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 05-28-2013, 06:36 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
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 A model of the membrane-bound cytochrome b5-cytochrome p450 complex from NMR and mutagenesis data.

A model of the membrane-bound cytochrome b5-cytochrome p450 complex from NMR and mutagenesis data.

A model of the membrane-bound cytochrome b5-cytochrome p450 complex from NMR and mutagenesis data.

J Biol Chem. 2013 May 24;

Authors: Ahuja S, Jahr N, Im SC, Vivekanandan S, Popovych N, Le Clair SV, Huang R, Soong R, Xu J, Yamamoto K, Nanga RP, Bridges A, Waskell L, Ramamoorthy A

Abstract
Microsomal cytochrome b5 (cytb5) is a membrane-bound protein that modulates the catalytic activity of its redox partner, cytochrome P4502B4 (cytP450). Here, we report the first structure of full-length rabbit ferric microsomal cytb5 (16-kDa), incorporated in two different membrane mimetics (detergent micelles and lipid bicelles). Differential line broadening of the cytb5 NMR resonances and site-directed mutagenesis data were used to characterize the cytb5 interaction epitope recognized by ferric microsomal cytP450 (56-kDa). Subsequently, a data-driven docking algorithm, HADDOCK, was used to generate the structure of the complex between cytP4502B4 and cytb5 using experimentally derived restraints from NMR, mutagenesis and double-mutant cycle data obtained on the full-length proteins. Our docking and experimental results point to the formation of a dynamic electron-transfer complex between the acidic, convex surface of cytb5 and the concave, basic proximal surface of cytP4502B4. The majority of the binding energy for the complex is provided by interactions between residues on the C-helix and ?-bulge of cytP450 and residues at the end of helix ?4 of cytb5. The structure of the complex allows us to propose an interprotein electron transfer pathway involving the highly conserved Arg125 on cytP450 serving as a salt bridge between the heme propionates of cytP450 and cytb5. We have also shown that the addition of a substrate to cytP450 likely strengthens the cytb5-cytP450 interaction. This study paves the way to obtaining valuable structural, functional and dynamic information on membrane-bound complexes.


PMID: 23709268 [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] Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR.
Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR. Related Articles Substrate-Modulated Cytochrome P450 17A1 and Cytochrome b5 Interactions Revealed by NMR. J Biol Chem. 2013 Apr 25; Authors: Estrada DF, Laurence JS, Scott EE Abstract The membrane heme protein cytochrome b5 (b5) can enhance, inhibit, or have no effect on cytochrome P450 (P450) catalysis, depending on the specific P450, substrate, and reaction conditions, but the structural basis remains unclear. Herein the interactions between the...
nmrlearner Journal club 0 04-27-2013 01:56 PM
NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation.
NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation. NMR-derived models of amidopyrine and its metabolites in complexes with rabbit cytochrome P450 2B4 reveal a structural mechanism of sequential N-dealkylation. Biochemistry. 2011 Mar 29;50(12):2123-34 Authors: Roberts AG, Sjögren SE, Fomina N, Vu KT, Almutairi A, Halpert JR To understand the molecular basis of sequential N-dealkylation by cytochrome P450 2B enzymes, we studied the binding of...
nmrlearner Journal club 0 05-20-2011 11:26 AM
NMR-Derived Models of Amidopyrine and Its Metabolites in Complexes with Rabbit Cytochrome P450 2B4 Reveal a Structural Mechanism of Sequential N-Dealkylation
NMR-Derived Models of Amidopyrine and Its Metabolites in Complexes with Rabbit Cytochrome P450 2B4 Reveal a Structural Mechanism of Sequential N-Dealkylation http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/bichaw/0/bichaw.ahead-of-print/bi101797v/aop/images/medium/bi-2010-01797v_0012.gif Biochemistry DOI: 10.1021/bi101797v http://feeds.feedburner.com/~ff/acs/bichaw?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/bichaw/~4/lT6iIRntwis More...
nmrlearner Journal club 0 03-05-2011 02:44 AM
[NMR paper] Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data.
Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data. Related Articles Characterization and calculation of a cytochrome c-cytochrome b5 complex using NMR data. Biochemistry. 2005 Aug 9;44(31):10654-68 Authors: Deep S, Im SC, Zuiderweg ER, Waskell L To identify the binding site for bovine cytochrome b(5) (cyt b(5)) on horse cytochrome c (cyt c), cross-saturation transfer NMR experiments were performed with (2)H- and (15)N-enriched cyt c and unlabeled cyt b(5). In addition, chemical shift changes of the cyt c...
nmrlearner Journal club 0 12-01-2010 06:56 PM
[NMR paper] The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 vis
The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Related Articles The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK. Protein Sci. 2005 Mar;14(3):799-811 Authors: Volkov AN, Ferrari D, Worrall JA, Bonvin AM, Ubbink M The interaction of bovine microsomal ferricytochrome b5 with yeast iso-1-ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical-shift...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] The substrate binding site of human liver cytochrome P450 2C9: an NMR study.
The substrate binding site of human liver cytochrome P450 2C9: an NMR study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles The substrate binding site of human liver cytochrome P450 2C9: an NMR study. Biochemistry. 1997 Oct 21;36(42):12672-82 Authors: Poli-Scaife S, Attias R, Dansette PM, Mansuy D Purified recombinant human liver cytochrome P450 2C9 was produced, from expression of the corresponding cDNA in yeast, in quantities large enough for UV-visible and 1H NMR experiments. Its...
nmrlearner Journal club 0 08-22-2010 05:08 PM
[NMR paper] A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of s
A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles A model for human cytochrome P450 2D6 based on homology modeling and NMR studies of substrate binding. Biochemistry. 1996 Apr 9;35(14):4540-50 Authors: Modi S, Paine MJ, Sutcliffe MJ, Lian LY, Primrose WU, Wolf CR, Roberts GC The cytochrome P450 responsible for the debrisoquine/sparteine polymorphism (P450 2D6) has been produced in large...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] 1H-NMR study of reduced heme proteins myoglobin and cytochrome P450.
1H-NMR study of reduced heme proteins myoglobin and cytochrome P450. 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 1H-NMR study of reduced heme proteins myoglobin and cytochrome P450. Eur J Biochem. 1993 Jul 15;215(2):431-7 Authors: Banci L, Bertini I, Marconi S, Pierattelli R The 1H-NMR spectra of deoxymyoglobin and reduced cytochrome P450 are analyzed by NOE spectroscopy. Progress has been made in the assignment of the...
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 - 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 01:36 PM.


Map