Related ArticlesUnraveling Allostery in a Knotted Minimal Methyltransferase by NMR Spectroscopy.
J Mol Biol. 2020 Mar 02;:
Authors: Capraro DT, Burban DJ, Jennings PA
Abstract
The methyltransferases that belong to the SpoU-TrmD family contain trefoil knots in their backbone fold. Recent structural dynamic and binding analyses of both free and bound homologs indicate that the knot within the polypeptide backbone plays a significant role in the biological activity of the molecule. The knot loops form the S-Adenosyl-Methionine (SAM)-binding pocket as well as participate in SAM-binding and catalysis. Knots contain both at once a stable core as well as moving parts that modulate long-range motions. Here, we sought to understand allosteric effects modulated by the knotted topology. Uncovering the residues that contribute to these changes and the functional aspects of these protein motions are essential to understanding the interplay between the knot, activation of the MTase and the implications in RNA interactions. The question we sought to address is how does the knot, which constricts the backbone as well as forms the SAM-binding pocket with its three distinctive loops, affect the binding mechanism? Using a minimally tied trefoil (MTT) protein as the framework for understanding the structure-function roles, we offer an unprecedented view of the conformational mechanics of the knot and its relationship to the activation of the ligand-molecule. Focusing on the biophysical characterization of the knot region by Nuclear Magnetic Resonance (NMR) spectroscopy, we identify the SAM-binding region, and observe changes in the dynamics of the loops that form the knot. Importantly, we also observe long-range allosteric changes in flanking helices consistent with winding/unwinding in helical propensity as the knot tightens to secure the SAM-cofactor.
PMID: 32135193 [PubMed - as supplied by publisher]
[NMR paper] 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii.
1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles 1H, 13C, 15N backbone NMR resonance assignments for the rRNA methyltransferase Dim1 from the hyperthermophilic archaeon Pyrococcus horikoshii.
Biomol NMR Assign. 2019 May 08;:
Authors: Kaiser M, Hacker C, Duchardt-Ferner E, Wöhnert J
Abstract
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[ASAP] Unraveling the Reaction Mechanisms of SiO Anodes for Li-Ion Batteries by Combining in Situ 7Li and ex Situ 7Li/29Si Solid-State NMR Spectroscopy
Unraveling the Reaction Mechanisms of SiO Anodes for Li-Ion Batteries by Combining in Situ 7Li and ex Situ 7Li/29Si Solid-State NMR Spectroscopy
Keitaro Kitada, Oliver Pecher, Pieter C. M. M. Magusin, Matthias F. Groh, Robert S. Weatherup, Clare P. Grey
https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.9b01589/20190423/images/medium/ja-2019-01589u_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/jacs.9b01589
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
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[NMR paper] Beyond the limit of assignment of metabolites using minimal serum samples and 1H NMR spectroscopy with cross-validation by mass spectrometry.
Beyond the limit of assignment of metabolites using minimal serum samples and 1H NMR spectroscopy with cross-validation by mass spectrometry.
Beyond the limit of assignment of metabolites using minimal serum samples and 1H NMR spectroscopy with cross-validation by mass spectrometry.
J Pharm Biomed Anal. 2018 Jan 09;151:356-364
Authors: Gupta A, Kumar D
Abstract
Identification of NMR-based metabolic indexes is limited by the deleterious effects of copious proteins and lipoproteins in the serum that accentuate the need for advance...
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02-08-2018 04:32 PM
[NMR paper] Relaxation dispersion NMR spectroscopy for the study of protein allostery.
Relaxation dispersion NMR spectroscopy for the study of protein allostery.
Related Articles Relaxation dispersion NMR spectroscopy for the study of protein allostery.
Biophys Rev. 2015 Jun;7(2):191-200
Authors: Farber PJ, Mittermaier A
Abstract
Allosteric transmission of information between distant sites in biological macromolecules often involves collective transitions between active and inactive conformations. Nuclear magnetic resonance (NMR) spectroscopy can yield detailed information on these dynamics. In particular,...
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[NMR paper] Solution NMR Spectroscopy for the Study of Enzyme Allostery.
Solution NMR Spectroscopy for the Study of Enzyme Allostery.
Related Articles Solution NMR Spectroscopy for the Study of Enzyme Allostery.
Chem Rev. 2016 Jan 6;
Authors: Lisi GP, Loria JP
Abstract
Allostery is a ubiquitous biological regulatory process in which distant binding sites within a protein or enzyme are functionally and thermodynamically coupled. Allosteric interactions play essential roles in many enzymological mechanisms, often facilitating formation of enzyme-substrate complexes and/or product release. Thus,...
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[NMR paper] Backbone NMR assignments of a topologically knotted protein in urea-denatured state.
Backbone NMR assignments of a topologically knotted protein in urea-denatured state.
Related Articles Backbone NMR assignments of a topologically knotted protein in urea-denatured state.
Biomol NMR Assign. 2013 Jul 3;
Authors: Hsieh SJ, Mallam AL, Jackson SE, Hsu ST
Abstract
YbeA is a 3-methylpseudoridine methyltransferase from Escherichia coli that forms a stable homodimer in solution. It is one of the deeply trefoil 31 knotted proteins, of which the knot encompasses the C-terminal helix that threads through a long loop. Recent...
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[NMR paper] Unraveling a phosphorylation event in a folded protein by NMR spectroscopy: phosphorylation of the Pin1 WW domain by PKA.
Unraveling a phosphorylation event in a folded protein by NMR spectroscopy: phosphorylation of the Pin1 WW domain by PKA.
Unraveling a phosphorylation event in a folded protein by NMR spectroscopy: phosphorylation of the Pin1 WW domain by PKA.
J Biomol NMR. 2013 Mar 2;
Authors: Smet-Nocca C, Launay H, Wieruszeski JM, Lippens G, Landrieu I
Abstract
The Pin1 protein plays a critical role in the functional regulation of the hyperphosphorylated neuronal Tau protein in Alzheimer's disease and is by itself regulated by phosphorylation. We have...
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[NMR paper] 67Zn solid-state NMR spectroscopy of the minimal dna binding domain of human nucleoti
67Zn solid-state NMR spectroscopy of the minimal dna binding domain of human nucleotide excision repair protein XPA.
Related Articles 67Zn solid-state NMR spectroscopy of the minimal dna binding domain of human nucleotide excision repair protein XPA.
J Am Chem Soc. 2001 Feb 7;123(5):992-3
Authors: Lipton AS, Buchko GW, Sears JA, Kennedy MA, Ellis PD
Unraveling Allostery in a Knotted Minimal Methyltransferase by NMR Spectroscopy.
Linear Mode
