[NMR paper] How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations
We review recent advances in modeling structural ensembles of transcription factors from nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopic data, integrated with molecular dynamics (MD) simulations. We focus on approaches that confirm computed conformational ensembles by sparse constraints obtained from magnetic resonance. This combination enables the deduction of functional and structural protein models even if nuclear Overhauser effects (NOEs) are too...
[NMR paper] OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
Related Articles OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring Flip Frequencies by Integrated Use of 1H-NMR and Molecular Dynamics Simulations.
Chembiochem. 2020 Sep 25;:
Authors: Martin BT, Malmstrom RD, Amaro RE, Wüthrich K
Abstract
* *The 55-residue OCRE domains of the splicing factors RBM5 and RBM10 contain 15 tyrosines in compact, globular folds. At 25?C all 15...
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[NMR paper] Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations.
Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--cdn.elifesciences.org-images-elife_oa@1x.png Related Articles Structure and dynamics of a nanodisc by integrating NMR, SAXS and SANS experiments with molecular dynamics simulations.
Elife. 2020 Jul 30;9:
Authors: Bengtsen T, Holm VL, Kjølbye LR, Midtgaard SR, Johansen NT, Tesei G, Bottaro S, Schiøtt B, Arleth L, Lindorff-Larsen K
Abstract
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08-01-2020 02:01 PM
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations - Science Advances
Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations Science AdvancesWe present an integrated experimental and computational approach for de novo protein structure determination in which short-distance cross-linking data are ...
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03-24-2019 10:41 PM
[NMR paper] Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.
Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.
Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein.
Biophys J. 2018 Feb 27;114(4):839-855
Authors: Debiec KT, Whitley MJ, Koharudin LMI, Chong LT, Gronenborn AM
Abstract
Multidomain proteins with two or more independently folded functional domains are prevalent in nature. Whereas most multidomain proteins are linked linearly in sequence, roughly one-tenth possess domain insertions where...
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03-01-2018 09:20 PM
[NMR paper] CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
Related Articles CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations.
J Phys Chem B. 2017 Feb 09;:
Authors: Perilla JR, Zhao G, Lu M, Ning J, Hou G, Byeon IL, Gronenborn AM, Polenova T, Zhang P
Abstract
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many...
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02-10-2017 04:19 PM
[NMR paper] Molecular dynamics simulations on PGLa using NMR orientational constraints.
Molecular dynamics simulations on PGLa using NMR orientational constraints.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Molecular dynamics simulations on PGLa using NMR orientational constraints.
J Biomol NMR. 2015 Nov;63(3):265-74
Authors: Sternberg U, Witter R
Abstract
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the...
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08-25-2016 06:10 PM
Molecular dynamics simulations on PGLa using NMR orientational constraints
Molecular dynamics simulations on PGLa using NMR orientational constraints
Abstract
NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics...
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09-11-2015 06:48 AM
[NMR paper] Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Assessment of the Use of NMR Chemical Shifts as Replica-Averaged Structural Restraints in Molecular Dynamics Simulations to Characterize the Dynamics of Proteins.
J Phys Chem B. 2013 Feb 1;
Authors: Camilloni C, Cavalli A, Vendruscolo M
Abstract
It has been recently...
How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations
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