NMR paper Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

		BioNMR > Educational resources > Journal club
[NMR paper] Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

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

09-29-2021, 12:23 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,733

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

Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and...

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Expanding the Structural Diversity of Protein Building Blocks with Noncanonical Amino Acids Biosynthesized from Aromatic Thiols Expanding the Structural Diversity of Protein Building Blocks with Noncanonical Amino Acids Biosynthesized from Aromatic Thiols Angewandte Chemie International Edition, EarlyView. More...	nmrlearner	Journal club	0	03-23-2021 07:56 PM
[NMR paper] Self-Assembly of DNA and RNA Building Blocks Explored by Nitrogen-14 NMR Crystallography: Structure and Dynamics. Self-Assembly of DNA and RNA Building Blocks Explored by Nitrogen-14 NMR Crystallography: Structure and Dynamics. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--media.wiley.com-assets-7388-69-wiley-full-text.png Related Articles Self-Assembly of DNA and RNA Building Blocks Explored by Nitrogen-14 NMR Crystallography: Structure and Dynamics. Chemphyschem. 2020 Mar 19;: Authors: Carnevale D, Hollenstein M, Bodenhausen G Abstract The isotopic enrichment of nucleic acids with nitrogen-15 is often carried out...	nmrlearner	Journal club	0	03-21-2020 12:53 AM
[ASAP] Proteins as Sustainable Building Blocks for the Next Generation of Bioinorganic Nanomaterials Proteins as Sustainable Building Blocks for the Next Generation of Bioinorganic Nanomaterials https://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.8b00966/20181003/images/medium/bi-2018-00966a_0001.gif Biochemistry DOI: 10.1021/acs.biochem.8b00966 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/_FMJp6mgx5Q More...	nmrlearner	Journal club	0	11-25-2018 06:02 AM
Production of isotope-labeled proteins in insect cells for NMR Production of isotope-labeled proteins in insect cells for NMR Abstract Baculovirus-infected insect cells have become a powerful tool to express recombinant proteins for structural and functional studies by NMR spectroscopy. This article provides an introduction into the insect cell/baculovirus expression system and its use for the production of recombinant isotope-labeled proteins. We discuss recent advances in inexpensive isotope-labeling methods using labeled algal or yeast extracts as the amino acid source and give examples of advanced NMR...	nmrlearner	Journal club	0	04-23-2018 05:00 PM
[NMR paper] Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR. Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR. Related Articles Synthesis and incorporation of 13C-labeled DNA building blocks to probe structural dynamics of DNA by NMR. Nucleic Acids Res. 2017 Sep 06;45(15):9178-9192 Authors: Nußbaumer F, Juen MA, Gasser C, Kremser J, Müller T, Tollinger M, Kreutz C Abstract We report the synthesis of atom-specifically 13C-modified building blocks that can be incorporated into DNA via solid phase synthesis to facilitate investigations...	nmrlearner	Journal club	0	09-16-2017 09:58 PM
Protein Assembly and Building Blocks: Beyond the Limitsof the LEGO Brick Metaphor Protein Assembly and Building Blocks: Beyond the Limitsof the LEGO Brick Metaphor http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.7b00666/20170830/images/medium/bi-2017-006667_0004.gif Biochemistry DOI: 10.1021/acs.biochem.7b00666 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/_mVOizsSYuA More...	nmrlearner	Journal club	0	09-01-2017 05:57 AM
[NMR paper] Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies. Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies. Related Articles Isotope-Labeled Amyloids via Synthesis, Expression, and Chemical Ligation for Use in FTIR, 2D IR, and NMR Studies. Methods Mol Biol. 2016;1345:21-41 Authors: Zhang TO, Grechko M, Moran SD, Zanni MT Abstract This chapter provides protocols for isotope-labeling the human islet amyloid polypeptide (hIAPP or amylin) involved in type II diabetes and ?D-crystallin involved in cataract formation. Because...	nmrlearner	Journal club	0	10-12-2015 01:04 AM
[NMR paper] NMR studies of structure and dynamics of isotope enriched proteins. NMR studies of structure and dynamics of isotope enriched proteins. Related Articles NMR studies of structure and dynamics of isotope enriched proteins. Biopolymers. 1992 Apr;32(4):381-90 Authors: Wagner G, Thanabal V, Stockman BJ, Peng JW, Nirmala NR, Hyberts SG, Goldberg MS, Detlefsen DJ, Clubb RT, Adler M Structural studies of globular proteins by nmr can be enhanced by the use of isotope enrichment. We have been working with proteins enriched with 15N, and with both 15N and 13C. Due to the isotope enrichment we could assign several large...	nmrlearner	Journal club	0	08-21-2010 11:41 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