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 08-21-2010, 11:45 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,134
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 Binding of the competitive inhibitor dCDP to ribonucleoside-diphosphate reductase fro

Binding of the competitive inhibitor dCDP to ribonucleoside-diphosphate reductase from Escherichia coli studied by 1H NMR. Different properties of the large protein subunit and the holoenzyme.

Related Articles Binding of the competitive inhibitor dCDP to ribonucleoside-diphosphate reductase from Escherichia coli studied by 1H NMR. Different properties of the large protein subunit and the holoenzyme.

Eur J Biochem. 1992 Sep 15;208(3):635-42

Authors: Allard P, Kuprin S, Shen B, Ehrenberg A

Ribonucleoside-diphosphate reductase (EC 1.17.4.1) from Escherichia coli consists of two nonidentical subunits, proteins R1 and R2. The binding of the product dCDP to protein R1 and to the holoenzyme R1R2 has been studied by means of 1H-NMR spectroscopy. In presence of the effector dTTP at 25 degrees C, dCDP was found to be in rapid exchange between the binding sites and the solvent which results in a broadening of the dCDP resonances. When both proteins R1 and R2 are present, so that the complex R1R2 is formed, a smaller broadening is observed than with protein R1 alone. No further linewidth decrease was observed when the [R2]/[R1] ratio exceeded 1. The binding constant of dCDP to R1 or R1R2 is the same, Kd = 0.9 mM. The smaller broadening of the dCDP resonances observed with the complex R1R2 as compared with R1 may be explained by the combination of two effects: (a) the overall tumbling time of the protein will increase when going from R1 to R1R2, which will cause the broadening to increase correspondingly, and (b) a twofold decrease of the number of binding sites in rapid exchange, which will decrease the broadening by a factor of 0.5. The effect of R2 without iron (apoR2) is reduced compared with native R2, probably because of some denatured proteins, while a C-terminal peptide from R2 did not cause any narrowing at all.

PMID: 1396671 [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 Studies Reveal anUnexpected Binding Site for a Redox Inhibitor of AP Endonuclease 1
NMR Studies Reveal anUnexpected Binding Site for a Redox Inhibitor of AP Endonuclease 1 http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi201071g/aop/images/medium/bi-2011-01071g_0007.gif Biochemistry DOI: 10.1021/bi201071g http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/rjOfEh_C8Bk More...
nmrlearner Journal club 0 11-10-2011 07:38 AM
Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase.
Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase. Thermodynamic and NMR analysis of inhibitor binding to dihydrofolate reductase. Bioorg Med Chem. 2010 Dec 15;18(24):8485-92 Authors: Batruch I, Javasky E, Brown ED, Organ MG, Johnson PE Isothermal titration calorimetry (ITC) was used to determine the thermodynamic driving force for inhibitor binding to the enzyme dihydrofolate reductase (DHFR) from Escherichia coli. 1,4-Bis-{sulfanylmethyl}-3,6-dimethyl-benzene (1) binds DHFR:NADPH with a K(d) of 13±5 nM while the...
nmrlearner Journal club 0 03-09-2011 02:20 PM
[NMR paper] Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion
Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. Related Articles Epitope mapping and competitive binding of HSA drug site II ligands by NMR diffusion measurements. J Am Chem Soc. 2004 Nov 3;126(43):14258-66 Authors: Lucas LH, Price KE, Larive CK It is important to characterize drug-albumin binding during drug discovery and lead optimization as strong binding may reduce bioavailability and/or increase the drug's in vivo half-life. Despite knowing about the location of human serum albumin (HSA)...
nmrlearner Journal club 0 11-24-2010 10:03 PM
[NMR paper] Analysis of competitive binding of ligands to human serum albumin using NMR relaxatio
Analysis of competitive binding of ligands to human serum albumin using NMR relaxation measurements. Related Articles Analysis of competitive binding of ligands to human serum albumin using NMR relaxation measurements. J Pharm Biomed Anal. 2004 Feb 4;34(2):247-54 Authors: Cui YF, Bai GY, Li CG, Ye CH, Liu ML The competitive binding of two ligands, ibuprofen (IBP) and salicylic acid (SAL), to human serum albumin (HSA) was studied by using nuclear magnetic resonance (NMR) relaxation measurements. When the concentration of one ligand was...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: cha
NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha). Related Articles NMR chemical shift mapping of the binding site of a protein proteinase inhibitor: changes in the (1)H, (13)C and (15)N NMR chemical shifts of turkey ovomucoid third domain upon binding to bovine chymotrypsin A(alpha). J Mol Recognit. 2001 May-Jun;14(3):166-71 Authors: Song J, Markley JL The substrate-like...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Selective NMR observation of inhibitor and sugar binding to the galactose-H(+) sympor
Selective NMR observation of inhibitor and sugar binding to the galactose-H(+) symport protein GalP, of Escherichia coli. Related Articles Selective NMR observation of inhibitor and sugar binding to the galactose-H(+) symport protein GalP, of Escherichia coli. Biochim Biophys Acta. 2000 Dec 20;1509(1-2):55-64 Authors: Appleyard AN, Herbert RB, Henderson PJ, Watts A, Spooner PJ The binding of the transport inhibitor forskolin, synthetically labelled with (13)C, to the galactose-H(+) symport protein GalP, overexpressed in its native inner...
nmrlearner Journal club 0 11-19-2010 08:29 PM
[NMR paper] NMR studies of binding of 5-FdUDP and dCDP to ribonucleoside-diphosphate reductase fr
NMR studies of binding of 5-FdUDP and dCDP to ribonucleoside-diphosphate reductase from Escherichia coli. Related Articles NMR studies of binding of 5-FdUDP and dCDP to ribonucleoside-diphosphate reductase from Escherichia coli. Biochim Biophys Acta. 1995 Mar 15;1247(2):284-92 Authors: Roy B, Decout JL, Béguin C, Fontecave M, Allard P, Kuprin S, Ehrenberg A 5-Fluoro-2'-deoxyuridine-5'-diphosphate (5-FdUDP) has been synthesised using an original route, previously applied to the synthesis of natural nucleoside diphosphates. The interaction...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] Studies on ribonucleoside-diphosphate reductase from Escherichia coli. The product dC
Studies on ribonucleoside-diphosphate reductase from Escherichia coli. The product dCDP is a competitive inhibitor and functions as a spectroscopic probe for the substrate binding site; demonstration by enzyme kinetics and 1H NMR. 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 Studies on ribonucleoside-diphosphate reductase from Escherichia coli. The product dCDP is a competitive inhibitor and functions as a spectroscopic probe for the substrate binding site;...
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 - 2024, 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 03:16 PM.


Map