experimental NMR Chemical Shifts of p-Menthane-3,9-diols. A Combination of Molecular Dynamics and Quantum Mechanics to Determine the Structure and the Solvent Effects.

ChemInform ◽  
2010 ◽  
Vol 32 (37) ◽  
pp. no-no
Author(s):  
Jordi Casanovas ◽  
Adriana M. Namba ◽  
Salvador Leon ◽  
Gilberto L. B. Aquino ◽  
Gil Valdo Jose da Silva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts

scholarly journals CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations

2017 ◽  
Vol 121 (15) ◽  
pp. 3853-3863 ◽  
Author(s):  
Juan R. Perilla ◽  
Gongpu Zhao ◽  
Manman Lu ◽  
Jiying Ning ◽  
Guangjin Hou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Structure Refinement ◽  
Nmr Chemical Shifts ◽  
Dynamics Simulations

Calculated and Experimental NMR Chemical Shifts ofp-Menthane-3,9-diols. A Combination of Molecular Dynamics and Quantum Mechanics to Determine the Structure and the Solvent Effects

2001 ◽  
Vol 66 (11) ◽  
pp. 3775-3782 ◽  
Author(s):  
Jordi Casanovas ◽  
Adriana M. Namba ◽  
Salvador León ◽  
Gilberto L. B. Aquino ◽  
Gil Valdo José da Silva ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Solvent Effects ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts

scholarly journals Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel

2020 ◽  
Author(s):  
Sergio Perez-Conesa ◽  
Eric G. Keeler ◽  
Dongyu Zhang ◽  
Lucie Delemotte ◽  
Ann E McDermott
Keyword(s):  
Molecular Dynamics ◽  
Chemical Shifts ◽  
Md Simulations ◽  
X Ray ◽  
Nmr Chemical Shifts ◽  
X Ray Crystallography ◽  
Activated State ◽  
State Present ◽  
Dynamics Simulations ◽  
Inference Techniques

As the first potassium channel with a X-ray structure determined, and given its homol- ogy to eukaryotic channels, the pH-gated prokaryotic channel KcsA has been extensively studied. Nevertheless, questions related in particular to the allosteric coupling between its gates remain open. The many currently available X-ray crystallography structures appear to correspond to various stages of activation and inactivation, offering insights into the molecular basis of these mechanisms. Since these studies have required mutations, com- plexation with antibodies, and substitution of detergents for lipids, examining the channel under more native conditions is desirable. Solid-state NMR (SSNMR) can be used to study the wild-type protein under activating conditions (low pH), at room temperature, and in bacteriomimetic liposomes. In this work, we sought to structurally assign the acti- vated state present in SSNMR experiments. We used a combination of molecular dynamics (MD) simulations, chemical shift prediction algorithms, and Bayesian inference techniques to determine which of the most plausible X-ray structures resolved to date best represents the activated state captured in SSNMR. We first identified specific nuclei with simulated NMR chemical shifts that differed significantly when comparing partially open vs. fully open ensembles from MD simulations. The simulated NMR chemical shifts for those spe- cific nuclei were then compared to experimental ones, revealing that the simulation of the partially open state was in good agreement with the SSNMR data. Nuclei that discrimi- nate effectively between partially and fully open states belong to residues spread over the sequence and provide a molecular level description of the conformational change.

Sign in / Sign up

Export Citation Format

Share Document