NMR paper In-Cell Protein Structures from 2D NMR Experiments.

		BioNMR > Educational resources > Journal club
[NMR paper] In-Cell Protein Structures from 2D NMR Experiments.

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

Rating:

Display Modes

07-06-2016, 03:13 PM

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

In-Cell Protein Structures from 2D NMR Experiments.

In-Cell Protein Structures from 2D NMR Experiments.

In-Cell Protein Structures from 2D NMR Experiments.

J Phys Chem Lett. 2016 Jul 5;

Authors: Müntener T, Häussinger D, Selenko P, Theillet FX

Abstract
In-cell NMR spectroscopy provides atomic resolution insights into the structural properties of proteins in cells. However, it is rarely used to solve entire protein structures de novo. Here, we introduce a paramagnetic lanthanide-tag to simultaneously measure protein pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) to be used as input for structure calculation routines within the Rosetta program. We employ this approach to determine the structure of the protein G B1 domain (GB1) in intact Xenopus laevis oocytes from 1H-15N 2D in-cell NMR experiments. Specifically, we derive well-defined GB1 ensembles from low concentration in-cell NMR samples (~50 ?M) measured at moderate magnetic field strengths (600 MHz), thus offering novel routes for intracellular structure determination with data from 2D in-cell NMR experiments.

PMID: 27379949 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Peering into cell structures - UD Daily http://www.bionmr.com//t0.gstatic.com/images?q=tbn:ANd9GcSCwT2cWE7tmsRZUKzKKIVOxl2OLMvleQvZJs4RDMPQCLWmqbLR3x7aYhw8hniT7-hqXgl8UJF- UD Daily <img alt="" height="1" width="1"> Peering into cell structures UD Daily The research team used magic-angle-spinning nuclear magnetic resonance spectrometry (NMR) in the Department of Chemistry and Biochemistry at UD to unveil the structure of the CAP-Gly protein assembled on polymerized microtubules. The CAP-Gly ... and more » Peering into cell structures - UD Daily	nmrlearner	Online News	0	11-25-2015 11:51 AM
[NMR paper] Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. Biophys J. 2015 Mar 24;108(6):1380-9 Authors: Nygaard R, Romaniuk JA, Rice DM, Cegelski L Abstract Gram-positive bacteria surround themselves with a thick cell wall that is essential to cell survival and is a major target of antibiotics. Quantifying alterations in cell-wall composition are crucial to evaluating drug...	nmrlearner	Journal club	0	03-27-2015 11:59 PM
[NMR paper] Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures. J Am Chem Soc. 2014 Jan 6; Authors: Mao B, Tejero R, Baker D, Montelione GT Abstract We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement...	nmrlearner	Journal club	0	01-08-2014 11:23 AM
[NMR paper] Investigation of proteins in living bacteria with in-cell NMR experiments. Investigation of proteins in living bacteria with in-cell NMR experiments. Related Articles Investigation of proteins in living bacteria with in-cell NMR experiments. Top Curr Chem. 2008;273:203-14 Authors: Dötsch V Abstract In recent years NMR methods have been developed that enable the observation of proteins insideliving bacterial cells. Because of the sensitivity of the chemical shift to environmental changesthese in-cell NMR experiments can be used to study protein conformation, molecular interaction ordynamics in a*protein's natural...	nmrlearner	Journal club	0	04-24-2013 09:48 PM
[NMR paper] Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. Related Articles Cell-free protein synthesis in an autoinduction system for NMR studies of protein-protein interactions. J Biomol NMR. 2005 Jul;32(3):235-41 Authors: Ozawa K, Jergic S, Crowther JA, Thompson PR, Wijffels G, Otting G, Dixon NA Cell-free protein synthesis systems provide facile access to proteins in a nascent state that enables formation of soluble, native protein-protein complexes even if one of the protein components is prone...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Related Articles Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray- and NMR-resolved protein structures? Proteins. 2005 Jul 1;60(1):139-47 Authors: Garbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Methyl groups as probes for proteins and complexes in in-cell NMR experiments. Methyl groups as probes for proteins and complexes in in-cell NMR experiments. Related Articles Methyl groups as probes for proteins and complexes in in-cell NMR experiments. J Am Chem Soc. 2004 Jun 9;126(22):7119-25 Authors: Serber Z, Straub W, Corsini L, Nomura AM, Shimba N, Craik CS, Ortiz de Montellano P, Dötsch V Studying protein components of large intracellular complexes by in-cell NMR has so far been impossible because the backbone resonances are unobservable due to their slow tumbling rates. We describe a methodology that overcomes...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[BMNRC community] In-cell NMR: three-dimensional protein structures In-cell NMR: three-dimensional protein structures http://www.nature.com/nature/journal/v458/n7234/edsumm/e090305-13.html Go to BMNRC community to find more info about this topic.	nmrlearner	News from other NMR forums	0	08-27-2010 07:58 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