[NMR paper] The Interaction of Fluorinated Glycomimetics with DC-SIGN: Multiple Binding Modes Disentangled by the Combination of NMR Methods and MD Simulations.
Related ArticlesThe Interaction of Fluorinated Glycomimetics with DC-SIGN: Multiple Binding Modes Disentangled by the Combination of NMR Methods and MD Simulations.
Abstract
Fluorinated glycomimetics are frequently employed to study and eventually modulate protein-glycan interactions. However, complex glycans and their glycomimetics may display multiple binding epitopes that enormously complicate the access to a complete picture of the protein-ligand complexes. We herein present a new methodology based on the synergic combination of experimental 19F-based saturation transfer difference (STD) NMR data with computational protocols, applied to analyze the interaction between DC-SIGN, a key lectin involved in inflammation and infection events with the trifluorinated glycomimetic of the trimannoside core, ubiquitous in human glycoproteins. A novel 2D-STD-TOCSYreF NMR experiment was employed to obtain the experimental STD NMR intensities, while the Complete Relaxation Matrix Analysis (CORCEMA-ST) was used to predict that expected for an ensemble of geometries extracted from extensive MD simulations. Then, an in-house built computer program was devised to find the ensemble of structures that provide the best fit between the theoretical and the observed STD data. Remarkably, the experimental STD profiles obtained for the ligand/DC-SIGN complex could not be satisfactorily explained by a single binding mode, but rather with a combination of different modes coexisting in solution. Therefore, the method provides a precise view of those ligand-receptor complexes present in solution.
[NMR paper] Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR.
Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Conformational Stability Study of a Therapeutic Peptide Plectasin Using Molecular Dynamics Simulations in Combination with NMR.
J Phys Chem B. 2019 06 13;123(23):4867-4877
Authors: Indrakumar S, Zalar M, Pohl C, Nørgaard A, Streicher W, Harris P, Golovanov AP, Peters GHJ
Abstract
...
[NMR paper] Structures of biomolecular complexes by combination of NMR and cryoEM methods.
Structures of biomolecular complexes by combination of NMR and cryoEM methods.
Related Articles Structures of biomolecular complexes by combination of NMR and cryoEM methods.
Curr Opin Struct Biol. 2017 Jan 02;43:104-113
Authors: Cuniasse P, Tavares P, Orlova EV, Zinn-Justin S
Abstract
CryoEM is presently providing structures of biocomplexes considered intractable to analysis by other structural techniques. NMR is playing an important role in delivering structural information on dynamics events and conformational heterogeneity....
nmrlearner
Journal club
0
01-06-2017 07:43 PM
[NMR paper] STD NMR and molecular modelling insights into interaction of novel mannose-based ligands with DC-SIGN.
STD NMR and molecular modelling insights into interaction of novel mannose-based ligands with DC-SIGN.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles STD NMR and molecular modelling insights into interaction of novel mannose-based ligands with DC-SIGN.
Org Biomol Chem. 2016 Jan 21;14(3):862-75
Authors: Kotar A, Tomaši? T, Lenar?i? Živkovi? M, Jug G, Plavec J, Anderluh M
Abstract
Study of interaction of mannose-based ligands with receptor...
nmrlearner
Journal club
0
09-27-2016 06:00 PM
[NMR paper] NMR insight into the multiple glycosaminoglycan binding modes of the Link module from human TSG-6.
NMR insight into the multiple glycosaminoglycan binding modes of the Link module from human TSG-6.
http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles NMR insight into the multiple glycosaminoglycan binding modes of the Link module from human TSG-6.
Biochemistry. 2015 Dec 18;
Authors: Park Y, Jowitt TA, Day AJ, Prestegard JH
Abstract
Tumor necrosis factor-stimulated gene-6 (TSG-6) is a hyaluronan (HA) binding protein that is essential for stabilizing and...
nmrlearner
Journal club
0
12-28-2015 12:26 AM
[NMR paper] Langerin-Heparin Interaction: Two Binding Sites for Small and Large Ligands as revealed by a combination of NMR Spectroscopy and Cross-Linking Mapping Experiments.
Langerin-Heparin Interaction: Two Binding Sites for Small and Large Ligands as revealed by a combination of NMR Spectroscopy and Cross-Linking Mapping Experiments.
Related Articles Langerin-Heparin Interaction: Two Binding Sites for Small and Large Ligands as revealed by a combination of NMR Spectroscopy and Cross-Linking Mapping Experiments.
J Am Chem Soc. 2015 Mar 6;
Authors: Muñoz-García JC, Chabrol E, Vives RR, Thomas A, de Paz JL, Rojo J, Imberty A, Fieschi F, Nieto PM, Angulo J
Abstract
Langerin is a C-type lectin present...
Very simple combination of TROSY, CRINEPT and multiple quantum coherence for signal enhancement in an HN(CO)CA experiment for large proteins
Very simple combination of TROSY, CRINEPT and multiple quantum coherence for signal enhancement in an HN(CO)CA experiment for large proteins
Publication year: 2011
Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 3 February 2011</br>
Monika, Bayrhuber , Roland, Riek</br>
Sensitivity enhancement in liquid state nuclear magnetic resonance (NMR) triple resonance experiments for the sequential assignment of proteins is important for the investigation of large proteins or protein complexes. We present here the 3D TROSY-MQ/CRINEPT-HN(CO)CA which makes...
The Interaction of Fluorinated Glycomimetics with DC-SIGN: Multiple Binding Modes Disentangled by the Combination of NMR Methods and MD Simulations.
Linear Mode
