NMR paper Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein

		BioNMR > Educational resources > Journal club
[NMR paper] Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein

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

03-31-2021, 11:21 PM

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

Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein

Impact of In-Cell and In-Vitro Crowding on the Conformations and Dynamics of an Intrinsically Disordered Protein

Angewandte Chemie International Edition, EarlyView.

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] In-Cell NMR of Intrinsically Disordered Proteins in Mammalian Cells. In-Cell NMR of Intrinsically Disordered Proteins in Mammalian Cells. Related Articles In-Cell NMR of Intrinsically Disordered Proteins in Mammalian Cells. Methods Mol Biol. 2020;2141:873-893 Authors: Gerez JA, Prymaczok NC, Riek R Abstract In-cell NMR enables structural insights at atomic resolution of proteins in their natural environment. To date, very few methods have been developed to study proteins by in-cell NMR in mammalian systems. Here we describe a detailed protocol to conduct in-cell NMR on the intrinsically...	nmrlearner	Journal club	0	07-23-2020 11:23 PM
[NMR paper] Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy. Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy. Related Articles Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy. Methods Mol Biol. 2020;2141:233-245 Authors: Isaksson L, Pedersen A Abstract Cell-free protein synthesis (CFPS) is an established method to produce recombinant proteins and has been used in a wide variety of applications. The use of CFPS has almost from the onset been favorably linked to the production of isotopically...	nmrlearner	Journal club	0	07-23-2020 11:23 PM
[ASAP] How Do Intrinsically Disordered Viral Proteins Hijack the Cell? How Do Intrinsically Disordered Viral Proteins Hijack the Cell? https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00622/20180627/images/medium/bi-2018-00622j_0003.gif Biochemistry DOI: 10.1021/acs.biochem.8b00622 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/P0xr0p5XaMU More...	nmrlearner	Journal club	0	06-29-2018 08:31 AM
[NMR paper] A bioresistant nitroxide spin label for in-cell EPR spectroscopy: in vitro and in oocytes protein structural dynamics studies. A bioresistant nitroxide spin label for in-cell EPR spectroscopy: in vitro and in oocytes protein structural dynamics studies. Approaching proteins structural dynamics and protein-protein interactions in the cellular environment is a fundamental challenge. Due to its absolute sensitivity and to its selectivity to paramagnetic species, Site-Directed Spin Labeling (SDSL) combined with Electron Paramagnetic Resonance (EPR) has the potential to evolve into an efficient method to follow conformational changes in proteins directly inside cells. Until now, the use of nitroxyde-based spin labels...	nmrlearner	Journal club	0	12-12-2017 02:12 AM
Conformations and Exchange Dynamics of FlgM, an Intrinsically Disordered Protein, in Dilute and Crowded Conditions Studied by NMR Spectroscopy Conformations and Exchange Dynamics of FlgM, an Intrinsically Disordered Protein, in Dilute and Crowded Conditions Studied by NMR Spectroscopy Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Pieter E.S. Smith, Huan-Xiang Zhou</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-17-2016 07:50 PM
[NMR paper] In-cell (13)C NMR spectroscopy for the study of intrinsically disordered proteins. In-cell (13)C NMR spectroscopy for the study of intrinsically disordered proteins. In-cell (13)C NMR spectroscopy for the study of intrinsically disordered proteins. Nat Protoc. 2014 Sep;9(9):2005-2016 Authors: Felli IC, Gonnelli L, Pierattelli R Abstract A large number of proteins carry out their function in highly flexible and disordered states, lacking a well-defined 3D structure. These proteins, referred to as intrinsically disordered proteins (IDPs), are now in the spotlight of modern structural biology. Nuclear magnetic...	nmrlearner	Journal club	0	08-01-2014 06:21 PM
[NMR paper] Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein. Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein. Related Articles Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of ?-Synuclein. Chembiochem. 2013 Jun 28; Authors: Roche J, Ying J, Maltsev AS, Bax A Abstract The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated ?-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close...	nmrlearner	Journal club	0	07-03-2013 01:46 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

« 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