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 03-04-2014, 06:37 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,617
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 NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters.

NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters.

Related Articles NMR Characterization of the Near Native and Unfolded States of the PTB Domain of Dok1: Alternate Conformations and Residual Clusters.

PLoS One. 2014;9(2):e90557

Authors: Gupta S, Bhattacharjya S

Abstract
BACKGROUND: Phosphotyrosine binding (PTB) domains are critically involved in cellular signaling and diseases. PTB domains are categorized into three distinct structural classes namely IRS-like, Shc-like and Dab-like. All PTB domains consist of a core pleckstrin homology (PH) domain with additional structural elements in Shc and Dab groups. The core PH fold of the PTB domain contains a seven stranded ?-sheet and a long C-terminal helix.
PRINCIPAL FINDINGS: In this work, the PTB domain of Dok1 protein has been characterized, by use of NMR spectroscopy, in solutions containing sub-denaturing and denaturing concentrations of urea. We find that the Dok1 PTB domain displays, at sub-denaturing concentrations of urea, alternate conformational states for residues located in the C-terminal helix and in the ?5 strand of the ?-sheet region. The ?5 strand of PTB domain has been found to be experiencing significant chemical shift perturbations in the presence of urea. Notably, many of these residues in the helix and in the ?5 strand are also involved in ligand binding. Structural and dynamical analyses at 7 M urea showed that the PTB domain is unfolded with islands of motionally restricted regions in the polypeptide chain. Further, the C-terminal helix appears to be persisted in the unfolded state of the PTB domain. By contrast, residues encompassing ?-sheets, loops, and the short N-terminal helix lack any preferred secondary structures. Moreover, these residues demonstrated an intimate contact with the denaturant.
SIGNIFICANCE: This study implicates existence of alternate conformational states around the ligand binding pocket of the PTB domain either in the native or in the near native conditions. Further, the current study demonstrates that the C-terminal helical region of PTB domain may be considered as a potential site for the initiation of folding.


PMID: 24587391 [PubMed - in process]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein.
Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Clusters of Branched Aliphatic Side Chains Serve As Cores of Stability in the Native State of the HisF TIM Barrel Protein. J Mol Biol. 2013 Jan 16; Authors: Gangadhara BN, Laine JM, Kathuria SV, Massi F, Matthews CR Abstract Imidazole-3-glycerol phosphate synthase is a heterodimeric allosteric...
nmrlearner Journal club 0 02-03-2013 10:19 AM
[NMR paper] Structural characterization by NMR of the natively unfolded extracellular domain of b
Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan. Related Articles Structural characterization by NMR of the natively unfolded extracellular domain of beta-dystroglycan: toward the identification of the binding epitope for alpha-dystroglycan. Biochemistry. 2003 Nov 25;42(46):13717-24 Authors: Bozzi M, Bianchi M, Sciandra F, Paci M, Giardina B, Brancaccio A, Cicero DO Dystroglycan (DG) is an adhesion molecule playing a...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Probing residual interactions in unfolded protein states using NMR spin relaxation te
Probing residual interactions in unfolded protein states using NMR spin relaxation techniques: an application to delta131delta. Related Articles Probing residual interactions in unfolded protein states using NMR spin relaxation techniques: an application to delta131delta. J Am Chem Soc. 2003 Oct 1;125(39):11988-92 Authors: Choy WY, Kay LE Residual interactions in delta131delta, a large disordered fragment of staphylococcal nuclease, have been probed at two different pHs using backbone (15)N and side-chain methyl (2)H NMR spin relaxation...
nmrlearner Journal club 0 11-24-2010 09:16 PM
[NMR paper] Dynamical characterization of residual and non-native structures in a partially folde
Dynamical characterization of residual and non-native structures in a partially folded protein by (15)N NMR relaxation using a model based on a distribution of correlation times. Related Articles Dynamical characterization of residual and non-native structures in a partially folded protein by (15)N NMR relaxation using a model based on a distribution of correlation times. Protein Sci. 2002 Apr;11(4):957-64 Authors: Ochsenbein F, Neumann JM, Guittet E, van Heijenoort C A spectral density model based on a truncated lorentzian distribution of...
nmrlearner Journal club 0 11-24-2010 08:49 PM
[NMR paper] Structural characterization of the molten globule and native states of ovalbumin: a 1
Structural characterization of the molten globule and native states of ovalbumin: a 1H NMR study. Related Articles Structural characterization of the molten globule and native states of ovalbumin: a 1H NMR study. J Pept Res. 1997 Dec;50(6):465-74 Authors: Sogami M, Era S, Koseki T, Nagai N Molecular characteristics of ovalbumin (OVA) in the acidic (pD 3.08, the E-form) and neutral regions were studied by measuring effective radii, 1H NMR spectra, spin-echo 1H NMR spectra and cross-relaxation times (TIS) from irradiated to observed protein...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing co
NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. Biochemistry. 1997 Apr 1;36(13):3959-70 Authors: Zhang O, Forman-Kay JD The isolated N-terminal SH3 domain of the Drosophila adapter protein drk (drkN SH3 domain) exists in a dynamic equilibrium between a folded (F(exch)) and an unfolded (U(exch)) state...
nmrlearner Journal club 0 08-22-2010 03:31 PM
[NMR paper] NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing co
NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles NMR studies of unfolded states of an SH3 domain in aqueous solution and denaturing conditions. Biochemistry. 1997 Apr 1;36(13):3959-70 Authors: Zhang O, Forman-Kay JD The isolated N-terminal SH3 domain of the Drosophila adapter protein drk (drkN SH3 domain) exists in a dynamic equilibrium between a folded (F(exch)) and an unfolded (U(exch)) state...
nmrlearner Journal club 0 08-22-2010 03:03 PM
[NMR paper] Side-chain conformations in an unfolded protein: chi1 distributions in denatured hen
Side-chain conformations in an unfolded protein: chi1 distributions in denatured hen lysozyme determined by heteronuclear 13C, 15N NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Side-chain conformations in an unfolded protein: chi1 distributions in denatured hen lysozyme determined by heteronuclear 13C, 15N NMR spectroscopy. J Mol Biol. 1999 May 14;288(4):705-23 Authors: Hennig M, Bermel W, Spencer A, Dobson CM, Smith LJ, Schwalbe H Using a 13C and...
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 08:54 AM.


Map