NMR paper NMR evidence for similarities between the DNA-binding regions of Drosophila melanogas

		BioNMR > Educational resources > Journal club
[NMR paper] NMR evidence for similarities between the DNA-binding regions of Drosophila melanogas

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

08-22-2010, 03:33 AM

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

NMR evidence for similarities between the DNA-binding regions of Drosophila melanogas

NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/forkhead families of transcription factors.

Related Articles NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/forkhead families of transcription factors.

Biochemistry. 1994 Jan 11;33(1):10-6

Authors: Vuister GW, Kim SJ, Wu C, Bax A

Heteronuclear multidimensional NMR experiments of residues 33-163 of the DNA-binding domain of Drosophila heat shock factor, dHSF(33-163), were recorded, using only 3 mg of uniformly 15N-labeled or 2 mg of uniformly 15N/13C-labeled protein. The polypeptide consists of a structured part comprising three helices, a three-stranded antiparallel beta-sheet, with the first two strands connected by a four-residue type I tight turn. The second helix is disrupted at its C-terminal end by a proline residue and is followed by an extended turn, leading to the third helix. The dHSF(33-163) protein is unstructured at its N- and C-termini, and a third unstructured region is found from Thr113 to Arg124. Exchange broadening of the 15N-1H correlations upon titration of 15N labeled HSF with a 13-base-pair DNA duplex suggests a DNA-binding motif in which the third helix acts as the recognition helix. Both the secondary structure and DNA-binding pattern of dHSF(33-163) suggest that the overall topology resembles that the helix-turn-helix bacterial activator CAP [Weber, I. T., & Steitz, T. A. (1987) J. Mol. Biol. 198, 311-326] and the liver-specific transcription factor HNF-3 gamma, the prototype of the HNF-3/forkhead protein family [Clark, K. L., Halay, E. D., Lai, E., & Burley, S. K. (1993) Nature 364, 412-420].

PMID: 8286326 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release) Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> Searching the protein structure database for ligand-binding site similarities ... 7thSpace Interactive (press release) CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the ... Read here	nmrlearner	Online News	0	01-27-2011 04:31 AM
[NMR paper] NMR and ICP spectroscopic analysis of the DNA-binding domain of the Drosophila GCM pr NMR and ICP spectroscopic analysis of the DNA-binding domain of the Drosophila GCM protein reveals a novel Zn2+ -binding motif. Related Articles NMR and ICP spectroscopic analysis of the DNA-binding domain of the Drosophila GCM protein reveals a novel Zn2+ -binding motif. Protein Eng. 2003 Apr;16(4):247-54 Authors: Shimizu M, Hiroaki H, Kohda D, Hosoya T, Akiyama-Oda Y, Hotta Y, Morita EH, Morikawa K Drosophila GCM (glial cell missing) is a novel DNA-binding protein that determines the fate of glial precursors from the neural default to glia....	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] Mapping the interacting regions between troponins T and C. Binding of TnT and TnI pep Mapping the interacting regions between troponins T and C. Binding of TnT and TnI peptides to TnC and NMR mapping of the TnT-binding site on TnC. Related Articles Mapping the interacting regions between troponins T and C. Binding of TnT and TnI peptides to TnC and NMR mapping of the TnT-binding site on TnC. J Biol Chem. 2001 Sep 28;276(39):36606-12 Authors: Blumenschein TM, Tripet BP, Hodges RS, Sykes BD Muscular contraction is triggered by an increase in calcium concentration, which is transmitted to the contractile proteins by the troponin...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
Evaluation of protein adsorption and preferred binding regions in multimodal chromato Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR. Related Articles Evaluation of protein adsorption and preferred binding regions in multimodal chromatography using NMR. Proc Natl Acad Sci U S A. 2010 Sep 13; Authors: Chung WK, Freed AS, Holstein MA, McCallum SA, Cramer SM NMR titration experiments with labeled human ubiquitin were employed in concert with chromatographic data obtained with a library of ubiquitin mutants to study the nature of protein adsorption in multimodal (MM) chromatography....	nmrlearner	Journal club	0	09-15-2010 02:26 PM
[NMR paper] NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reve NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR solution structure of a dsRNA binding domain from Drosophila staufen protein reveals homology to the N-terminal domain of ribosomal protein S5. EMBO J. 1995 Jul 17;14(14):3563-71 Authors: Bycroft M, Grünert S, Murzin AG, Proctor M, St Johnston D The...	nmrlearner	Journal club	0	08-22-2010 03:50 AM
[NMR paper] NMR studies of peptides derived from the putative binding regions of cartilage protei NMR studies of peptides derived from the putative binding regions of cartilage proteins. No evidence for binding to hyaluronan. Related Articles NMR studies of peptides derived from the putative binding regions of cartilage proteins. No evidence for binding to hyaluronan. J Biol Chem. 1994 Jan 21;269(3):1699-704 Authors: Horita DA, Hajduk PJ, Goetinck PF, Lerner LE Previous work has implicated sequences within the tandem repeats of cartilage link protein in the interaction of link protein with hyaluronan. This conclusion was based on...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] NMR studies of peptides derived from the putative binding regions of cartilage protei NMR studies of peptides derived from the putative binding regions of cartilage proteins. No evidence for binding to hyaluronan. Related Articles NMR studies of peptides derived from the putative binding regions of cartilage proteins. No evidence for binding to hyaluronan. J Biol Chem. 1994 Jan 21;269(3):1699-704 Authors: Horita DA, Hajduk PJ, Goetinck PF, Lerner LE Previous work has implicated sequences within the tandem repeats of cartilage link protein in the interaction of link protein with hyaluronan. This conclusion was based on...	nmrlearner	Journal club	0	08-22-2010 03:33 AM
[NMR paper] NMR evidence for similarities between the DNA-binding regions of Drosophila melanogas NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/forkhead families of transcription factors. Related Articles NMR evidence for similarities between the DNA-binding regions of Drosophila melanogaster heat shock factor and the helix-turn-helix and HNF-3/forkhead families of transcription factors. Biochemistry. 1994 Jan 11;33(1):10-6 Authors: Vuister GW, Kim SJ, Wu C, Bax A Heteronuclear multidimensional NMR experiments of residues 33-163 of the...	nmrlearner	Journal club	0	08-22-2010 03:33 AM

« 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