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: 17,578
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 Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-

Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-LTR by high resolution 2D-NMR.

Related Articles Conformational characteristics of high affinity Sp1 binding enhancer elements of HIV-LTR by high resolution 2D-NMR.

J Biomol Struct Dyn. 1995 Dec;13(3):553-64

Authors: Singh MP, Pon RT, Lown JW

The understanding of early events in the expression of genes has vastly improved in recent years with the identification of a variety of gene- and sequence-specific DNA binding transcription factors. One such protein, Sp1, has been implicated in activating transcription of various cellular and viral genes including those of HIV, and SIV types of retroviruses. The basic recognition site for Sp1 has been identified as variants of a 10 base-pairs long GC-rich DNA, often containing a hexanucleotide segment 5'-GGGCGG (termed GC-box). However, variations in both the relative protein-DNA binding affinity and the nature of binding sequences have been noted. Two-dimensional 1H-NMR experiments (500 MHz) were employed for conformational studies of two decadeoxyribonucleotide duplexes, d(GAGGCGTGGC).d(GCCACGCCTC), termed Sp1-III, and d(GGGAGTGGCG).d(CGCCACTCCC), termed Sp1-I. These are two of the highest affinity Sp1 binding sites and consist of diverse positioning of the tri- and tetranucleotide segments GAG, GTG, GCG, GGCG, GTGG and GGAG, that occur frequently in other Sp1 binding sites as well, and may form specific contacts with the protein. Phase-sensitive nuclear Overhauser enhancement (2D-NOESY and MINSY) and correlation (COSY) spectra were obtained for the assignment of the exchangeable and nonexchangeable protons in a sequence-specific fashion. As a prelude to determination of the detailed solution structures of the selected sequences, numerous structural constraints were obtained from angle-dependent coupling constants and relative intensities of distance-dependent intra- and internucleotide NOEs. Overall, each duplex adopts a structure similar to B-DNA with predominantly C2'-endo/S-type sugar conformation and anti-glycosidic torsion angles. A selective disruption of sequential NOE connectivities at the GAG.CAC and GTG.CAC steps, irrespective of the flanking sequence, suggests that conformational changes at these sites may act as unique determinants of sequence specific recognition/binding of Sp1. Implications for a specific inhibition of Sp1-mediated transcription by minor groove binding class of drugs, designed to recognize GC-rich sequences, are also briefly discussed.

PMID: 8825736 [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] Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of
Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin. Related Articles Binding affinity difference induced by the stereochemistry of the sulfoxide bridge of the cyclic peptide inhibitors of Grb2-SH2 domain: NMR studies for the structural origin. Biochem Biophys Res Commun. 2005 May 20;330(4):1254-61 Authors: Shi YH, Song YL, Lin DH, Tan J, Roller PP, Li Q, Long YQ, Song GQ The SAR study on a phage library-derived...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Determination of protein-ligand binding affinity by NMR: observations from serum albu
Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems. Related Articles Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems. Magn Reson Chem. 2005 Jun;43(6):463-70 Authors: Fielding L, Rutherford S, Fletcher D The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] QSAR-by-NMR: quantitative insights into structural determinants for binding affinity
QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Related Articles QSAR-by-NMR: quantitative insights into structural determinants for binding affinity by analysis of 1H/15N chemical shift differences in MMP-3 ligands. Bioorg Med Chem Lett. 2005 Apr 1;15(7):1779-83 Authors: Matter H, Schudok M, Elshorst B, Jacobs DM, Saxena K, Kogler H A novel strategy is applied to obtain quantitative insights on factors influencing biological affinity in...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] Competition STD NMR for the detection of high-affinity ligands and NMR-based screenin
Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Related Articles Competition STD NMR for the detection of high-affinity ligands and NMR-based screening. Magn Reson Chem. 2004 Jun;42(6):485-9 Authors: Wang YS, Liu D, Wyss DF The reported competition STD NMR method combines saturation transfer difference (STD) NMR with competition binding experiments to allow the detection of high-affinity ligands that undergo slow chemical exchange on the NMR time-scale. With this technique, the presence of a competing...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12.
Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12. Related Articles Solution NMR structure of S100B bound to the high-affinity target peptide TRTK-12. J Mol Biol. 2002 Dec 13;324(5):1003-14 Authors: Inman KG, Yang R, Rustandi RR, Miller KE, Baldisseri DM, Weber DJ The solution NMR structure is reported for Ca(2+)-loaded S100B bound to a 12-residue peptide, TRTK-12, from the actin capping protein CapZ (alpha1 or alpha2 subunit, residues 265-276: TRTKIDWNKILS). This peptide was discovered by Dimlich and co-workers...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] Discovering high-affinity ligands for proteins: SAR by NMR.
Discovering high-affinity ligands for proteins: SAR by NMR. Related Articles Discovering high-affinity ligands for proteins: SAR by NMR. Science. 1996 Nov 29;274(5292):1531-4 Authors: Shuker SB, Hajduk PJ, Meadows RP, Fesik SW A nuclear magnetic resonance (NMR)-based method is described in which small organic molecules that bind to proximal subsites of a protein are identified, optimized, and linked together to produce high-affinity ligands. The approach is called "SAR by NMR" because structure-activity relationships (SAR) are obtained from...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu
NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain. Related Articles NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain. Biochemistry. 1991 Nov 12;30(45):10872-7 Authors: Lowry DF, Cool RH, Redfield AG, Parmeggiani A The phosphoryl-binding elements in the GDP-binding domain of elongation factor Tu were studied by heteronuclear proton observe methods. Five proton resonances were found below 10.5 ppm. Two of these were assigned to the amide...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu
NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain. Related Articles NMR study of the phosphate-binding elements of Escherichia coli elongation factor Tu catalytic domain. Biochemistry. 1991 Nov 12;30(45):10872-7 Authors: Lowry DF, Cool RH, Redfield AG, Parmeggiani A The phosphoryl-binding elements in the GDP-binding domain of elongation factor Tu were studied by heteronuclear proton observe methods. Five proton resonances were found below 10.5 ppm. Two of these were assigned to the amide...
nmrlearner Journal club 0 08-21-2010 11:12 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 04:41 PM.


Map