NMR paper An Endoplasmic Reticulum (ER)-Targeting DNA Nanodevice for Autophagy-Dependent Degradation of Proteins in Membrane-Bound Organelles

		BioNMR > Educational resources > Journal club
[NMR paper] An Endoplasmic Reticulum (ER)-Targeting DNA Nanodevice for Autophagy-Dependent Degradation of Proteins in Membrane-Bound Organelles

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

09-13-2022, 11:49 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

An Endoplasmic Reticulum (ER)-Targeting DNA Nanodevice for Autophagy-Dependent Degradation of Proteins in Membrane-Bound Organelles

An Endoplasmic Reticulum (ER)-Targeting DNA Nanodevice for Autophagy-Dependent Degradation of Proteins in Membrane-Bound Organelles

Angewandte Chemie International Edition, Volume 61, Issue 38, September 19, 2022.

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Tuning Protein Dynamics to Sense Rapid Endoplasmic-Reticulum Calcium Dynamics Tuning Protein Dynamics to Sense Rapid Endoplasmic-Reticulum Calcium Dynamics Angewandte Chemie International Edition, Volume 60, Issue 43, Page 23289-23298, October 18, 2021. More...	nmrlearner	Journal club	0	10-11-2021 03:57 PM
[ASAP] Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy–Lysosome Pathway Redefining the Scope of Targeted Protein Degradation: Translational Opportunities in Hijacking the Autophagy–Lysosome Pathway https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00330/20210927/images/medium/bi1c00330_0002.gif Biochemistry DOI: 10.1021/acs.biochem.1c00330 http://feeds.feedburner.com/~r/acs/bichaw/~4/joOGR6eQNhs More...	nmrlearner	Journal club	0	09-27-2021 10:14 PM
[NMR paper] From medium to endoplasmic reticulum: Tracing anticancer phenolato titanium(IV) complex by (19)F NMR detection From medium to endoplasmic reticulum: Tracing anticancer phenolato titanium(IV) complex by (19)F NMR detection Titanium(IV) complexes of diaminobis(phenolato)-bis(alkoxo) ligands are promising anticancer drugs, showing marked in-vivo efficacy with no toxic side-effects in mice, hence, it is of interest to elucidate their mechanism of action. Herein, we employed a fluoro-substituted derivative, FenolaTi, for mechanistic analysis of the active species and its cellular target by quantitative ^(19)F NMR detection to reveal its biodistribution and reactivity in extracellular and intracellular...	nmrlearner	Journal club	0	05-30-2021 06:35 AM
[NMR paper] Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acspubs.jpg Related Articles Helix Fraying and Lipid-Dependent Structure of a Short Amphipathic Membrane-Bound Peptide Revealed by Solid-State NMR. J Phys Chem B. 2018 06 14;122(23):6236-6250 Authors: Strandberg E, Grau-Campistany A, Wadhwani P, Bürck J, Rabanal F, Ulrich AS Abstract The amphipathic ?-helical...	nmrlearner	Journal club	0	04-19-2019 10:31 AM
[NMR paper] Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy. Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy. Related Articles Elucidating ligand-bound structures of membrane proteins using solid-state NMR spectroscopy. Curr Opin Struct Biol. 2019 Mar 20;57:103-109 Authors: Elkins MR, Hong M Abstract Magic-angle-spinning (MAS) solid-state NMR spectroscopy is a versatile technique to elucidate functionally important protein-ligand interactions in lipid membranes. Here, we review recent solid-state NMR studies of membrane protein interactions with...	nmrlearner	Journal club	0	03-25-2019 08:37 PM
[NMR paper] Simplifying solid-state NMR spectra for biophysical studies on membrane proteins: selective targeting of sites and interactions. Simplifying solid-state NMR spectra for biophysical studies on membrane proteins: selective targeting of sites and interactions. Related Articles Simplifying solid-state NMR spectra for biophysical studies on membrane proteins: selective targeting of sites and interactions. Biophys J. 2014 May 20;106(10):2083-4 Authors: Huster D, Madhu PK PMID: 24853736	nmrlearner	Journal club	0	05-24-2014 04:50 PM
Simplifying Solid-State NMR Spectra for Biophysical Studies on Membrane Proteins: Selective Targeting of Sites and Interactions Simplifying Solid-State NMR Spectra for Biophysical Studies on Membrane Proteins: Selective Targeting of Sites and Interactions Publication date: 20 May 2014 Source:Biophysical Journal, Volume 106, Issue 10</br> Author(s): Daniel Huster , Perunthiruthy*K. Madhu</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	05-21-2014 11:52 AM
[NMR paper] Solution NMR Studies on the Orientation of Membrane-Bound Peptides and Proteins by Paramagnetic Probes. Solution NMR Studies on the Orientation of Membrane-Bound Peptides and Proteins by Paramagnetic Probes. Solution NMR Studies on the Orientation of Membrane-Bound Peptides and Proteins by Paramagnetic Probes. Molecules. 2013;18(7):7407-7435 Authors: Schrank E, Wagner GE, Zangger K Abstract Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often...	nmrlearner	Journal club	0	06-27-2013 02:10 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