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 04-23-2016, 09:24 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 17,704
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 Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.

Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.

Related Articles Difference in the structures of alanine tri- and tetra-peptides with antiparallel ?-sheet assessed by X-ray diffraction, solid-state NMR and chemical shift calculations by GIPAW.

Biopolymers. 2014 Jan;101(1):13-20

Authors: Asakura T, Yazawa K, Horiguchi K, Suzuki F, Nishiyama Y, Nishimura K, Kaji H

Abstract
Alanine oligomers provide a key structure for silk fibers from spider and wild silkworms.We report on structural analysis of L-alanyl-L-alanyl-L-alanyl-L-alanine (Ala)4 with anti-parallel (AP) ?-structures using X-ray and solid-state NMR. All of the Ala residues in the (Ala)4 are in equivalent positions, whereas for alanine trimer (Ala)3 there are two alternative locations in a unit cell as reported previously (Fawcett and Camerman, Acta Cryst., 1975, 31, 658-665). (Ala)4 with AP ?-structure is more stable than AP-(Ala)3 due to formation of the stronger hydrogen bonds. The intermolecular structure of (Ala)4 is also different from polyalanine fiber structure, indicating that the interchain arrangement of AP ?-structure changes with increasing alanine sequencelength. Furthermore the precise (1)H positions, which are usually inaccesible by X-ray diffraction method, are determined by high resolution (1)H solid state NMR combined with the chemical shift calculations by the gauge-including projector augmented wave method.


PMID: 23526402 [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] Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations.
Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Determining hydrogen-bond interactions in spider silk with 1H-13C HETCOR fast MAS solid-state NMR and DFT proton chemical shift calculations. Chem Commun (Camb). 2013 Jul 28;49(59):6680-2 Authors: Holland GP, Mou Q, Yarger JL Abstract Two-dimensional (2D) (1)H-(13)C...
nmrlearner Journal club 0 01-18-2014 11:31 AM
[NMR paper] Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel ? sheet fusion peptide structure in the final six-helix bundle state.
Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel ? sheet fusion peptide structure in the final six-helix bundle state. Related Articles Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel ? sheet fusion peptide structure in the final six-helix bundle state. J Mol Biol. 2013 Nov 15; Authors: Sackett K, Nethercott MJ, Zheng Z, Weliky DP Abstract The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although...
nmrlearner Journal club 0 11-20-2013 12:52 PM
Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel ? sheet fusion peptide structure in the final six-helix bundle state
Solid-state NMR spectroscopy of the HIV gp41 membrane fusion protein supports intermolecular antiparallel ? sheet fusion peptide structure in the final six-helix bundle state Publication date: Available online 16 November 2013 Source:Journal of Molecular Biology</br> Author(s): Kelly Sackett , Matthew J. Nethercott , Zhaoxiong Zheng , David P. Weliky</br> The HIV gp41 protein catalyzes fusion between viral and target cell membranes. Although the ~20-residue N-terminal fusion peptide (FP) region is critical for fusion, the structure of this region is not...
nmrlearner Journal club 0 11-16-2013 03:14 PM
[Question from NMRWiki Q&A forum] Capillary vs bulk solvent chemical shift difference
Capillary vs bulk solvent chemical shift difference I have prepared a sealed DMSO-d6 capillary tube (3mmOD) to use as an internal reference for an undergraduate prac using Evans method. When I run the capillary with DMSO-d6 only in the outer tube (ie no sample) there is a small difference in the shift of the residual DMSO solvent peak of the outer tube vs the capillary (~0.005ppm, 300MHz). The difference is not great enough to effect the result of the experiment but I would like to be able to explain the discrepancy to the students. Due to the large number of samples it is...
nmrlearner News from other NMR forums 0 11-12-2013 03:33 AM
[NMR paper] Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy.
Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy. Identifying inter-residue resonances in crowded 2D (13)C- (13)C chemical shift correlation spectra of membrane proteins by solid-state MAS NMR difference spectroscopy. J Biomol NMR. 2013 May 25; Authors: Miao Y, Cross TA, Fu R Abstract The feasibility of using difference spectroscopy, i.e. subtraction of two correlation spectra at different mixing times, for substantially...
nmrlearner Journal club 0 05-28-2013 06:36 PM
[NMR paper] Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.
Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information. J Biomol NMR. 2013 Apr 28; Authors: Fritzsching KJ, Yang Y, Schmidt-Rohr K, Hong M Abstract We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic...
nmrlearner Journal club 0 04-30-2013 10:21 PM
[NMR paper] Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation.
Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Determination of accurate 1H positions of an alanine tripeptide with anti-parallel and parallel ?-sheet structures by high resolution 1H solid state NMR and GIPAW chemical shift calculation. Chem Commun (Camb). 2012 Nov 25;48(91):11199-201 ...
nmrlearner Journal club 0 03-30-2013 12:59 PM
[NMR paper] Transmembrane 19F NMR chemical shift difference of fluorinated solutes in liposomes,
Transmembrane 19F NMR chemical shift difference of fluorinated solutes in liposomes, erythrocytes and erythrocyte ghosts. Related Articles Transmembrane 19F NMR chemical shift difference of fluorinated solutes in liposomes, erythrocytes and erythrocyte ghosts. NMR Biomed. 1993 Mar-Apr;6(2):136-43 Authors: Xu AS, Waldeck AR, Kuchel PW In erythrocytes suspended in isotonic medium, a number of fluorinated anions showed well resolved 19F NMR resonances from the solute populations in the intra- and extracellular compartments; the intracellular...
nmrlearner Journal club 0 08-21-2010 11:53 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 - 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 02:51 PM.


Map