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 03-29-2020, 12:14 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,995
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 Nucleotide Binding and Active Site Gate Dynamics for the Hsp90 Chaperone ATPase Domain from Benchtop and High Field 19F NMR Spectroscopy.

Nucleotide Binding and Active Site Gate Dynamics for the Hsp90 Chaperone ATPase Domain from Benchtop and High Field 19F NMR Spectroscopy.

Related Articles Nucleotide Binding and Active Site Gate Dynamics for the Hsp90 Chaperone ATPase Domain from Benchtop and High Field 19F NMR Spectroscopy.

J Phys Chem B. 2020 Mar 25;:

Authors: Rashid S, Lee BL, Wajda B, Spyracopoulos L

Abstract
Protein turnover in cells is regulated by the ATP dependent activity of the Hsp90 chaperone. In concert with accessory proteins, ATP hydrolysis drives the obligate Hsp90 dimer through a cycle between open and closed states that is critical for assisting the folding and stability of hundreds of proteins. Cycling is initiated by ATP binding to the ATPase domain, with the chaperone and the active site gates in the dimer in open states. The chaperone then adopts a short-lived, ATP bound closed state with a closed active site gate. The structural and dynamic changes induced in the ATPase domain and active site gate upon nucleotide binding, and their impact on dimer closing are not well understood. We site-specifically 19F-labeled the ATPase domain at the active site gate to enable benchtop and high field 19F NMR spectroscopic studies. Combined with MD simulations, this allowed accurate characterization of pico- to nanosecond timescale motions of the active site gate, as well as slower micro- to millisecond timescale processes resulting from nucleotide binding. ATP binding induces increased flexibility at one of the hinges of the active site gate, a necessary prelude to release of the second hinge, and eventual gate closure in the intact chaperone.


PMID: 32212608 [PubMed - as supplied by publisher]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Synergic Effect of Active Sites in Zinc-Modified ZSM-5 Zeolites as Revealed by High-Field Solid-State NMR Spectroscopy
Synergic Effect of Active Sites in Zinc-Modified ZSM-5 Zeolites as Revealed by High-Field Solid-State NMR Spectroscopy Understanding the nature of active sites in metal-supported catalysts is of great importance towards establishing their structure–property relationships. The outstanding catalytic performance of metal-supported catalysts is frequently ascribed to the synergic effect of different active sites, which is however not well spectroscopically characterized. Herein, we report the direct detection of surface Zn species and 1H–67Zn internuclear interaction between Zn2+ ions and...
nmrlearner Journal club 0 11-19-2016 08:35 PM
NMR and Fluorescence Studiesof Drug Binding to theFirst Nucleotide Binding Domain of SUR2A
NMR and Fluorescence Studiesof Drug Binding to theFirst Nucleotide Binding Domain of SUR2A http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi301019e/aop/images/medium/bi-2012-01019e_0008.gif Biochemistry DOI: 10.1021/bi301019e http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/VpjFg9eH8kQ More...
nmrlearner Journal club 0 11-01-2012 10:38 PM
Characterization of Sarcoplasmic Reticulum Ca(2+) ATPase Nucleotide Binding Domain Mutants using NMR spectroscopy.
Characterization of Sarcoplasmic Reticulum Ca(2+) ATPase Nucleotide Binding Domain Mutants using NMR spectroscopy. Characterization of Sarcoplasmic Reticulum Ca(2+) ATPase Nucleotide Binding Domain Mutants using NMR spectroscopy. Biochem Biophys Res Commun. 2010 Dec 24; Authors: Myint W, Gong Q, Ahn J, Ishima R Sarcoplasmic reticulum Ca(2+) ATPase (SERCA) is essential for muscle function by transporting Ca(2+) from the cytosol into the sarcoplasmic reticulum through ATP hydrolysis. In this report, the effects of substitution mutations on the...
nmrlearner Journal club 0 12-29-2010 04:04 PM
[NMR paper] NMR study of nucleotide-induced changes in the nucleotide binding domain of Thermus t
NMR study of nucleotide-induced changes in the nucleotide binding domain of Thermus thermophilus Hsp70 chaperone DnaK: implications for the allosteric mechanism. Related Articles NMR study of nucleotide-induced changes in the nucleotide binding domain of Thermus thermophilus Hsp70 chaperone DnaK: implications for the allosteric mechanism. J Biol Chem. 2004 Aug 6;279(32):33958-67 Authors: Revington M, Holder TM, Zuiderweg ER We present an NMR investigation of the nucleotide-dependent conformational properties of a 44-kDa nucleotide binding...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding
NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol. Related Articles NMR chemical shift perturbation study of the N-terminal domain of Hsp90 upon binding of ADP, AMP-PNP, geldanamycin, and radicicol. Chembiochem. 2003 Sep 5;4(9):870-7 Authors: Dehner A, Furrer J, Richter K, Schuster I, Buchner J, Kessler H Hsp90 is one of the most abundant chaperone proteins in the cytosol. In an ATP-dependent manner it plays an essential role in the folding and activation of a...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Biochemical characterization and NMR studies of the nucleotide-binding domain 1 of mu
Biochemical characterization and NMR studies of the nucleotide-binding domain 1 of multidrug-resistance-associated protein 1: evidence for interaction between ATP and Trp653. Related Articles Biochemical characterization and NMR studies of the nucleotide-binding domain 1 of multidrug-resistance-associated protein 1: evidence for interaction between ATP and Trp653. Biochem J. 2003 Dec 15;376(Pt 3):749-56 Authors: Ramaen O, Masscheleyn S, Duffieux F, Pamlard O, Oberkampf M, Lallemand JY, Stoven V, Jacquet E Multidrug-resistance-associated...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] A model of reversible inhibitors in the gastric H+/K+-ATPase binding site determined
A model of reversible inhibitors in the gastric H+/K+-ATPase binding site determined by rotational echo double resonance NMR. Related Articles A model of reversible inhibitors in the gastric H+/K+-ATPase binding site determined by rotational echo double resonance NMR. J Biol Chem. 2001 Nov 16;276(46):43197-204 Authors: Watts JA, Watts A, Middleton DA Several close analogues of the noncovalent H(+)/K(+)-ATPase inhibitor SCH28080 (2-methyl-3-cyanomethyl-8-(phenylmethoxy)imidazopyridine) have been screened for activity and examined in the...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain:
NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain: a preview of chaperone-protein interaction. Related Articles NMR solution structure of the 21 kDa chaperone protein DnaK substrate binding domain: a preview of chaperone-protein interaction. Biochemistry. 1998 Jun 2;37(22):7929-40 Authors: Wang H, Kurochkin AV, Pang Y, Hu W, Flynn GC, Zuiderweg ER The solution structure of the 21 kDa substrate-binding domain of the Escherichia coli Hsp70-chaperone protein DnaK (DnaK 386-561) has been determined to a precision...
nmrlearner Journal club 0 11-17-2010 11:06 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 - 2020, 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 04:26 AM.


Map