Peptides or proteins containing small biomolecular aggregates, such as micelles, bicelles, droplets and nanodiscs, are pivotal in many fields ranging from structural biology to pharmaceutics. Monitoring dynamics of such systems has been limited by the lack of experimental methods that could directly detect their fast (picosecond to nanosecond) timescale dynamics. Spin relaxation times from NMR experiments are sensitive to such motions, but their interpretation for biomolecular aggregates is not...
[NMR paper] Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations
Probing Methyl Group Dynamics in Proteins by NMR Cross-Correlated Dipolar Relaxation and Molecular Dynamics Simulations
Nuclear magnetic resonance (NMR) spin relaxation is the most informative approach to experimentally probe the internal dynamics of proteins on the picosecond to nanosecond time scale. At the same time, molecular dynamics (MD) simulations of biological macromolecules are steadily improving through better physical models, enhanced sampling methods, and increased computational power, and they provide exquisite information about flexibility and its role in protein stability...
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11-04-2022 12:15 AM
[NMR paper] Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel
As the first potassium channel with an x-ray structure determined, and given its homology 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...
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05-05-2021 09:22 AM
[NMR paper] Effects of a Hydrophilic/Hydrophobic Interface on Amyloid-? Peptides Studied by Molecular Dynamics Simulations and NMR Experiments.
Effects of a Hydrophilic/Hydrophobic Interface on Amyloid-? Peptides Studied by Molecular Dynamics Simulations and NMR Experiments.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Effects of a Hydrophilic/Hydrophobic Interface on Amyloid-? Peptides Studied by Molecular Dynamics Simulations and NMR Experiments.
J Phys Chem B. 2019 01 10;123(1):160-169
Authors: Itoh SG, Yagi-Utsumi M, Kato K, Okumura H
Abstract
Oligomer formation of amyloid-? peptides...
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06-03-2020 09:31 AM
[NMR paper] The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7315-19-Wiley_FullText_120x30_orange.png Related Articles The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
Biopolymers. 2013 Aug;99(8):548-61
Authors: Clark TD,...
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04-23-2016 09:24 PM
[NMR paper] Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.
Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.
Related Articles Probing the Interaction between cHAVc3 Peptide and the EC1 Domain of E-cadherin using NMR and Molecular Dynamics Simulations.
J Biomol Struct Dyn. 2016 Jan 5;:1-48
Authors: Alaofi A, Farokhi E, Prasasty VD, Anbanandam A, Kuczera K, Siahaan TJ
Abstract
The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic...
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01-07-2016 08:36 AM
[NMR paper] Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
Related Articles Motions and Entropies in Proteins as Seen in NMR Relaxation Experiments and Molecular Dynamics Simulations.
J Phys Chem B. 2014 Oct 28;
Authors: Allnér O, Foloppe N, Nilsson L
Abstract
Molecular dynamics simulations of E. coli glutaredoxin1 in water have been performed to relate the dynamical parameters and entropy obtained in NMR relaxation experiments, with results extracted from simulated trajectory...
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10-29-2014 03:51 PM
Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Structure and Dynamics of the A?21–30 Peptide from the Interplay of NMR Experiments and Molecular Simulations
Nicolas L. Fawzi, Aaron H. Phillips, Jory Z. Ruscio, Michaeleen Doucleff, David E. Wemmer and Teresa Head-Gordon
Journal of the American Chemical Society
DOI: 10.1021/ja204315n
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/bEQEah_ik60
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[NMR paper] Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Related Articles Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations.
Biophys J. 2005 Sep;89(3):2113-20
Authors: Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M
An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and...
Probing the dynamic landscape of peptides in molecular assemblies by synergized NMR experiments and MD simulations
Linear Mode
