Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins

2013 ◽  
Vol 117 (6) ◽  
pp. 1838-1843 ◽  
Author(s):  
Carlo Camilloni ◽  
Andrea Cavalli ◽  
Michele Vendruscolo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts ◽  
Structural Restraints ◽  
Dynamics Simulations

scholarly journals Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins

Structure ◽  
2010 ◽  
Vol 18 (8) ◽  
pp. 923-933 ◽  
Author(s):  
Paul Robustelli ◽  
Kai Kohlhoff ◽  
Andrea Cavalli ◽  
Michele Vendruscolo
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Nmr Chemical Shifts ◽  
Structural Restraints ◽  
Dynamics Simulations

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.

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

scholarly journals Combining enhanced sampling with experiment-directed simulation of the GYG peptide

2018 ◽  
Vol 17 (03) ◽  
pp. 1840007 ◽  
Author(s):  
Dilnoza B. Amirkulova ◽  
Andrew D. White
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Shifts ◽  
Parallel Tempering ◽  
Collective Variables ◽  
Novel Approach ◽  
Sampling Problem ◽  
Combination Of Methods ◽  
Dynamics Simulations ◽  
Explicit Water

Experiment-directed simulation (EDS) is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics simulations of large systems. This work combines EDS with both the parallel-tempering or parallel-tempering well-tempered ensemble replica-exchange methods to enhance sampling. These methods are demonstrated on the GYG tripeptide in explicit water. The collective variables biased by EDS are chemical shifts, where the set-points are determined by NMR experiments. The results show that it is possible to enhance sampling with either parallel-tempering and parallel-tempering well-tempered ensemble in the EDS method. This combination of methods provides a novel approach for both accurately and exhaustively simulating biological systems.

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