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 05-02-2018, 11:57 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,208
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 Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation.

Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation.

Related Articles Dynamic Structure and Orientation of Melittin Bound to Acidic Lipid Bilayers, As Revealed by Solid-State NMR and Molecular Dynamics Simulation.

J Phys Chem B. 2017 03 02;121(8):1802-1811

Authors: Norisada K, Javkhlantugs N, Mishima D, Kawamura I, Saitô H, Ueda K, Naito A

Abstract
Melittin is a venom peptide that disrupts lipid bilayers at temperatures below the liquid-crystalline to gel phase transition temperature (Tc). Notably, the ability of melittin to disrupt acidic dimyristoylphosphatidylglycerol (DMPG) bilayers was weaker than its ability to disrupt neutral dimyristoylphosphatidylcholine bilayers. The structure and orientation of melittin bound to DMPG bilayers were revealed by analyzing the 13C chemical shift anisotropy of [1-13C]-labeled melittin obtained from solid-state 13C NMR spectra. 13C chemical shift anisotropy showed oscillatory shifts with the index number of residues. Analysis of the chemical shift oscillation properties indicated that melittin bound to a DMPG membrane adopts a bent ?-helical structure with tilt angles for the N- and C-terminal helices of -32 and +30°, respectively. The transmembrane melittin in DMPG bilayers indicates that the peptide protrudes toward the C-terminal direction from the core region of the lipid bilayer to show a pseudotransmembrane bent ?-helix. Molecular dynamics simulation was performed to characterize the structure and interaction of melittin with lipid molecules in DMPG bilayers. The simulation results indicate that basic amino acid residues in melittin interact strongly with lipid head groups to generate a pseudo-transmembrane alignment. The N-terminus is located within the lipid core region and disturbs the lower surface of the lipid bilayer.


PMID: 28165239 [PubMed - indexed for MEDLINE]



More...
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] Transmembrane Interactions of Full-length Mammalian Bitopic Cytochrome-P450-Cytochrome-b5 Complex in Lipid Bilayers Revealed by Sensitivity-Enhanced Dynamic Nuclear Polarization Solid-state NMR Spectroscopy.
Transmembrane Interactions of Full-length Mammalian Bitopic Cytochrome-P450-Cytochrome-b5 Complex in Lipid Bilayers Revealed by Sensitivity-Enhanced Dynamic Nuclear Polarization Solid-state NMR Spectroscopy. Related Articles Transmembrane Interactions of Full-length Mammalian Bitopic Cytochrome-P450-Cytochrome-b5 Complex in Lipid Bilayers Revealed by Sensitivity-Enhanced Dynamic Nuclear Polarization Solid-state NMR Spectroscopy. Sci Rep. 2017 Jun 23;7(1):4116 Authors: Yamamoto K, Caporini MA, Im SC, Waskell L, Ramamoorthy A Abstract...
nmrlearner Journal club 0 06-25-2017 02:42 PM
[NMR paper] Orientation and Location of the Cyclotide Kalata B1 in Lipid Bilayers Revealed by Solid-State NMR.
Orientation and Location of the Cyclotide Kalata B1 in Lipid Bilayers Revealed by Solid-State NMR. Related Articles Orientation and Location of the Cyclotide Kalata B1 in Lipid Bilayers Revealed by Solid-State NMR. Biophys J. 2017 Feb 28;112(4):630-642 Authors: Grage SL, Sani MA, Cheneval O, Henriques ST, Schalck C, Heinzmann R, Mylne JS, Mykhailiuk PK, Afonin S, Komarov IV, Separovic F, Craik DJ, Ulrich AS Abstract Cyclotides are ultra-stable cyclic disulfide-rich peptides from plants. Their biophysical effects and medically...
nmrlearner Journal club 0 03-04-2017 12:19 PM
MembraneInsertion of a Dinuclear Polypyridylruthenium(II)Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation:Implications for Selective Antibacterial Activity
MembraneInsertion of a Dinuclear Polypyridylruthenium(II)Complex Revealed by Solid-State NMR and Molecular Dynamics Simulation:Implications for Selective Antibacterial Activity Daniel K. Weber, Marc-Antoine Sani, Matthew T. Downton, Frances Separovic, F. Richard Keene and J. Grant Collins http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/jacs.6b09996/20161109/images/medium/ja-2016-099965_0009.gif Journal of the American Chemical Society DOI: 10.1021/jacs.6b09996 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...
nmrlearner Journal club 0 11-19-2016 08:35 PM
[NMR paper] Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation.
Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-cellhub.gif Related Articles Structure and orientation of bovine lactoferrampin in the mimetic bacterial membrane as revealed by solid-state NMR and molecular dynamics simulation. Biophys J. 2012 Oct 17;103(8):1735-43 Authors: Tsutsumi A, Javkhlantugs N, Kira A, Umeyama M, Kawamura I, Nishimura K, Ueda K,...
nmrlearner Journal club 0 03-21-2013 02:58 PM
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide.
Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. Combined Use of Replica-Exchange Molecular Dynamics and Magic-Angle-Spinning Solid-State NMR Spectral Simulations for Determining the Structure and Orientation of Membrane-Bound Peptide. J Phys Chem B. 2011 Jun 13; Authors: Ikeda K, Kameda T, Harada E, Akutsu H, Fujiwara T We report an approach to determining membrane-peptides and -protein complex structures by...
nmrlearner Journal club 0 06-15-2011 01:15 PM
Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR.
Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR. Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR. J Am Chem Soc. 2011 Mar 14; Authors: Yang J, Aslimovska L, Glaubitz C Environmental factors such as temperature, hydration, and lipid bilayer properties are tightly coupled to the dynamics of membrane proteins. So far, site-resolved data visualizing the protein's response to alterations in these factors are rare, and conclusions had to be drawn from dynamic data averaged over the whole protein...
nmrlearner Journal club 0 03-16-2011 04:15 PM
Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR
Molecular Dynamics of Proteorhodopsin in Lipid Bilayers by Solid-State NMR Jun Yang, Lubica Aslimovska and Clemens Glaubitz http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja109766n/aop/images/medium/ja-2010-09766n_0011.gif Journal of the American Chemical Society DOI: 10.1021/ja109766n http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/VmNlca5pCIw
nmrlearner Journal club 0 03-15-2011 05:56 AM
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation.
Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation. Dynamic structure of bombolitin II bound to lipid bilayers as revealed by solid-state NMR and molecular-dynamics simulation. Biophys J. 2010 Nov 17;99(10):3282-9 Authors: Toraya S, Javkhlantugs N, Mishima D, Nishimura K, Ueda K, Naito A Bombolitin II (BLT2) is one of the hemolytic heptadecapeptides originally isolated from the venom of a bumblebee. Structure and orientation of BLT2 bound to...
nmrlearner Journal club 0 03-03-2011 12:34 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 04:52 AM.


Map