NMR paper 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins

		BioNMR > Educational resources > Journal club
[NMR paper] 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins

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

07-03-2021, 08:12 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

1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins

1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins

Angewandte Chemie International Edition, EarlyView.

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR. Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles Altered Domain Structure of the Prion Protein Caused by Cu2+ Binding and Functionally Relevant Mutations: Analysis by Cross-Linking, MS/MS, and NMR. Structure. 2019 Mar 28;: Authors: McDonald AJ, Leon DR, Markham KA, Wu B, Heckendorf CF, Schilling K, Showalter HD,...	nmrlearner	Journal club	0	04-09-2019 11:33 PM
[NMR paper] Reversible DNA-protein cross-linking at epigenetic DNA marks Reversible DNA-protein cross-linking at epigenetic DNA marks 5-Formylcytosine (5fC) is an endogenous DNA modification frequently found within regulatory elements of mammalian genes. Although 5fC is an oxidation product of 5-methylcytosine (5mC), the two epigenetic marks show distinct genome-wide distributions and protein affinities, suggesting that they perform different functions in epigenetic signaling. A unique feature of 5fC is the presence of a potentially reactive aldehyde group in its structure. Here, we show that 5fC bases in DNA readily form Schiff base conjugates with Lys side...	nmrlearner	Journal club	0	09-12-2017 01:45 PM
Use of Protein Cross-Linking and Radiolytic LabelingTo Elucidate the Structure of PsbO withinHigher-Plant Photosystem II Use of Protein Cross-Linking and Radiolytic LabelingTo Elucidate the Structure of PsbO withinHigher-Plant Photosystem II http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00365/20160603/images/medium/bi-2016-003659_0004.gif Biochemistry DOI: 10.1021/acs.biochem.6b00365 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/LGXqWsWM1bg More...	nmrlearner	Journal club	0	06-04-2016 11:08 AM
Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry - Nature.com Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry - Nature.com http://www.bionmr.com//t2.gstatic.com/images?q=tbn:ANd9GcSCXR38-W1skwr6nJyTpI7ekwp0MTCyjWVm3-nHyO5fN0ai5Hxu348VoeOV77NUFQBjMN6RfXbk Nature.com <img alt="" height="1" width="1"> Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry Nature.com We describe an integrated workflow that robustly identifies cross-links from endogenous protein complexes in human cellular lysates. Our approach is based on the application of mass spectrometry (MS)-cleavable cross-linkers,...	nmrlearner	Online News	0	09-29-2015 07:59 AM
Langerin–HeparinInteraction: Two Binding Sitesfor Small and Large Ligands As Revealed by a Combination of NMR Spectroscopyand Cross-Linking Mapping Experiments Langerin–HeparinInteraction: Two Binding Sitesfor Small and Large Ligands As Revealed by a Combination of NMR Spectroscopyand Cross-Linking Mapping Experiments Juan C. Mun?oz-Garci?a, Eric Chabrol, Romain R. Vive?s, Aline Thomas, Jose? L. de Paz, Javier Rojo, Anne Imberty, Franck Fieschi, Pedro M. Nieto and Jesu?s Angulo http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja511529x/20150319/images/medium/ja-2014-11529x_0009.gif Journal of the American Chemical Society DOI: 10.1021/ja511529x...	nmrlearner	Journal club	0	03-23-2015 08:22 PM
Interactions between CusF and CusB Identified by NMR Spectroscopy and Chemical Cross-Linking Coupled to Mass Spectrometry Interactions between CusF and CusB Identified by NMR Spectroscopy and Chemical Cross-Linking Coupled to Mass Spectrometry http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi102012j/aop/images/medium/bi-2010-02012j_0006.gif Biochemistry DOI: 10.1021/bi102012j http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/1zthtU6QJBQ More...	nmrlearner	Journal club	0	03-09-2011 04:19 AM
Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Interactions between CusF and CusB identified by NMR spectroscopy and chemical cross-linking coupled to mass spectrometry. Biochemistry. 2011 Feb 16; Authors: Mealman TD, Bagai I, Singh P, Goodlet DR, Rensing C, Zhou H, Wysocki VH, McEvoy MM The E. coli periplasmic proteins CusF and CusB, as part of the CusCFBA efflux system, aid in the resistance of elevated levels of copper and silver by direct metal transfer between the...	nmrlearner	Journal club	0	02-18-2011 08:07 PM
Effect of protein structural integrity on cross-linking by tyrosinase evidenced by mu Effect of protein structural integrity on cross-linking by tyrosinase evidenced by multidimensional heteronuclear NMR spectroscopy. Effect of protein structural integrity on cross-linking by tyrosinase evidenced by multidimensional heteronuclear NMR spectroscopy. J Biotechnol. 2010 Nov 15; Authors: Hellman M, Mattinen ML, Fu B, Buchert J, Permi P Enzymatic cross-linking of proteins can be catalyzed either by transferase-type enzymes, e.g., transglutaminases, or by oxidoreductases, e.g, tyrosinases or laccases. Three-dimensional structure of...	nmrlearner	Journal club	0	11-20-2010 06:01 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