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 11-19-2010, 08:32 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 Solution-state NMR investigations of triosephosphate isomerase active site loop motio

Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics.

Related Articles Solution-state NMR investigations of triosephosphate isomerase active site loop motion: ligand release in relation to active site loop dynamics.

J Mol Biol. 2001 Jun 29;310(1):271-80

Authors: Rozovsky S, Jogl G, Tong L, McDermott AE

Product release is partially rate determining in the isomerization reaction catalyzed by Triosephosphate Isomerase, the conversion of dihydroxyacetone phosphate to D-glyceraldehyde 3-phosphate, probably because an active-site loop movement is necessary to free the product from confinement in the active-site. The timescale of the catalytic loop motion and of ligand release were studied using 19F and 31P solution-state NMR. A 5'-fluorotryptophan was incorporated in the loop N-terminal hinge as a reporter of loop motion timescale. Crystallographic studies confirmed that the structure of the fluorinated enzyme is indistinguishable from the wild-type; the fluorine accepts a hydrogen bond from water and not from a protein residue, with minimal perturbation to the flexible loop stability. Two distinct loop conformations were observed by 19F NMR. Both for unligated (empty) and ligated enzyme samples a single species was detected, but the chemical shifts of these two distinct species differed by 1.2 ppm. For samples in the presence of subsaturating amounts of a substrate analogue, glycerol 3-phosphate, both NMR peaks were present, with broadened lineshapes at 0 degrees C. In contrast, a single NMR peak representing a rapid average of the two species was observed at 30 degrees C. We conclude that the rate of loop motion is less than 1400 s(-1) at 0 degrees C and more than 1400 s(-1) at 30 degrees C. Ligand release was studied under similar sample conditions, using 31P NMR of the phosphate group of the substrate analogue. The rate of ligand release is less than 1000 s(-1) at 0 degrees C and more than 1000 s(-1) at 30 degrees C. Therefore, loop motion and product release are probably concerted and likely to represent a rate limiting step for chemistry.

PMID: 11419952 [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] Solution 1H NMR study of the active site molecular structure and magnetic properties
Solution 1H NMR study of the active site molecular structure and magnetic properties of the cyanomet complex of the isolated, tetrameric beta-chain from human adult hemoglobin. Related Articles Solution 1H NMR study of the active site molecular structure and magnetic properties of the cyanomet complex of the isolated, tetrameric beta-chain from human adult hemoglobin. Biochim Biophys Acta. 2004 Sep 1;1701(1-2):75-87 Authors: Tran AT, Kolczak U, La Mar GN The solution molecular structure and the electronic and magnetic properties of the heme...
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Two-dimensional NMR study of the heme active site structure of chloroperoxidase.
Two-dimensional NMR study of the heme active site structure of chloroperoxidase. Related Articles Two-dimensional NMR study of the heme active site structure of chloroperoxidase. J Biol Chem. 2003 Mar 7;278(10):7765-74 Authors: Wang X, Tachikawa H, Yi X, Manoj KM, Hager LP The heme active site structure of chloroperoxidase (CPO), a glycoprotein that displays versatile catalytic activities isolated from the marine mold Caldariomyces fumago, has been characterized by two-dimensional NMR spectroscopic studies. All hyperfine shifted resonances...
nmrlearner Journal club 0 11-24-2010 08:58 PM
[NMR paper] NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain
NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding protein. Related Articles NMR solution structure and dynamics of the peptidyl-prolyl cis-trans isomerase domain of the trigger factor from Mycoplasma genitalium compared to FK506-binding protein. J Mol Biol. 2002 May 10;318(4):1097-115 Authors: Vogtherr M, Jacobs DM, Parac TN, Maurer M, Pahl A, Saxena K, Rüterjans H, Griesinger C, Fiebig KM We have solved the solution structure of the...
nmrlearner Journal club 0 11-24-2010 08:49 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] Structural determination of the active site of a sweet protein. A 1H NMR investigatio
Structural determination of the active site of a sweet protein. A 1H NMR investigation of pMNEI. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Structural determination of the active site of a sweet protein. A 1H NMR investigation of pMNEI. FEBS Lett. 1992 Sep 21;310(1):27-30 Authors: Tancredi T, Iijima H, Saviano G, Amodeo P, Temussi PA pMNEI, a single chain sweet protein related to monellin, has been studied by means of 1H NMR at 500 MHz. A partial sequential...
nmrlearner Journal club 0 08-21-2010 11:45 PM
[NMR paper] NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase
NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. Related Articles NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. J Biol Chem. 1991 Aug 15;266(23):15001-8 Authors: de Ropp JS, La Mar GN, Wariishi H, Gold MH One- and two-dimensional 1H NMR spectroscopy has been used to probe the active site of the high spin ferric resting...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase
NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. Related Articles NMR study of the active site of resting state and cyanide-inhibited lignin peroxidase from Phanerochaete chrysosporium. Comparison with horseradish peroxidase. J Biol Chem. 1991 Aug 15;266(23):15001-8 Authors: de Ropp JS, La Mar GN, Wariishi H, Gold MH One- and two-dimensional 1H NMR spectroscopy has been used to probe the active site of the high spin ferric resting...
nmrlearner Journal club 0 08-21-2010 11:12 PM
[NMR paper] Location of a cation-binding site in the loop between helices F and G of bacteriorhod
Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR. Biophys J. 1999 Mar;76(3):1523-31 Authors: Tuzi S, Yamaguchi S, Tanio M, Konishi H, Inoue S, Naito A,...
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 - 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 12:59 PM.


Map