BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 12-29-2020, 04:50 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Biomolecular phase separation through the lens of sodium-23 NMR

Biomolecular phase separation through the lens of sodium-23 NMR

Abstract

Phase separation is a fundamental physicochemical process underlying the spatial arrangement and coordination of cellular events. Detailed characterization of biomolecular phase separation requires experimental access to the internal environment of dilute and especially condensed phases at high resolution. In this study, we take advantage from the ubiquitous presence of sodium ions in biomolecular samples and present the potentials of 23Na NMR as a proxy to report the internal fluidity of biomolecular condensed phases. After establishing the temperature and viscosity dependence of 23Na NMR relaxation rates and translational diffusion coefficient, we demonstrate that 23Na NMR probes of rotational and translational mobility of sodium ions are capable of capturing the increasing levels of confinement in agarose gels in dependence of agarose concentration. The 23Na NMR approach is then applied to a gel-forming phenylalanine-glycine (FG)-containing peptide, part of the nuclear pore complex involved in controlling the traffic between cytoplasm and cell nucleus. It is shown that the 23Na NMR together with the 17O NMR provide a detailed picture of the sodium ion and water mobility within the interior of the FG peptide hydrogel. As another example, we study phase separation in water-triethylamine (TEA) mixture and provide evidence for the presence of multiple microscopic environments within the TEA-rich phase. Our results highlight the potentials of 23Na NMR in combination with 17O NMR in studying biological phase separation, in particular with regards to the molecular properties of biomolecular condensates and their regulation through various physico- and biochemical factors.



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
'Reading' proteins for new properties: Researchers can now translate patterns to determine how a protein will condense during phase separation - Science Daily
'Reading' proteins for new properties: Researchers can now translate patterns to determine how a protein will condense during phase separation Science Daily 'Reading' proteins for new properties: Researchers can now translate patterns to determine how a protein will condense during phase separation - Science Daily More...
nmrlearner Online News 0 02-29-2020 09:52 PM
[ASAP] Pressure-Sensitive and Osmolyte-Modulated Liquid–Liquid Phase Separation of Eye-Lens ?-Crystallins
Pressure-Sensitive and Osmolyte-Modulated Liquid–Liquid Phase Separation of Eye-Lens ?-Crystallins Süleyman Cinar, Hasan Cinar, Hue Sun Chan, Roland Winter https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.8b13636/20190423/images/medium/ja-2018-13636x_0006.gif Journal of the American Chemical Society DOI: 10.1021/jacs.8b13636 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/0k8PRwEgdm4
nmrlearner Journal club 0 04-24-2019 09:00 AM
Relationship of Sequence and Phase Separation in ProteinLow-Complexity Regions
Relationship of Sequence and Phase Separation in ProteinLow-Complexity Regions https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00008/20180316/images/medium/bi-2018-00008n_0006.gif Biochemistry DOI: 10.1021/acs.biochem.8b00008 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/8TxFxS7r55U More...
nmrlearner Journal club 0 03-17-2018 12:12 PM
Phase Separation Behavior of Supercharged Proteinsand Polyelectrolytes
Phase Separation Behavior of Supercharged Proteinsand Polyelectrolytes http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00990/20171227/images/medium/bi-2017-00990x_0008.gif Biochemistry DOI: 10.1021/acs.biochem.7b00990 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/vZ7f8dKcbeE More...
nmrlearner Journal club 0 12-29-2017 02:19 AM
[NMR paper] Investigating liquid-liquid phase separation of a monoclonal antibody using solution-state NMR spectroscopy: effect of Arg·Glu and Arg·HCl.
Investigating liquid-liquid phase separation of a monoclonal antibody using solution-state NMR spectroscopy: effect of Arg·Glu and Arg·HCl. Investigating liquid-liquid phase separation of a monoclonal antibody using solution-state NMR spectroscopy: effect of Arg·Glu and Arg·HCl. Mol Pharm. 2017 Jun 14;: Authors: Kheddo P, Bramham JE, Dearman RJ, Uddin S, van der Walle CF, Golovanov AP Abstract Liquid-liquid phase separation (LLPS) of monoclonal antibody (mAb) formulations involves spontaneous separation into dense...
nmrlearner Journal club 0 06-15-2017 03:37 PM
[NMR paper] Characterization of Sodium Mobility and Binding by (23) Na NMR Spectroscopy in a Model Lipoproteic Emulsion Gel for Sodium Reduction.
Characterization of Sodium Mobility and Binding by (23) Na NMR Spectroscopy in a Model Lipoproteic Emulsion Gel for Sodium Reduction. Related Articles Characterization of Sodium Mobility and Binding by (23) Na NMR Spectroscopy in a Model Lipoproteic Emulsion Gel for Sodium Reduction. J Food Sci. 2017 May 27;: Authors: Okada KS, Lee Y Abstract The effects of formulation and processing parameters on sodium availability in a model lipid/protein-based emulsion gel were studied for purposes of sodium reduction. Heat-set model gels...
nmrlearner Journal club 0 05-31-2017 09:18 PM
Phosphate–WaterInterplay Tunes Amorphous CalciumCarbonate Metastability: Spontaneous Phase Separation and Crystallizationvs Stabilization Viewed by Solid State NMR
Phosphate–WaterInterplay Tunes Amorphous CalciumCarbonate Metastability: Spontaneous Phase Separation and Crystallizationvs Stabilization Viewed by Solid State NMR Shifi Kababya, Assaf Gal, Keren Kahil, Steve Weiner, Lia Addadi and Asher Schmidt http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja511869g/20150105/images/medium/ja-2014-11869g_0007.gif Journal of the American Chemical Society DOI: 10.1021/ja511869g http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 01-06-2015 07:59 PM
[NMR paper] A solid-state NMR study of molecular mobility and phase separation in co-spray-dried
A solid-state NMR study of molecular mobility and phase separation in co-spray-dried protein-sugar particles. Related Articles A solid-state NMR study of molecular mobility and phase separation in co-spray-dried protein-sugar particles. Eur J Pharm Sci. 2005 May;25(1):105-12 Authors: Suihko EJ, Forbes RT, Apperley DC Molecular mobility and physical form of co-spray-dried sugar-lysozyme formulations were evaluated. Co-spray-dried trehalose:lysozyme and sucrose:lysozyme formulations in 1:9, 1:1 and 9:1 ratios (w:w) were stored at 0% RH and 75%...
nmrlearner Journal club 0 11-25-2010 08:21 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 05:35 PM.


Map