[NMR paper] Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
Related ArticlesConformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
Chembiochem. 2017 Feb 16;18(4):396-401
Authors: Suzuki T, Kajino M, Yanaka S, Zhu T, Yagi H, Satoh T, Yamaguchi T, Kato K
Abstract
Exploration of the conformational spaces of flexible oligosaccharides is essential to gain deeper insights into their functional mechanisms. Here we characterised dynamic conformation of a high-mannose-type dodecasaccharide with a terminal glucose residue, a critical determinant recognised by molecular chaperones. The dodecasaccharide was prepared by our developed chemoenzymatic technique, which uses (13) C labelling and lanthanide tagging to detect conformation-dependent paramagnetic effects by NMR spectroscopy. The NMR-validated molecular dynamics simulation produced the dynamic conformational ensemble of the dodecasaccharide. This determined its spatial distribution as well as the glycosidic linkage conformation of the terminal glucose determinant. Moreover, comparison of our results with previously reported crystallographic data indicates that the chaperone binding to its target oligosaccharides involves an induced-fit mechanism.
[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.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.
Adv Exp Med Biol. 2015;842:217-30
Authors: Zhang Y, Yamaguchi T, Satoh T, Yagi-Utsumi M, Kamiya Y,...
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[NMR paper] Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation.
Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation.
Mapping Protein Conformational Energy Landscapes Using NMR and Molecular Simulation.
Chemphyschem. 2013 May 23;
Authors: Guerry P, Mollica L, Blackledge M
Abstract
Nuclear magnetic resonance (NMR) spectroscopy provides detailed understanding of the nature and extent of protein dynamics on physiologically important timescales. We present recent advances in the combination of NMR with state-of-the-art molecular simulation that are providing unique new...
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NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101896j/aop/images/medium/bi-2010-01896j_0004.gif
Biochemistry
DOI: 10.1021/bi101896j
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NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
NMR Spectroscopy and Molecular Dynamics Simulation of r(CCGCUGCGG)2 Reveal a Dynamic UU Internal Loop Found in Myotonic Dystrophy Type 1.
Biochemistry. 2011 Jan 4;
Authors: Parkesh R, Disney MD, Fountain M
The NMR structure of an RNA with a copy of the 5'CUG/3'GUC motif found in the triplet repeating disorder myotonic dystrophy type 1 (DM1) is disclosed. The lowest energy conformation of the UU pair is a single...
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Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Alanine Methyl Groups as NMR Probes of Molecular Structure and Dynamics in High-Molecular-Weight Proteins
Raquel Godoy-Ruiz, Chenyun Guo and Vitali Tugarinov
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja1083656/aop/images/medium/ja-2010-083656_0009.gif
Journal of the American Chemical Society
DOI: 10.1021/ja1083656
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[NMR paper] Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics sim
Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide
Related Articles Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide
J Comput Aided Mol Des. 1996 Jun;10(3):213-32
Authors: Buono RA, Kucharczyk N, Neuenschwander M, Kemmink J, Hwang LY, Fauchère JL, Venanzi CA
The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several...
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[NMR paper] Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation wit
Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Molecular dynamics simulation of E. coli ribonuclease H1 in solution: correlation with NMR and X-ray data and insights into biological function.
J Mol Biol. 1995 Dec 8;254(4):771-92
Authors: Philippopoulos M, Lim C
A 500 ps molecular dynamics simulation of Escherichia coli RNase...
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[NMR paper] A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation:
A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Related Articles A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.
Proteins. 1993 Dec;17(4):375-90
Authors: Eriksson MA, Berglund H, Härd T, Nilsson L
The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using...
Conformational Analysis of a High-Mannose-Type Oligosaccharide Displaying Glucosyl Determinant Recognised by Molecular Chaperones Using NMR-Validated Molecular Dynamics Simulation.
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