Abstract
An ever-increasing number of functional RNAs require mechanistic understanding. RNA function relies on changes in its structure, so-called dynamics. To reveal dynamic processes and higher energy structures, new Nuclear Magnetic Resonance (NMR) methods have been developed to elucidate these dynamics in RNA with atomic resolution. In this review, we provide an introduction to dynamics novices and an overview of methods that access most dynamic timescales, from picoseconds to hours. Examples are provided as well as insight into theory, data acquisition and analysis for these different methods. Using this broad spectrum of methodology, unprecedented details and invisible structures have been obtained and are reviewed here. RNA, though often more complicated and therefore neglected, also provides a great system to study structural changes, as RNA structural changes are easier definable than in proteins, hence the numerous revelations of RNA excited states.
PMID: 30997719 [PubMed - as supplied by publisher]
[NMR paper] Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
Related Articles Side Chain Dynamics of the Trifluoroacetone Cysteine Derivative Characterized by 19F NMR Relaxation and Molecular Dynamics Simulations.
J Phys Chem B. 2019 Apr 11;:
Authors: Rashid S, Lee BL, Wajda B, Spyracopoulos L
Abstract
19F NMR spectroscopy is a powerful tool for the study of the structures, dynamics, and interactions of proteins bearing cysteine residues chemically...
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04-12-2019 05:25 PM
[NMR paper] Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.
Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Structure and Dynamics of Extracellular Loops in Human Aquaporin-1 from Solid-State NMR and Molecular Dynamics.
J Phys Chem B. 2016 09 22;120(37):9887-902
Authors: Wang S, Ing C, Emami S, Jiang Y, Liang H, Pomès R, Brown LS, Ladizhansky V
Abstract
Multiple moderate-resolution crystal structures...
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04-19-2018 01:52 PM
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
NMR Relaxation and Molecular Dynamics Simulations of Side Chain Dynamics in Proteins
Publication date: 2 February 2018
Source:Biophysical Journal, Volume 114, Issue 3, Supplement 1</br>
Author(s): Falk Hoffmann, Mengjun Xue, Frans Mulder, Lars Schäfer</br>
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02-07-2018 03:41 PM
[NMR paper] Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation.
Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation.
Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation.
J Inorg Biochem. 2018 Jan 12;181:65-73
Authors: Zhao J, Xue M, Gudanis D, Gracz H, Findenegg GH, Gdaniec Z, Franzen S
Abstract
Dehaloperoxidase-hemoglobin is the first hemoglobin identified with biologically-relevant oxidative functions, which include peroxidase, peroxygenase and oxidase...
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Conformational Dynamics and Protein–SubstrateInteraction of ABC Transporter BtuCD at the Occluded State Revealedby Molecular Dynamics Simulations
Conformational Dynamics and Protein–SubstrateInteraction of ABC Transporter BtuCD at the Occluded State Revealedby Molecular Dynamics Simulations
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00386/20161201/images/medium/bi-2016-00386h_0007.gif
Biochemistry
DOI: 10.1021/acs.biochem.6b00386
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[NMR paper] Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
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Adv Exp Med Biol. 2015;842:217-30
Authors: Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y,...
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05-02-2015 09:41 PM
[NMR paper] Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations.
Lipid dynamics studied by calculation of 31P solid-state NMR spectra using ensembles from molecular dynamics simulations.
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J Phys Chem B. 2014 May 15;118(19):5119-29
Authors: Hansen SK, Vestergaard M, Thøgersen L, Schiøtt B, Nielsen NC, Vosegaard T
Abstract
We present a method to...
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04-22-2015 03:33 PM
[NMR paper] Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
Related Articles Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure.
J Biomol Struct Dyn. 2013 Jun 3;
Authors: Mahajan S, de Brevern AG, Offmann B, Srinivasan N
Abstract
Conformational changes in proteins are extremely important for their biochemical functions. Correlation between inherent conformational...