Data supporting beta-amyloid dimer structural transitions and protein-lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

		BioNMR > Educational resources > Journal club
Data supporting beta-amyloid dimer structural transitions and protein-lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

03-10-2016, 08:12 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Data supporting beta-amyloid dimer structural transitions and protein-lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

Data supporting beta-amyloid dimer structural transitions and protein-lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

Publication date: Available online 10 March 2016
Source:Data in Brief

Author(s): Sara Y. Cheng, George Chou, Creighton Buie, Mark W. Vaughn, Campbell Compton, Kwan H. Cheng

This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface”[1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR. Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR. Related Articles Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR. J Biomol NMR. 2015 Jan 30; Authors: Eddy MT, Su Y, Silvers R, Andreas L, Clark L, Wagner G, Pintacuda G, Emsley L, Griffin RG Abstract	nmrlearner	Journal club	0	01-31-2015 04:16 PM
Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR Lipid bilayer-bound conformation of an integral membrane beta barrel protein by multidimensional MAS NMR Abstract The human voltage dependent anion channel 1 (VDAC) is a 32Â*kDa Î²-barrel integral membrane protein that controls the transport of ions across the outer mitochondrial membrane. Despite the determination of VDAC solution and diffraction structures, a structural basis for the mechanism of its function is not yet fully understood. Biophysical studies suggest VDAC requires a lipid bilayer to achieve full function, motivating the need...	nmrlearner	Journal club	0	01-30-2015 12:15 PM
[NMR paper] Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation. J Biomol NMR. 2015 Jan 13; Authors: Ding Y, Fujimoto LM, Yao Y, Marassi FM Abstract Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the...	nmrlearner	Journal club	0	01-13-2015 02:31 PM
Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation Solid-state NMR of the Yersinia pestis outer membrane protein Ail in lipid bilayer nanodiscs sedimented by ultracentrifugation Abstract Solid-state NMR studies of sedimented soluble proteins has been developed recently as an attractive approach for overcoming the size limitations of solution NMR spectroscopy while bypassing the need for sample crystallization or precipitation (Bertini et al. Proc Natl Acad Sci USA 108(26):10396â??10399, 2011). Inspired by the potential benefits of this method, we have investigated the ability to sediment lipid bilayer...	nmrlearner	Journal club	0	01-12-2015 11:31 PM
[NMR paper] Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles. Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles. Related Articles Solution-NMR Characterization of Outer-Membrane Protein A from E. coli in Lipid Bilayer Nanodiscs and Detergent Micelles. Chembiochem. 2014 Apr 1; Authors: Sušac L, Horst R, Wüthrich K Abstract X-ray crystallography and solution NMR of detergent-reconstituted OmpA (outer membrane protein A from E. coli) had shown that this protein forms an eight-stranded transmembrane ?-barrel, but only...	nmrlearner	Journal club	0	04-03-2014 12:59 PM
[NMR paper] Solid-State NMR Investigations of Peptide-Lipid Interactions of the Transmembrane Domain of A Plant-Derived Protein, Hcf106. Solid-State NMR Investigations of Peptide-Lipid Interactions of the Transmembrane Domain of A Plant-Derived Protein, Hcf106. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solid-State NMR Investigations of Peptide-Lipid Interactions of the Transmembrane Domain of A Plant-Derived Protein, Hcf106. Chem Phys Lipids. 2013 Sep 24; Authors: Zhang L, Liu L, Maltsev S, Lorigan GA, Dabney-Smith C Abstract The chloroplast twin arginine translocation...	nmrlearner	Journal club	0	10-01-2013 11:15 PM
Solid-State NMR Investigations of Peptide-Lipid Interactions of the Transmembrane Domain of A Plant-Derived Protein, Hcf106 Solid-State NMR Investigations of Peptide-Lipid Interactions of the Transmembrane Domain of A Plant-Derived Protein, Hcf106 Publication date: Available online 24 September 2013 Source:Chemistry and Physics of Lipids</br> Author(s): Lei Zhang , Lishan Liu , Sergey Maltsev , Gary A. Lorigan , Carole Dabney-Smith</br> The chloroplast twin arginine translocation system transports highly folded precursor proteins across the thylakoid using the protonmotive force as its only energy source. Hcf106 and another thylakoid protein, cpTatC compose the precursor receptor...	nmrlearner	Journal club	0	09-25-2013 11:15 AM
[NMR paper] Investigating structural changes in the lipid bilayer upon insertion of the transmemb Investigating structural changes in the lipid bilayer upon insertion of the transmembrane domain of the membrane-bound protein phospholamban utilizing 31P and 2H solid-state NMR spectroscopy. Related Articles Investigating structural changes in the lipid bilayer upon insertion of the transmembrane domain of the membrane-bound protein phospholamban utilizing 31P and 2H solid-state NMR spectroscopy. Biophys J. 2004 Mar;86(3):1564-73 Authors: Dave PC, Tiburu EK, Damodaran K, Lorigan GA Phospholamban (PLB) is a 52-amino acid integral membrane...	nmrlearner	Journal club	0	11-24-2010 09:25 PM

« Previous Thread | Next 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