NMR paper Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?

		BioNMR > Educational resources > Journal club
[NMR paper] Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?

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

08-10-2021, 10:54 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

Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?

Structural biology of RNA-binding proteins in the context of phase separation: What NMR and EPR can bring?

Liquid-liquid phase separation of RNA-binding proteins underlies the formation of membraneless organelles, whose composition is dynamic and whose existence may be transient. These organelles are involved in regulation of RNA processing and translation and, if they behave abnormally, in pathologies. Because disorder phenomena are essential in their formation and dynamics, established methodology is insufficient for characterizing their structure. In this review, we consider the current and...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase The role of biomolecular condensates in regulating biological function and the importance of dynamic interactions involving intrinsically disordered protein regions (IDRs) in their assembly are increasingly appreciated. While computational and theoretical approaches have provided significant insights into IDR phase behavior, establishing the critical interactions that govern condensation with atomic resolution through experiment is more difficult, given the lack of applicability of standard... ...	nmrlearner	Journal club	0	06-02-2021 05:10 PM
Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase [Biophysics and Computational Biology] Interaction hot spots for phase separation revealed by NMR studies of a CAPRIN1 condensed phase Tae Hun Kim, Brandon J. Payliss, Michael L. Nosella, Ian T. W. Lee, Yuki Toyama, Julie D. Forman-Kay, Lewis E. Kay... Date: 2021-06-01 The role of biomolecular condensates in regulating biological function and the importance of dynamic interactions involving intrinsically disordered protein regions (IDRs) in their assembly are increasingly appreciated. While computational and theoretical approaches have provided significant insights into IDR phase behavior, establishing the critical...	nmrlearner	Journal club	0	06-01-2021 11:42 PM
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...	nmrlearner	Journal club	0	01-28-2021 02:26 AM
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...	nmrlearner	Journal club	0	12-29-2020 04:50 AM
'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
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
Structural biology Structure in the cellular context - Nature.com <img alt="" height="1" width="1"> Structural biology Structure in the cellular context Nature.com Researchers develop an approach based on solid-state nuclear magnetic resonance (NMR) to study the structure of an intrinsically disordered protein under near-native conditions. Traditionally, investigations into the molecular structure of a protein ... Structural biology Structure in the cellular context - Nature.com More...	nmrlearner	Online News	0	12-09-2015 09:03 AM
Structural biology Structure in the cellular context - Nature.com <img alt="" height="1" width="1"> Structural biology Structure in the cellular context Nature.com Researchers develop an approach based on solid-state nuclear magnetic resonance (NMR) to study the structure of an intrinsically disordered protein under near-native conditions. Traditionally, investigations into the molecular structure of a protein ... Structural biology Structure in the cellular context - Nature.com More...	nmrlearner	Online News	0	12-01-2015 11:22 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