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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 11-17-2010, 11:06 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 Refolding of [6-19F]tryptophan-labeled Escherichia coli dihydrofolate reductase in th

Refolding of [6-19F]tryptophan-labeled Escherichia coli dihydrofolate reductase in the presence of ligand: a stopped-flow NMR spectroscopy study.

Related Articles Refolding of [6-19F]tryptophan-labeled Escherichia coli dihydrofolate reductase in the presence of ligand: a stopped-flow NMR spectroscopy study.

Biochemistry. 1998 Jan 6;37(1):387-98

Authors: Hoeltzli SD, Frieden C

Escherichia coli dihydrofolate reductase contains five tryptophan residues that are spatially distributed throughout the protein and located in different secondary structural elements. When these tryptophans are replaced with [6-19F]tryptophan, distinct native and unfolded resonances can be resolved in the 1-D 19F NMR spectra. Using site-directed mutagenesis, these resonances have been assigned to individual tryptophans [Hoeltzli, S. D., and Frieden, C. (1994) Biochemistry 33, 5502-5509], allowing both the native and unfolded environments of each tryptophan to be monitored during the refolding process. We have previously used these assignments and stopped-flow NMR to investigate the behavior of specific regions of the protein during refolding of apo dihydrofolate reductase from urea in real time. These studies now have been extended to investigate the real time behavior of specific regions of the protein during refolding of dihydrofolate reductase in the presence of either NADP+ or dihydrofolate. As observed for the apoprotein, in the presence of either ligand, unfolded resonance intensities present at the first observed time point (1.5 s) disappear in two phases similar to those monitored by either stopped-flow fluorescence or circular dichroism spectroscopy. The existence of unfolded resonances which disappear slowly indicates that an equilibrium exists between the unfolded side chain environment and one or more intermediates, and that formation of at least one intermediate is cooperative. The results of this study are consistent with previous fluorescence studies demonstrating that dihydrofolate binds at an earlier step in the folding process than does NADP+ [Frieden, C. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 4413-4416] and provide a structural interpretation of the previous results. In the apoprotein as well as in the presence of either ligand, the protein folds via at least one cooperatively formed, solvent-protected intermediate which contains secondary structure. In the presence of NADP+, a stable native-like side chain environment forms in the regions around tryptophans 30, 133, and 47 in an intermediate which cannot bind NADP+ tightly. Native side chain environment forms in the regions around tryptophans 22 and 74 only in the structure which is able to bind NADP+ tightly. In the presence of dihydrofolate, stable native-like side chain environment forms cooperatively in the regions around each tryptophan in a non-native intermediate which must undergo a conformational change prior to binding NADP+. The presence of ligands influences the processes which occur during the folding of dihydrofolate reductase, and the ligand may in effect serve as part of the hydrophobic core.

PMID: 9425060 [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 structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions.
NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand hydrophobic interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif NMR structures of apo L. casei dihydrofolate reductase and its complexes with trimethoprim and NADPH: contributions to positive cooperative binding from ligand-induced refolding, conformational changes, and interligand...
nmrlearner Journal club 0 07-13-2011 06:42 PM
NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions
NMR Structures of Apo L. casei Dihydrofolate Reductase and Its Complexes with Trimethoprim and NADPH: Contributions to Positive Cooperative Binding from Ligand-Induced Refolding, Conformational Changes, and Interligand Hydrophobic Interactions http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi200067t/aop/images/medium/bi-2011-00067t_0002.gif Biochemistry DOI: 10.1021/bi200067t http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/sLQe7ipMThM More...
nmrlearner Journal club 0 04-15-2011 01:40 AM
[NMR paper] Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolat
Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolate reductase using stopped-flow NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Real-time refolding studies of 6-19F-tryptophan labeled Escherichia coli dihydrofolate reductase using stopped-flow NMR spectroscopy. Biochemistry. 1996 Dec 24;35(51):16843-51 Authors: Hoeltzli SD, Frieden C Escherichia coli dihydrofolate reductase (ecDHFR, EC1.5.1.3) contains 5 tryptophan residues that have...
nmrlearner Journal club 0 08-22-2010 02:20 PM
[NMR paper] 19F NMR spectroscopy of [6-19F]tryptophan-labeled Escherichia coli dihydrofolate redu
19F NMR spectroscopy of tryptophan-labeled Escherichia coli dihydrofolate reductase: equilibrium folding and ligand binding studies. Related Articles 19F NMR spectroscopy of tryptophan-labeled Escherichia coli dihydrofolate reductase: equilibrium folding and ligand binding studies. Biochemistry. 1994 May 10;33(18):5502-9 Authors: Hoeltzli SD, Frieden C Escherichia coli dihydrofolate reductase contains five tryptophan residues distributed throughout its structure. In order to examine the regions of the protein surrounding these tryptophan...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] 19F NMR spectroscopy of [6-19F]tryptophan-labeled Escherichia coli dihydrofolate redu
19F NMR spectroscopy of tryptophan-labeled Escherichia coli dihydrofolate reductase: equilibrium folding and ligand binding studies. Related Articles 19F NMR spectroscopy of tryptophan-labeled Escherichia coli dihydrofolate reductase: equilibrium folding and ligand binding studies. Biochemistry. 1994 May 10;33(18):5502-9 Authors: Hoeltzli SD, Frieden C Escherichia coli dihydrofolate reductase contains five tryptophan residues distributed throughout its structure. In order to examine the regions of the protein surrounding these tryptophan...
nmrlearner Journal club 0 08-22-2010 03:33 AM
[NMR paper] The interactions of Escherichia coli trp repressor with tryptophan and with an operat
The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. NMR studies using selectively 15N-labelled protein. 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 The interactions of Escherichia coli trp repressor with tryptophan and with an operator oligonucleotide. NMR studies using selectively 15N-labelled protein. Eur J Biochem. 1994 Oct 15;225(2):601-8 Authors: Ramesh V, Frederick RO, Syed SE,...
nmrlearner Journal club 0 08-22-2010 03:29 AM
[NMR paper] 13C NMR studies of complexes of Escherichia coli dihydrofolate reductase formed with
13C NMR studies of complexes of Escherichia coli dihydrofolate reductase formed with methotrexate and with folic acid. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles 13C NMR studies of complexes of Escherichia coli dihydrofolate reductase formed with methotrexate and with folic acid. FEBS Lett. 1992 Nov 9;312(2-3):147-51 Authors: Cheung HT, Birdsall B, Feeney J 13C NMR studies of 13C-labelled ligands bound to dihydrofolate reductase provide (DHFR) a powerful means of...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] The conformations of trimethoprim/E. coli dihydrofolate reductase complexes. A 15N an
The conformations of trimethoprim/E. coli dihydrofolate reductase complexes. A 15N and 31P NMR study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The conformations of trimethoprim/E. coli dihydrofolate reductase complexes. A 15N and 31P NMR study. FEBS Lett. 1991 May 20;283(1):44-6 Authors: Huang FY, Yang QX, Huang TH, Gelbaum L, Kuyper LF We have employed 15N and 31P NMR techniques to characterize the conformations of trimethoprim (TMP)/E. coli dihydrofolate...
nmrlearner Journal club 0 08-21-2010 11:16 PM



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 12:45 AM.


Map