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 12-02-2014, 01:59 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 18,079
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 Elucidation of the Interaction Loci of the Human Pyruvate Dehydrogenase Complex E2·E3BP Core with Pyruvate Dehydrogenase Kinase 1 and Kinase 2 by H/D Exchange Mass Spectrometry and NMR.

Elucidation of the Interaction Loci of the Human Pyruvate Dehydrogenase Complex E2·E3BP Core with Pyruvate Dehydrogenase Kinase 1 and Kinase 2 by H/D Exchange Mass Spectrometry and NMR.

Elucidation of the Interaction Loci of the Human Pyruvate Dehydrogenase Complex E2·E3BP Core with Pyruvate Dehydrogenase Kinase 1 and Kinase 2 by H/D Exchange Mass Spectrometry and NMR.

Biochemistry. 2014 Dec 1;

Authors: Wang J, Kumaran S, Zhou J, Tao H, Nemeria NS, Kakalis L, Patel MS, Park YH, Birkaya B, Jordan F

Abstract
The human pyruvate dehydrogenase complex (PDC) comprises three principal catalytic components for its mission: E1, E2 and E3. The core of the complex is a strong sub-complex between E2 and an E3-binding protein (E3BP). The PDC is subject to regulation at E1 by serine phosphorylation by four kinases (PDK1-4), an inactivation reversed by the action of two phosphatases (PDP1-2). We report H/D exchange mass spectrometric (HDX-MS) and nuclear magnetic resonance (NMR) studies in the first attempt to define the interaction loci between PDK1 and PDK2 with the intact E2.E3BP core and their C-terminally truncated proteins. While the three lipoyl domains (LD1 and LD2 on E2 and LD3 on E3BP) lend themselves to NMR studies and determination of interaction maps with the PDK1 and PDK2 at the individual residue level, HDX-MS enabled studies of interaction loci on both partners in the complexes, PDKs and other regions of the E2.E3BP as well, at the peptide level. The HDX-MS suggested that intact E2.E3BP core enhances the binding specificity of L2 for PDK2 over PDK1, while NMR studies detected lipoyl domain residues unique to interaction with PDK1 and PDK2. The E2.E3BP core induced more changes on PDKs than any C-terminally truncated protein, with clear evidence for greater plasticity of PDK1 than PDK2. The effect of L1L2S paralleled HDX-MS results obtained with intact E2.E3BP, hence, L1L2S is an excellent candidate with which to define interaction loci with these two PDKs. Surprisingly, L3S' induced moderate interaction with both PDKs according to both methods.


PMID: 25436986 [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
Hyperpolarized singlet lifetimes of pyruvate in human blood and in the mouse
From The DNP-NMR Blog: Hyperpolarized singlet lifetimes of pyruvate in human blood and in the mouse Marco-Rius, I., et al., Hyperpolarized singlet lifetimes of pyruvate in human blood and in the mouse. NMR Biomed, 2013. 26(12): p. 1696-704. http://www.ncbi.nlm.nih.gov/pubmed/23946252
nmrlearner News from NMR blogs 0 03-19-2014 10:43 PM
[NMR paper] Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme com
Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Use of a truncated protein domain in NMR spectroscopy. Related Articles Interaction of the E2 and E3 components of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus. Use of a truncated protein domain in NMR spectroscopy. FEBS J. 2005 Jan;272(1):259-68 Authors: Allen MD, Broadhurst RW, Solomon RG, Perham RN A (15)N-labelled peripheral-subunit binding domain (PSBD) of the dihydrolipoyl...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Lipid analysis of human HDL and LDL by MALDI-TOF mass spectrometry and (31)P-NMR.
Lipid analysis of human HDL and LDL by MALDI-TOF mass spectrometry and (31)P-NMR. Related Articles Lipid analysis of human HDL and LDL by MALDI-TOF mass spectrometry and (31)P-NMR. J Lipid Res. 2001 Sep;42(9):1501-8 Authors: Schiller J, Zschörnig O, Petkovi? M, Müller M, Arnhold J, Arnold K The analysis of HDL and LDL is important for the further understanding of atherosclerosis because changes of the protein and lipid moieties occur under pathological conditions. Because destruction of lipids leads to the formation of well-defined products...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] 13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid form
13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in Bacillus subtilis. Related Articles 13C NMR evidence for pyruvate kinase flux attenuation underlying suppressed acid formation in Bacillus subtilis. Biotechnol Prog. 2000 Mar-Apr;16(2):169-75 Authors: Phalakornkule C, Fry B, Zhu T, Kopesel R, Ataai MM, Domach MM When batch and continuous Bacillus subtilis cultures are provided with a small amount of citrate, acid production ceases, carbon yield increases by more than 2-fold, and the productivity of...
nmrlearner Journal club 0 11-18-2010 09:15 PM
[NMR paper] Identification of reaction products and intermediates of aromatic-amine dehydrogenase
Identification of reaction products and intermediates of aromatic-amine dehydrogenase by 15N and 13C NMR. Related Articles Identification of reaction products and intermediates of aromatic-amine dehydrogenase by 15N and 13C NMR. Biochem J. 1998 Mar 15;330 ( Pt 3):1159-63 Authors: Bishop GR, Zhu Z, Whitehead TL, Hicks RP, Davidson VL 13C- and 15N-NMR studies of the reaction of aromatic amine dehydrogenase (AADH) with methylamine demonstrated that the products of the reductive half-reaction are an equivalent of formaldehyde hydrate and a reduced...
nmrlearner Journal club 0 11-17-2010 11:06 PM
Insights into the Mechanism of Ligand Binding to Octopine Dehydrogenase from Pecten m
Insights into the Mechanism of Ligand Binding to Octopine Dehydrogenase from Pecten maximus by NMR and Crystallography. Related Articles Insights into the Mechanism of Ligand Binding to Octopine Dehydrogenase from Pecten maximus by NMR and Crystallography. PLoS One. 2010;5(8): Authors: Smits SH, Meyer T, Mueller A, van Os N, Stoldt M, Willbold D, Schmitt L, Grieshaber MK Octopine dehydrogenase (OcDH) from the adductor muscle of the great scallop, Pecten maximus, catalyzes the NADH dependent, reductive condensation of L-arginine and pyruvate to...
nmrlearner Journal club 0 09-03-2010 02:30 PM
[NMR paper] C-NMR study on the interaction of medium-chain acyl-CoA dehydrogenase with acetoacety
C-NMR study on the interaction of medium-chain acyl-CoA dehydrogenase with acetoacetyl-CoA. Related Articles C-NMR study on the interaction of medium-chain acyl-CoA dehydrogenase with acetoacetyl-CoA. J Biochem. 1996 Mar;119(3):512-9 Authors: Miura R, Nishina Y, Fuji S, Shiga K The change-transfer interaction in the complex of pig kidney medium-chain acyl-CoA dehydrogenase (MCAD) with acetoacetyl-CoA was investigated by 13C-NMR spectroscopy and molecular orbital treatment. The acyl carbons of acetoacetyl-CoA were separately 13C-labeled and...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] A 19F-NMR study of the membrane-binding region of D-lactate dehydrogenase of Escheric
A 19F-NMR study of the membrane-binding region of D-lactate dehydrogenase of Escherichia coli. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles A 19F-NMR study of the membrane-binding region of D-lactate dehydrogenase of Escherichia coli. Protein Sci. 1993 Nov;2(11):1938-47 Authors: Sun ZY, Truong HT, Pratt EA, Sutherland DC,...
nmrlearner Journal club 0 08-22-2010 03:01 AM


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 - 2017, 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