[ASAP] The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

		BioNMR > Educational resources > Journal club
[ASAP] The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

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

05-05-2022, 11:49 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

[ASAP] The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

[ASAP] The DNA-Binding High-Mobility Group Box Domain of Sox Family Proteins Directly Interacts with RNA In Vitro

Biochemistry
DOI: 10.1021/acs.biochem.2c00218

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[ASAP] Characterization of the High-Affinity Fuzzy Complex between the Disordered Domain of the E7 Oncoprotein from High-Risk HPV and the TAZ2 Domain of CBP Characterization of the High-Affinity Fuzzy Complex between the Disordered Domain of the E7 Oncoprotein from High-Risk HPV and the TAZ2 Domain of CBP https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00669/20211214/images/medium/bi1c00669_0011.gif Biochemistry DOI: 10.1021/acs.biochem.1c00669 More...	nmrlearner	Journal club	0	12-15-2021 08:23 AM
[ASAP] Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter Formation of the Metal-Binding Core of the ZRT/IRT-like Protein (ZIP) Family Zinc Transporter https://pubs.acs.org/na101/home/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.1c00415/20210829/images/medium/bi1c00415_0010.gif Biochemistry DOI: 10.1021/acs.biochem.1c00415 http://feeds.feedburner.com/~r/acs/bichaw/~4/XQASJU_ZjZI More...	nmrlearner	Journal club	0	08-31-2021 10:53 AM
The CopC Family: Structural and Bioinformatic Insightsinto a Diverse Group of Periplasmic Copper Binding Proteins The CopC Family: Structural and Bioinformatic Insightsinto a Diverse Group of Periplasmic Copper Binding Proteins http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00175/20160406/images/medium/bi-2016-001758_0008.gif Biochemistry DOI: 10.1021/acs.biochem.6b00175 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/NhUil9uehKc More...	nmrlearner	Journal club	0	04-06-2016 10:29 PM
[NMR paper] Real-time kinetics of high-mobility group box 1 oxidation in extracellular fluids studied by in situ protein NMR spectroscopy. Real-time kinetics of high-mobility group box 1 oxidation in extracellular fluids studied by in situ protein NMR spectroscopy. Real-time kinetics of high-mobility group box 1 oxidation in extracellular fluids studied by in situ protein NMR spectroscopy. J Biol Chem. 2013 Feb 27; Authors: Zandarashvili L, Sahu D, Lee K, Lee YS, Singh P, Rajarathnam K, Iwahara J Abstract Some extracellular proteins are initially secreted in the reduced form via a non-canonical pathway bypassing the endoplasmic reticulum, and become oxidized in the...	nmrlearner	Journal club	0	03-01-2013 09:57 PM
[NMR paper] NMR studies of a new family of DNA binding proteins: the THAP proteins. NMR studies of a new family of DNA binding proteins: the THAP proteins. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--production.springer.de-OnlineResources-Logos-springerlink.gif Related Articles NMR studies of a new family of DNA binding proteins: the THAP proteins. J Biomol NMR. 2013 Jan 11; Authors: Gervais V, Campagne S, Durand J, Muller I, Milon A Abstract The THAP (THanatos-Associated Protein) domain is an evolutionary conserved C2CH zinc-coordinating domain shared with a large family of cellular factors (THAP proteins)....	nmrlearner	Journal club	0	02-03-2013 10:22 AM
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR [Biophysics and Computational Biology] Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR Kato, H., van Ingen, H., Zhou, B.-R., Feng, H., Bustin, M., Kay, L. E., Bai, Y.... Date: 2011-07-26 Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility group nucleosomal (HMGN) protein family that regulates various chromatin functions, including transcription. Here, we report the architecture of the HMGN2-nucleosome...	nmrlearner	Journal club	0	07-26-2011 11:22 PM
Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Architecture of the high mobility group nucleosomal protein 2-nucleosome complex as revealed by methyl-based NMR. Proc Natl Acad Sci U S A. 2011 Jul 5; Authors: Kato H, van Ingen H, Zhou BR, Feng H, Bustin M, Kay LE, Bai Y Chromatin structure and function are regulated by numerous proteins through specific binding to nucleosomes. The structural basis of many of these interactions is unknown, as in the case of the high mobility...	nmrlearner	Journal club	0	07-07-2011 05:12 PM
[NMR paper] Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protei Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protein kinases. An isolated but fully functional Gbeta binding domain from Ste20p is only partially folded as shown by heteronuclear NMR spectroscopy. Related Articles Molecular interactions of the Gbeta binding domain of the Ste20p/PAK family of protein kinases. An isolated but fully functional Gbeta binding domain from Ste20p is only partially folded as shown by heteronuclear NMR spectroscopy. J Biol Chem. 2001 Nov 2;276(44):41205-12 Authors: Song J, Chen Z, Xu P, Gingras R,...	nmrlearner	Journal club	0	11-19-2010 08:44 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