NMR paper NMR studies of protein folding and binding in cells and cell-like environments.

		BioNMR > Educational resources > Journal club
[NMR paper] NMR studies of protein folding and binding in cells and cell-like environments.

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

12-06-2014, 05:18 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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 studies of protein folding and binding in cells and cell-like environments.

NMR studies of protein folding and binding in cells and cell-like environments.

NMR studies of protein folding and binding in cells and cell-like environments.

Curr Opin Struct Biol. 2014 Dec 2;30C:7-16

Authors: Smith AE, Zhang Z, Pielak GJ, Li C

Abstract
Proteins function in cells where the concentration of macromolecules can exceed 300g/L. The ways in which this crowded environment affects the physical properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded conditions. Many of the observations can be understood in terms of interactions between proteins and the rest of the intracellular environment (i.e. quinary interactions). Nevertheless, NMR studies of folding and binding in cells and cell-like environments remain in their infancy. The frontier involves investigations of larger proteins and further efforts in higher eukaryotic cells.

PMID: 25479354 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
NMR studies of protein folding and binding in cells and cell-like environments NMR studies of protein folding and binding in cells and cell-like environments Publication date: February 2015 Source:Current Opinion in Structural Biology, Volume 30</br> Author(s): Austin E Smith , Zeting Zhang , Gary J Pielak , Conggang Li</br> Proteins function in cells where the concentration of macromolecules can exceed 300g/L. The ways in which this crowded environment affects the physical properties of proteins remain poorly understood. We summarize recent NMR-based studies of protein folding and binding conducted in cells and in vitro under crowded...	nmrlearner	Journal club	0	12-04-2014 04:37 AM
[NMR paper] Quantitation of Recombinant Protein in Whole Cells and Cell Extracts with Solid-State NMR Spectroscopy. Quantitation of Recombinant Protein in Whole Cells and Cell Extracts with Solid-State NMR Spectroscopy. Related Articles Quantitation of Recombinant Protein in Whole Cells and Cell Extracts with Solid-State NMR Spectroscopy. Biochemistry. 2013 Jun 6; Authors: Vogel EP, Weliky DP Abstract Recombinant proteins (RPs) are commonly expressed in bacteria followed by solubilization and chromatography. Purified RP yield can be diminished by losses at any step with very different changes in methods needed to try to improve yield. Time and...	nmrlearner	Journal club	0	06-08-2013 02:18 PM
[NMR paper] Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Chem Commun (Camb). 2013 Feb 26; Authors: Takaoka Y, Kioi Y, Morito A, Otani J, Arita K, Ashihara E, Ariyoshi M, Tochio H, Shirakawa M, Hamachi I Abstract Here we describe how a (19)F-probe incorporated into an endogenous protein by a chemical biology method revealed protein dynamics. By explicit determination of ligand-bound and unbound structures with...	nmrlearner	Journal club	0	02-27-2013 06:47 PM
[NMR paper] Protein dynamics in living cells studied by in-cell NMR spectroscopy. Protein dynamics in living cells studied by in-cell NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Protein dynamics in living cells studied by in-cell NMR spectroscopy. FEBS Lett. 2013 Jan 11; Authors: Li C, Liu M Abstract Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques...	nmrlearner	Journal club	0	02-03-2013 10:22 AM
Protein dynamics in living cells studied by in-cell NMR spectroscopy Protein dynamics in living cells studied by in-cell NMR spectroscopy Available online 11 January 2013 Publication year: 2013 Source:FEBS Letters</br> </br> Most proteins function in cells where protein concentrations can reach 400g/l. However, most quantitative studies of protein properties are performed in idealized, dilute conditions. Recently developed in-cell NMR techniques can provide protein structure and other biophysical properties inside living cells at atomic resolution. Here we review how protein dynamics, including global and internal motions have been...	nmrlearner	Journal club	0	02-03-2013 10:13 AM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these interactions...	nmrlearner	Journal club	0	09-30-2011 06:00 AM
Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Exploring weak, transient protein-protein interactions in crowded in vivo environments by in-cell NMR spectroscopy. Biochemistry. 2011 Sep 26; Authors: Wang Q, Zhuravleva A, Gierasch LM Abstract Biology relies on functional interplay of proteins in the crowded and heterogeneous environment inside cells, and functional protein interactions are often weak and transient. Thus, methods are needed that preserve these...	nmrlearner	Journal club	0	09-30-2011 05:59 AM

« 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