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, 03:50 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,577
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 Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.

Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.

Related Articles Backbone dynamics of the A-domain of HMG1 as studied by 15N NMR spectroscopy.

Biochemistry. 1995 Dec 26;34(51):16608-17

Authors: Broadhurst RW, Hardman CH, Thomas JO, Laue ED

The HMG-box sequence motif (approximately 80 residues) occurs in a number of abundant eukaryotic chromosomal proteins such as HMG1, which binds DNA without sequence specificity, but with "structure specificity", as well as in several sequence-specific transcription factors. HMG1 has two such boxes, A and B, which show approximately 30% sequence identity, and an acidic C-terminal tail. The boxes are responsible for the ability of the protein to bend DNA and bind to bent or distorted DNA. The structure of the HMG box has been determined by NMR spectroscopy for the B-domain of HMG1 [Weir et al. (1993) EMBO J. 12, 1311-1319; Read et al. (1993) Nucleic Acids Res. 21, 3427-3436) and for Drosophila HMG-D (Jones et al. (1994) Structure 2, 609-627]. It has an unusual twisted L-shape, suggesting that the protein might tumble anisotropically in solution. In this paper we report studies of the A-domain from HMG1 using 15N NMR spectroscopy which show that the backbone dynamics of the protein can be described by two different rotational correlation times of 9.0 +/- 0.5 and 10.8 +/- 0.5 ns. We show that the relaxation data can be analyzed by assuming that the protein is a rigid, axially symmetric ellipsoid undergoing anisotropic rotational diffusion; the global rotational diffusion constants, D parallel and D perpendicular, were estimated as 2.47 x 10(7) and 1.49 x 10(7) s-1, respectively. By estimating the angle between the amide bond vectors and the major axis of the rotational diffusion tensor from the family of structures determined by NMR spectroscopy [see accompanying paper, Hardman et al. (1995) Biochemistry 34, 16596-16607], we were able to show that the ellipsoid spectral density equation can reproduce the major features of the 15N T1 and T2 profiles of the three helices in the HMG1 A-domain. The backbone dynamics of the A-domain were then compared with those of the B-domain and the HMG box from HMG-D. This comparison strongly supported the differences observed in the orientation of helix I in the three structures, where the B-domain appears to be more similar to HMG-D than it is to the A-domain. These differences may turn out to be related to subtle differences in the DNA-binding properties of the A- and B-domains of HMG1.

PMID: 8527433 [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
[NMR paper] Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements.
Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements. Related Articles Backbone dynamics of the olfactory marker protein as studied by 15N NMR relaxation measurements. Biochemistry. 2005 Jul 19;44(28):9673-9 Authors: Gitti RK, Wright NT, Margolis JW, Varney KM, Weber DJ, Margolis FL Nuclear magnetic resonance (NMR) (15)N relaxation measurements of the olfactory marker protein (OMP) including longitudinal relaxation (T(1)), transverse relaxation (T(2)), and (15)N-{(1)H} NOE data were collected at low...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR
Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Related Articles Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1rho relaxation experiments. Protein Sci. 2005 Mar;14(3):735-42 Authors: Massi F, Grey MJ, Palmer AG NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on- and off-resonance...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implicati
Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains. Related Articles Backbone dynamics of the human MIA protein studied by (15)N NMR relaxation: implications for extended interactions of SH3 domains. Protein Sci. 2003 Mar;12(3):510-9 Authors: Stoll R, Renner C, Buettner R, Voelter W, Bosserhoff AK, Holak TA The melanoma inhibitory activity (MIA) protein is a clinically valuable marker in patients with malignant melanoma as enhanced values diagnose metastatic...
nmrlearner Journal club 0 11-24-2010 09:01 PM
[NMR paper] Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronu
Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy. Related Articles Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy. Biochemistry. 1995 Dec 26;34(51):16596-607 Authors: Hardman CH, Broadhurst RW, Raine AR, Grasser KD, Thomas JO, Laue ED HMG1 has two homologous, folded DNA-binding domains ("HMG boxes"), A and B, linked by a short basic region to an acidic C-terminal domain....
nmrlearner Journal club 0 08-22-2010 03:50 AM
[NMR paper] Backbone dynamics of trp repressor studied by 15N NMR relaxation.
Backbone dynamics of trp repressor studied by 15N NMR relaxation. Related Articles Backbone dynamics of trp repressor studied by 15N NMR relaxation. Biochemistry. 1995 Apr 18;34(15):5212-23 Authors: Zheng Z, Czaplicki J, Jardetzky O Backbone dynamics of trp repressor, a 25 kDa DNA binding protein, have been studied using 15N relaxation data measured by proton-detected two-dimensional 1H-15N NMR spectroscopy. 15N spin-lattice relaxation time (T1), spin-spin relaxation time (T2), and heteronuclear NOEs were determined for all visible backbone...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectr
Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N 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 Related Articles Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectroscopy. Eur J Biochem. 1994 Feb 1;219(3):887-96 Authors: Orekhov VYu , Pervushin KV, Arseniev AS The backbone dynamics of a uniformly 15N-labelled proteolytic fragment (residues 1-71) of bacteriorhodopsin,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectr
Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N 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 Related Articles Backbone dynamics of (1-71)bacterioopsin studied by two-dimensional 1H-15N NMR spectroscopy. Eur J Biochem. 1994 Feb 1;219(3):887-96 Authors: Orekhov VYu , Pervushin KV, Arseniev AS The backbone dynamics of a uniformly 15N-labelled proteolytic fragment (residues 1-71) of bacteriorhodopsin,...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spe
Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Superslow backbone protein dynamics as studied by 1D solid-state MAS exchange NMR spectroscopy. J Magn Reson. 1999 Jun;138(2):244-55 Authors: Krushelnitsky A, Reichert D, Hempel G, Fedotov V, Schneider H, Yagodina L, Schulga A Superslow backbone dynamics of the protein barstar and the polypeptide polyglycine was studied by...
nmrlearner Journal club 0 08-21-2010 04:03 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 01:17 AM.


Map