NMR paper Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.

		BioNMR > Educational resources > Journal club
[NMR paper] Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

02-14-2018, 02:43 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,175

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

Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.

Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.

Characterisation of an aptamer against the Runt domain of AML1 (RUNX1) by NMR and mutational analyses.

FEBS Open Bio. 2018 Feb;8(2):264-270

Authors: Takada K, Amano R, Nomura Y, Tanaka Y, Sugiyama S, Nagata T, Katahira M, Nakamura Y, Kozu T, Sakamoto T

Abstract
Since the invention of systematic evolution of ligands by exponential enrichment, many short oligonucleotides (or aptamers) have been reported that can bind to a wide range of target molecules with high affinity and specificity. Previously, we reported an RNA aptamer that shows high affinity to the Runt domain (RD) of the AML1 protein, a transcription factor with roles in haematopoiesis and immune function. From kinetic and thermodynamic studies, it was suggested that the aptamer recognises a large surface area of the RD, using numerous weak interactions. In this study, we identified the secondary structure by nuclear magnetic resonance spectroscopy and performed a mutational study to reveal the residue critical for binding to the RD. It was suggested that the large contact area was formed by a DNA-mimicking motif and a multibranched loop, which confers the high affinity and specificity of binding.

PMID: 29435416 [PubMed]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Journal Highlight: Prediction of beef color using time-domain nuclear magnetic resonance (TD-NMR) relaxometry data and multivariate analyses Journal Highlight: Prediction of beef color using time-domain nuclear magnetic resonance (TD-NMR) relaxometry data and multivariate analyses http://www.spectroscopynow.com/common/images/thumbnails/1577fd80b7a.jpgTime-domain NMR and chemometrics were used to predict color parameters, such as lightness, redness and yellowness of beef in bulk samples and through packages. Read the rest at Spectroscopynow.com	nmrlearner	General	0	11-19-2016 08:35 PM
Mutational Analysis of the Binding-Induced FoldingReaction of the Mixed-Lineage Leukemia Protein to the KIX Domain Mutational Analysis of the Binding-Induced FoldingReaction of the Mixed-Lineage Leukemia Protein to the KIX Domain http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/acs.biochem.6b00505/20160705/images/medium/bi-2016-00505d_0006.gif Biochemistry DOI: 10.1021/acs.biochem.6b00505 http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/cvEVUbCsgRo More...	nmrlearner	Journal club	0	07-07-2016 04:21 AM
[NMR paper] NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain. NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain. Related Articles NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain. Protein Sci. 2014 Aug 21; Authors: Leung HT, Kukic P, Camilloni C, Bemporad F, DeSimone A, Aprile FA, Kumita J, Vendruscolo M Abstract Lymphocyte function-associated antigen-1 (LFA-1) is an integrin protein that transmits information across the plasma membrane through the...	nmrlearner	Journal club	0	08-26-2014 01:25 PM
NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain NMR characterisation of the conformational fluctuations of the human lymphocyte function associated antigen-1 i domain Abstract Lymphocyte function-associated antigen-1 (LFA-1) is an integrin protein that transmits information across the plasma membrane through the so-called ‘inside-out’ and ‘outside-in’ signalling mechanism. To investigate this mechanism, we carried out an NMR analysis of the dynamics of the LFA-1 I-domain, which has enabled us to characterise the motions of this domain on a broad range of timescales. We studied first the internal motions on the nanosecond timescale...	nmrlearner	Journal club	0	08-21-2014 06:43 PM
[NMR paper] NMR Spectroscopic and Bioinformatic Analyses of the LTBP1 C-Terminus Reveal a Highly Dynamic Domain Organisation. NMR Spectroscopic and Bioinformatic Analyses of the LTBP1 C-Terminus Reveal a Highly Dynamic Domain Organisation. Related Articles NMR Spectroscopic and Bioinformatic Analyses of the LTBP1 C-Terminus Reveal a Highly Dynamic Domain Organisation. PLoS One. 2014;9(1):e87125 Authors: Robertson IB, Handford PA, Redfield C Abstract Proteins from the LTBP/fibrillin family perform key structural and functional roles in connective tissues. LTBP1 forms the large latent complex with TGF? and its propeptide LAP, and sequesters the latent growth factor...	nmrlearner	Journal club	0	02-04-2014 04:22 PM
Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data [Letters (Online Only)] Evaluation of competing J domain:Hsp70 complex models in light of existing mutational and NMR data Sousa, R., Jiang, J., Lafer, E. M., Hinck, A. P., Wang, L., Taylor, A. B., Maes, E. G.... Date: 2012-03-27 The work by Ahmad et al. (1) presented an NMR-based model for a bacterial DnaJ J domain:DnaK(Hsp70):ADP complex that differs from our crystal structure of a disulfide-linked bovine Hsc70:auxilin J domain complex (2). The work by Ahmad et al. (1) claimed that their model can better account for published mutational data, that their model is in better agreement with a previous NMR...	nmrlearner	Journal club	0	03-27-2012 08:41 PM
Structural Characterisation of a Histone Domain by Projection-Decomposition Structural Characterisation of a Histone Domain by Projection-Decomposition Publication year: 2012 Source:Journal of Magnetic Resonance</br> Jonas Fredriksson, Wolfgang Bermel, Martin Billeter</br> We demonstrate that two projection experiments, a 15N-HSQC–NOESY–15N-HSQC and a 13C-HSQC–NOESY–15N-HSQC, recorded for a histone domain from yeast, contain enough information to support a structural characterisation of the protein. At the temperature used, 298K, the histone domain exhibits a very high extent of chemical shift degeneracy that is uncharacteristic for a fully...	nmrlearner	Journal club	0	03-09-2012 09:16 AM
Structural Characterisation of a Histone Domain by Projection-Decomposition Structural Characterisation of a Histone Domain by Projection-Decomposition Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 23 February 2012</br> JonasFredriksson, WolfgangBermel, Martin*Billeter</br> We demonstrate that two projection experiments, aN-HSQC–NOESY–N-HSQC and aC-HSQC–NOESY–N-HSQC, recorded for a histone domain from yeast, contain enough information to support a structural characterisation of the protein. At the temperature used, 298K, the histone domain exhibits a very high extent of chemical shift degeneracy that is uncharacteristic for...	nmrlearner	Journal club	0	02-25-2012 04:20 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