NMR paper NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions

		BioNMR > Educational resources > Journal club
[NMR paper] NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-17-2022, 11:19 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions

NMR Methods for Characterization of Glycosaminoglycan-Chemokine Interactions

Humans express around 50 chemokines that play crucial roles in human pathophysiology from combating infection to immune surveillance by directing and trafficking leukocytes to the target tissue. Glycosaminoglycans (GAGs) regulate chemokine function by tuning monomer/dimer levels, chemotactic/haptotactic gradients, and how they are presented to their receptors. Knowledge of the structural features of the chemokine-GAG complexes and GAG properties that define chemokine interactions is essential...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions Solid-state NMR methods for the characterization of bioconjugations and protein-material interactions Protein solid-state NMR has evolved dramatically over the last two decades, with the development of new hardware and sample preparation methodologies. This technique is now ripe for complex applications, among which one can count bioconjugation, protein chemistry and functional biomaterials. In this review, we provide our account on this aspect of protein solid-state NMR. More...	nmrlearner	Journal club	0	10-16-2022 03:12 AM
[NMR paper] Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions Solution NMR Spectroscopy for Characterizing Protein-Glycosaminoglycan Interactions Solution nuclear magnetic resonance (NMR) spectroscopy and, in particular, chemical shift perturbation (CSP) titration experiments are ideally suited for mapping and characterizing the binding interface of macromolecular complexes. ¹H-^(15)N-HSQC-based CSP studies have become the method of choice due to their simplicity, short-time requirements, and minimal working knowledge of NMR. CSP studies for characterizing protein-glycosaminoglycan (GAG) interactions can be challenging due to... More...	nmrlearner	Journal club	0	10-10-2021 07:56 PM
[NMR paper] Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)-Ligand Interactions on Living Cancer Cells. Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)-Ligand Interactions on Living Cancer Cells. Ligand-Based NMR Study of C-X-C Chemokine Receptor Type 4 (CXCR4)-Ligand Interactions on Living Cancer Cells. J Med Chem. 2018 Mar 09;: Authors: Brancaccio D, Diana D, Di Maro S, Di Leva FS, Tomassi S, Fattorusso R, Russo L, Scala S, Trotta AM, Portella L, Novellino E, Marinelli L, Carotenuto A Abstract Peptides-binding G protein-coupled receptors play an important role in many pathological and physiological pathways....	nmrlearner	Journal club	0	03-10-2018 04:36 PM
[NMR paper] Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-highwire.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates...	nmrlearner	Journal club	0	04-02-2016 09:55 PM
[NMR paper] Characterizing protein-glycosaminoglycan interactions using solution NMR spectroscopy. Characterizing protein-glycosaminoglycan interactions using solution NMR spectroscopy. Characterizing protein-glycosaminoglycan interactions using solution NMR spectroscopy. Methods Mol Biol. 2015;1229:325-33 Authors: Joseph PR, Poluri KM, Sepuru KM, Rajarathnam K Abstract Solution nuclear magnetic resonance (NMR) spectroscopy and, in particular, chemical shift perturbation (CSP) titration experiments are ideally suited for characterizing the binding interface of macromolecular complexes. (1)H-(15) N-HSQC-based CSP studies have...	nmrlearner	Journal club	0	10-19-2014 01:27 PM
[NMR paper] NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions. NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR and computational methods in the structural and dynamic characterization of ligand-receptor interactions. Adv Exp Med Biol. 2014;805:271-304 Authors: Ghitti M, Musco G, Spitaleri A Abstract The recurrent failures in drug discovery campaigns, the asymmetry between the...	nmrlearner	Journal club	0	05-31-2014 01:47 AM
13C-Labeled Heparan Sulfate Analogue as a Tool To Study Protein/Heparan Sulfate Interactions by NMR Spectroscopy: Application to the CXCL12? Chemokine 13C-Labeled Heparan Sulfate Analogue as a Tool To Study Protein/Heparan Sulfate Interactions by NMR Spectroscopy: Application to the CXCL12? Chemokine Ce?dric Laguri, Nicolas Sapay, Jean-Pierre Simorre, Bernhard Brutscher, Anne Imberty, Pierre Gans and Hugues Lortat-Jacob http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201753e/aop/images/medium/ja-2011-01753e_0006.gif Journal of the American Chemical Society DOI: 10.1021/ja201753e http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...	nmrlearner	Journal club	0	06-09-2011 01:32 AM
[NMR paper] Characterization of tertiary interactions in a folded protein by NMR methods: studies Characterization of tertiary interactions in a folded protein by NMR methods: studies of pH-induced structural changes in human growth hormone. Related Articles Characterization of tertiary interactions in a folded protein by NMR methods: studies of pH-induced structural changes in human growth hormone. Biochemistry. 1992 Sep 15;31(36):8587-96 Authors: Abildgaard F, JÃ¸rgensen AM, Led JJ, Christensen T, Jensen EB, Junker F, DalbÃ¸ge H The pH-induced conformational changes in human growth hormone (hGH) have been studied, using a new...	nmrlearner	Journal club	0	08-21-2010 11:45 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off