BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 08-22-2010, 02:27 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,589
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus

Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy.

Related Articles Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy.

Biopolymers. 1996;40(5):553-9

Authors: Boelens R, Vis H, Vorgias CE, Wilson KS, Kaptein R

The DNA-binding protein HU from Bacillus stearothermophilus (HUBst) is a dimer with a molecular weight of 195 kDa that is capable of bending DNA. An x-ray structure has been determined previously [Tanaka et al. 1984) Nature, vol. 310, pp. 376-381], but no structure could be established for a large part of the supposed DNA-binding beta-arms. Distance geometry and restrained molecular dynamics using nmr restraints were used to generate a set of 25 structures. These structures display a backbone rms deviation (RMSD) of 0.36 A for the well-defined region (residues 2-54 and 75-90). The structure of the core is very similar to that observed in the x-ray structure, with a pairwise RMSD of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Heteronuclear 15N relaxation measurements indicate that the beta-arm and the tip of the beta-arm is flexible. This explains the disorder observed in the solution and x-ray structures of the beta-arm with respect to the core of the protein. Overlayed onto itself the beta-arm is better defined, with a backbone RMSD of 1.0 A calculated for residues 54-59 and 69-74. The tip of the arm adopts a well-defined 4 : 6 beta-hairpin conformation. Changes in amide 15N and 1H chemical shifts upon titrating DNA are most pronounced for the residues in the beta-hairpin arm and for the residues in the second half of the third alpha-helix. Heteronuclear 15N relaxation data for free and complexed HUBst show that that the arms become structured upon DNA binding. Together with chemically induced nuclear polarization measurements on a mutant HUBst (M69Y; V76Y) this shows that the beta-hairpin arm is involved in direct DNA interaction.

PMID: 9101760 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Structure, dynamics, and ionization equilibria of the tyrosine residues in Bacillus circulans xylanase
Structure, dynamics, and ionization equilibria of the tyrosine residues in Bacillus circulans xylanase Abstract We have developed NMR spectroscopic methods to investigate the tyrosines within Bacillus circulans xylanase (BcX). Four slowly exchanging buried tyrosine hydroxyl protons with chemical shifts between 7.5 and 12.5 ppm were found using a long-range 13C-HSQC experiment that exploits the 3JCH coupling between the ring 1Hη and 13Cε nuclei. The NMR signals from these protons were assigned via 13C-tyrosine selective labelling and a suite of scalar and 13C,15N-filtered/edited NOE...
nmrlearner Journal club 0 09-17-2011 10:20 AM
[NMR paper] Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR.
Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR. Related Articles Solution structure of the peptidoglycan binding domain of Bacillus subtilis cell wall lytic enzyme CwlC: characterization of the sporulation-related repeats by NMR. Biochemistry. 2005 Aug 2;44(30):10153-63 Authors: Mishima M, Shida T, Yabuki K, Kato K, Sekiguchi J, Kojima C Bacillus subtilis CwlC is a cell wall lytic N-acetylmuramoyl-l-alanine amidase that plays an...
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...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Cobalt(II) and copper(II) binding of Bacillus cereus trinuclear phospholipase C: a no
Cobalt(II) and copper(II) binding of Bacillus cereus trinuclear phospholipase C: a novel 1H NMR spectrum of a 'Tri-Cu(II)' center in protein. Related Articles Cobalt(II) and copper(II) binding of Bacillus cereus trinuclear phospholipase C: a novel 1H NMR spectrum of a 'Tri-Cu(II)' center in protein. J Inorg Biochem. 2001 Dec 1;87(3):149-56 Authors: Epperson JD, Ming LJ The phosphatidylcholine-preferring phospholipase C from Bacillus cereus (PC-PLC(Bc)) is a tri-Zn enzyme with two 'tight binding' and one 'loose binding' sites. The Zn2+ ions can...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response
High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles High-resolution NMR structure and backbone dynamics of the Bacillus subtilis response regulator, Spo0F: implications for phosphorylation and molecular recognition. Biochemistry. 1997 Aug 19;36(33):10015-25 Authors: Feher VA, Zapf JW, Hoch JA, Whiteley JM, McIntosh LP, Rance M, Skelton NJ,...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] NMR characterization of structure, backbone dynamics, and glutathione binding of the
NMR characterization of structure, backbone dynamics, and glutathione binding of the human macrophage migration inhibitory factor (MIF). http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR characterization of structure, backbone dynamics, and glutathione binding of the human macrophage migration inhibitory factor (MIF). Protein Sci. 1996...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] Symmetry and secondary structure of the replication terminator protein of Bacillus su
Symmetry and secondary structure of the replication terminator protein of Bacillus subtilis: sedimentation equilibrium and circular dichroic, infrared, and NMR spectroscopic studies. Related Articles Symmetry and secondary structure of the replication terminator protein of Bacillus subtilis: sedimentation equilibrium and circular dichroic, infrared, and NMR spectroscopic studies. Biochemistry. 1993 Sep 28;32(38):10216-23 Authors: Kralicek AV, Vesper NA, Ralston GB, Wake RG, King GF We have used analytical ultracentrifugation in combination...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-di
Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Solution structure of the phosphocarrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy. Protein Sci. 1992 Oct;1(10):1363-76 Authors: Wittekind...
nmrlearner Journal club 0 08-21-2010 11:45 PM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 08:22 AM.


Map