Related ArticlesOn the Use of Side-Chain NMR Relaxation Data to Derive Structural and Dynamical Information on Proteins: A Case Study using Hen Lysozyme.
Chembiochem. 2020 Nov 04;:
Authors: Smith LJ, van Gunsteren WF, Hansen N
Abstract
Values of S2CH and S2NH order parameters derived from NMR relaxation measurements on proteins cannot straightforwardly be used to determine protein structure, because they cannot be related to a single protein structure, but are defined in terms of an average over a conformational ensemble. MD simulation can generate a conformational ensemble and thus be used to restrain S2CH and S2NH order parameters towards experimentally derived target values S2CH(exp) and S2NH(exp). Application of S2CH and S2NH order-parameter restraining MD simulation to bond vectors in 63 side chains of the protein hen egg white lysozyme using 51 S2CH(exp) target values and 28 S2NH(exp) target values shows that a conformational ensemble compatible with the experimentally derived data can be obtained using this technique. It is observed that S2CH order-parameter restraining of C-H bonds in methyl groups is less reliable than S2NH order-parameter restraining, because of possibly less valid assumptions and approximations used to derive experimental S2CH(exp)-values from NMR relaxation measurements and the necessity to adopt the assumption of uniform rotational motion of methyl C-H bonds around their symmetry axis and of the independence of these motions from each other. The restrained simulations demonstrate that side chains on the protein surface are highly dynamic. Any hydrogen bonds they form and that appear in any of four different crystal structures, are fluctuating with short lifetimes in solution.
PMID: 33146424 [PubMed - as supplied by publisher]
[NMR paper] NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).
NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR study of non-structural proteins-part III: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Chikungunya virus (CHIKV).
Biomol NMR Assign. 2017 Sep 05;:
Authors: Lykouras MV, Tsika AC, Lichière J,...
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[NMR paper] Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.
Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.
Related Articles Solvent-Driven Dynamical Cross-Over in the Phenylalanine Side-Chain from the Hydrophobic Core of Amyloid Fibrils Detected by (2)H NMR Relaxation.
J Phys Chem B. 2017 Jul 12;:
Authors: Vugmeyster L, Ostrovsky D, Hoatson GL, Qiang W, Falconer IB
Abstract
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we...
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[NMR paper] NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).
NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).
Related Articles NMR study of non-structural proteins-part II: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Venezuelan equine encephalitis virus (VEEV).
Biomol NMR Assign. 2014 Oct 8;
Authors: Makrynitsa GI, Ntonti D, Marousis KD, Tsika AC, Lichière J, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA
Abstract
Macro...
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[NMR paper] NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).
NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).
Related Articles NMR study of non-structural proteins-part I: (1)H, (13)C, (15)N backbone and side-chain resonance assignment of macro domain from Mayaro virus (MAYV).
Biomol NMR Assign. 2014 Sep 13;
Authors: Melekis E, Tsika AC, Lichière J, Chasapis CT, Margiolaki I, Papageorgiou N, Coutard B, Bentrop D, Spyroulias GA
Abstract
Macro domains are ADP-ribose-binding modules present...
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09-14-2014 02:26 PM
[NMR paper] Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain (1)H Probes.
From Mendeley Biomolecular NMR group:
Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain (1)H Probes.
Journal of the American Chemical Society (2012). Volume: 134, Issue: 6. Pages: 3178-3189. Alexandar L Hansen, Patrik Lundström, Algirdas Velyvis, Lewis E Kay et al.
A Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for quantifying millisecond time-scale chemical exchange at side-chain (1)H positions in proteins. Such experiments are not possible in a fully protonated molecule because of magnetization...
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[NMR paper] Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain (1)H Probes.
From Mendeley Biomolecular NMR group:
Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain (1)H Probes.
Journal of the American Chemical Society (2012). Volume: 134, Issue: 6. Pages: 3178-3189. Alexandar L Hansen, Patrik Lundström, Algirdas Velyvis, Lewis E Kay et al.
A Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for quantifying millisecond time-scale chemical exchange at side-chain (1)H positions in proteins. Such experiments are not possible in a fully protonated molecule because of magnetization...
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Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain 1H Probes
Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain 1H Probes
Alexandar L. Hansen, Patrik Lundstrom, Algirdas Velyvis and Lewis E. Kay
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja210711v/aop/images/medium/ja-2011-10711v_0008.gif
Journal of the American Chemical Society
DOI: 10.1021/ja210711v
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http://feeds.feedburner.com/~r/acs/jacsat/~4/jaMjjnA_QTw
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[NMR paper] Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study
Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.
Related Articles Side chain dynamics in unfolded protein states: an NMR based 2H spin relaxation study of delta131delta.
J Am Chem Soc. 2003 Feb 19;125(7):1748-58
Authors: Choy WY, Shortle D, Kay LE
NMR relaxation data on disordered proteins can provide insight into both structural and dynamic properties of these molecules. Because of chemical shift degeneracy in correlation spectra, detailed site-specific analyses of side chain dynamics...