Related ArticlesBinding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.
Biochemistry. 2014 Oct 28;53(42):6706-16
Authors: Ferguson FM, Dias DM, Rodrigues JP, Wienk H, Boelens R, Bonvin AM, Abell C, Ciulli A
Abstract
Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective targeting of the BAZ2B bromodomain by small molecule inhibitors has been recently reported, but no structural information is yet available on the interaction with its natural binding partner, acetylated histone H3K14ac. We have assigned the BAZ2B bromodomain and studied its interaction with H3K14ac acetylated peptides by NMR spectroscopy using both chemical shift perturbation (CSP) data and clean chemical exchange (CLEANEX-PM) NMR experiments. The latter was used to characterize water molecules known to play an important role in mediating interactions. Besides the anticipated Kac binding site, we consistently found the bromodomain BC loop as hotspots for the interaction. This information was used to create a data-driven model for the complex using HADDOCK. Our findings provide both structure and dynamics characterization that will be useful in the quest for potent and selective inhibitors to probe the function of the BAZ2B bromodomain.
[NMR paper] Contribution of protein phosphorylation to binding-induced folding of the SLBP-histone mRNA complex probed by phosphorus-31 NMR.
Contribution of protein phosphorylation to binding-induced folding of the SLBP-histone mRNA complex probed by phosphorus-31 NMR.
Contribution of protein phosphorylation to binding-induced folding of the SLBP-histone mRNA complex probed by phosphorus-31 NMR.
FEBS Open Bio. 2014;4:853-7
Authors: Thapar R
Abstract
Phosphorus-31 ((31)P) NMR can be used to characterize the structure and dynamics of phosphorylated proteins. Here, I use (31)P NMR to report on the chemical nature of a phosphothreonine that lies in the RNA binding domain...
nmrlearner
Journal club
0
11-08-2014 12:43 PM
Contribution of protein phosphorylation to binding-induced folding of the SLBP–histone mRNA complex probed by phosphorus-31 NMR
Contribution of protein phosphorylation to binding-induced folding of the SLBP–histone mRNA complex probed by phosphorus-31 NMR
Publication date: Available online 16 October 2014
Source:FEBS Open Bio</br>
Author(s): Roopa Thapar</br>
Phosphorus-31 (31P) NMR can be used to characterize the structure and dynamics of phosphorylated proteins. Here, I use 31P NMR to report on the chemical nature of a phosphothreonine that lies in the RNA binding domain of SLBP (stem-loop binding protein). SLBP is an intrinsically disordered protein and phosphorylation at this threonine...
nmrlearner
Journal club
0
10-16-2014 01:09 PM
Binding Hotspots of BAZ2B Bromodomain: Histone InteractionRevealed by Solution NMR Driven Docking
Binding Hotspots of BAZ2B Bromodomain: Histone InteractionRevealed by Solution NMR Driven Docking
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi500909d/20141015/images/medium/bi-2014-00909d_0011.gif
Biochemistry
DOI: 10.1021/bi500909d
http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/bichaw/~4/VdojweDGLHw
More...
nmrlearner
Journal club
0
10-16-2014 12:12 AM
[NMR paper] Study of interaction of human serum albumin with curcumin by NMR and docking.
Study of interaction of human serum albumin with curcumin by NMR and docking.
Study of interaction of human serum albumin with curcumin by NMR and docking.
J Mol Model. 2014 Aug;20(8):2365
Authors: Singh DV, Bharti SK, Agarwal S, Roy R, Misra K
Abstract
Curcumin has been reported to be therapeutically active but has poor bioavailability, half life, and high rate of metabolic detoxifcation. Most of the hydrophobic and acidic drugs get transported through human serum albumin (HSA). Binding of drugs to serum protein increases their...
nmrlearner
Journal club
0
07-18-2014 01:02 PM
[NMR paper] Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.
Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.
Related Articles Solution NMR Structure and Histone Binding of the PHD Domain of Human MLL5.
PLoS One. 2013;8(10):e77020
Authors: Lemak A, Yee A, Wu H, Yap D, Zeng H, Dombrovski L, Houliston S, Aparicio S, Arrowsmith CH
Abstract
Mixed Lineage Leukemia 5 (MLL5) is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. In addition to its catalytic domain, MLL5 contains a PHD finger domain, a protein module that...
nmrlearner
Journal club
0
10-17-2013 04:57 PM
[NMR paper] Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations.
Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations.
Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations.
PLoS One. 2013;8(9):e74040
Authors: Huan X, Shi J, Lim L, Mitra S, Zhu W, Qin H, Pasquale EB, Song J
Abstract
The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions...
nmrlearner
Journal club
0
10-03-2013 03:31 PM
[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data.
Proteins. 2005 Aug 15;60(3):367-81
Authors: van Dijk AD, Fushman D, Bonvin AM
When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop bin
NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
Related Articles NMR structure and dynamics of the RNA-binding site for the histone mRNA stem-loop binding protein.
RNA. 2002 Jan;8(1):83-96
Authors: DeJong ES, Marzluff WF, Nikonowicz EP
The 3' end of replication-dependent histone mRNAs terminate in a conserved sequence containing a stem-loop. This 26-nt sequence is the binding site for a protein, stem-loop binding protein (SLBP), that is involved in multiple aspects of histone mRNA metabolism...
Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking.
Linear Mode
