NMR paper 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

		BioNMR > Educational resources > Journal club
[NMR paper] 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

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

11-24-2010, 09:51 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

Related Articles 2D solid state NMR spectral simulation of 3(10), alpha, and pi-helices.

J Magn Reson. 2004 Jun;168(2):187-93

Authors: Kim S, Cross TA

Transmembrane helices are more uniform in structure than similar helices in water soluble proteins. Solid state NMR of aligned bilayer samples is being increasingly used to characterize helical membrane protein structures. Traditional spectroscopic methods have difficulty distinguishing between helices with i to i + 3 (3(10)), i to i + 4 (alpha), and i to i + 5 (pi) hydrogen bonding topology. Here, we show that resonance patterns in PISEMA spectra simulated for these different helices show unique and striking features. The size and shape of these Polar Index Slant Angle (PISA) wheels, as well as the resonances per turn and clockwise versus counter-clockwise sequential connectivity of the resonances demonstrate how these different helical structures, if present as a uniform structure, will be readily distinguished, and characterized.

PMID: 15140426 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Packing Interactions inHydrated and Anhydrous Formsof the Antibiotic Ciprofloxacin: a Solid-State NMR, X-ray Diffraction,and Computer Simulation Study Packing Interactions inHydrated and Anhydrous Formsof the Antibiotic Ciprofloxacin: a Solid-State NMR, X-ray Diffraction,and Computer Simulation Study Lui?s Mafra, Se?rgio M. Santos, Rene?e Siegel, Ine?s Alves, Filipe A. Almeida Paz, Dmytro Dudenko and Hans W. Spiess http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja208647n/aop/images/medium/ja-2011-08647n_0005.gif Journal of the American Chemical Society DOI: 10.1021/ja208647n http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...	nmrlearner	Journal club	0	12-10-2011 02:38 AM
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
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
[NMR paper] NMR conformational analyses on (des-bromo) neuropeptide B [1-23] and neuropeptide W [1-23]: the importance of alpha-helices, a cation-pi interaction and a beta-turn. NMR conformational analyses on (des-bromo) neuropeptide B and neuropeptide W : the importance of alpha-helices, a cation-pi interaction and a beta-turn. Related Articles NMR conformational analyses on (des-bromo) neuropeptide B and neuropeptide W : the importance of alpha-helices, a cation-pi interaction and a beta-turn. J Biomol Struct Dyn. 2005 Aug;23(1):77-90 Authors: Lucyk S, Miskolzie M, Kotovych G The preferred conformations of the orphan G-protein coupled receptor agonists (des-bromo) neuropeptide B and neuropeptide W , referred to...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Solid-state dipolar INADEQUATE NMR spectroscopy with a large double-quantum spectral Solid-state dipolar INADEQUATE NMR spectroscopy with a large double-quantum spectral width. Related Articles Solid-state dipolar INADEQUATE NMR spectroscopy with a large double-quantum spectral width. J Magn Reson. 1999 Jan;136(1):86-91 Authors: Hong M A technique for obtaining dipolar-mediated INADEQUATE NMR spectra with a large spectral window in the double-quantum dimension is presented. Using the dipolar recoupling sequence C7 to excite the double-quantum coherence under magic-angle spinning, the technique involves incrementing the...	nmrlearner	Journal club	0	11-18-2010 07:05 PM
[NMR paper] Elucidating the folding problem of alpha-helices: local motifs, long-range electrosta Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. Related Articles Elucidating the folding problem of alpha-helices: local motifs, long-range electrostatics, ionic-strength dependence and prediction of NMR parameters. J Mol Biol. 1998 Nov 20;284(1):173-91 Authors: Lacroix E, Viguera AR, Serrano L The information about the conformational behavior of monomeric helical peptides in solution, as well as the alpha-helix stability in proteins, has...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] Orientational distribution of alpha-helices in the colicin B and E1 channel domains: Orientational distribution of alpha-helices in the colicin B and E1 channel domains: a one and two dimensional 15N solid-state NMR investigation in uniaxially aligned phospholipid bilayers. Related Articles Orientational distribution of alpha-helices in the colicin B and E1 channel domains: a one and two dimensional 15N solid-state NMR investigation in uniaxially aligned phospholipid bilayers. Biochemistry. 1998 Jan 6;37(1):16-22 Authors: Lambotte S, Jasperse P, Bechinger B Thermolytic fragments of the channel-forming bacterial toxins colicin...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
[NMR paper] Stability of alpha-helices in a molten globule state of cytochrome c by hydrogen-deut Stability of alpha-helices in a molten globule state of cytochrome c by hydrogen-deuterium exchange and two-dimensional NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Stability of alpha-helices in a molten globule state of cytochrome c by hydrogen-deuterium exchange and two-dimensional NMR spectroscopy. J Mol Biol. 1995 Apr 7;247(4):682-8 Authors: Kuroda Y, Endo S, Nagayama K, Wada A To distinguish between intrinsically stable helices and those...	nmrlearner	Journal club	0	08-22-2010 03:41 AM

« 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