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 02-27-2018, 12:30 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 19,916
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 Packing arrangement of 13C selectively labeled sequence model peptides of Samia cynthia ricini silk fibroin fibers studied by solid-state NMR.

Packing arrangement of 13C selectively labeled sequence model peptides of Samia cynthia ricini silk fibroin fibers studied by solid-state NMR.

Related Articles Packing arrangement of 13C selectively labeled sequence model peptides of Samia cynthia ricini silk fibroin fibers studied by solid-state NMR.

Phys Chem Chem Phys. 2017 May 24;19(20):13379-13386

Authors: Asakura T, Miyazawa K, Tasei Y, Kametani S, Nakazawa Y, Aoki A, Naito A

Abstract
Samia cynthia ricini (S. c. ricini) is one of the wild silkworms. Their silk fibroins have been paid attention as potentially valuable biomedical materials as well as Bombyx mori silk fibroins, but detailed information on the packing arrangement of the fibers is still not currently well understood at a molecular level. In this study, 34 mer model peptides, GGAGGGYGGDGG(A)12GGAGDGYGAG with different 13C labeled positions have been synthesized as a typical sequence of the primary structure of S. c. ricini silk fibroins made up of tandemly repeated sequences of polyalanine as the crystalline region and glycin-rich sequences as the non-crystalline region. The heterogeneous structure was obtained from the determination of the fraction of several conformations depending on the position of the Ala residue by 13C cross polarization/magic angle spinning NMR. The packing arrangement was studied by 13C dipolar assisted rotational resonance NMR and packing in a staggered arrangement rather than a rectangular arrangement of this peptide with an anti-parallel ?-sheet structure was clarified, which is in good agreement with our previous report on the packing arrangement of (Ala)7 with an anti-parallel ?-sheet structure.


PMID: 28492687 [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] Distinct solvent- and temperature-dependent packing arrangements of anti-parallel ?-sheet polyalanines studied with solid-state 13C NMR and MD simulation.
Distinct solvent- and temperature-dependent packing arrangements of anti-parallel ?-sheet polyalanines studied with solid-state 13C NMR and MD simulation. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.rsc.org-images-entities-char_z_RSClogo.gif Related Articles Distinct solvent- and temperature-dependent packing arrangements of anti-parallel ?-sheet polyalanines studied with solid-state 13C NMR and MD simulation. Phys Chem Chem Phys. 2017 Aug 09;19(31):20829-20838 Authors: Kametani S, Tasei Y, Nishimura A, Asakura T ...
nmrlearner Journal club 0 02-14-2018 02:43 AM
[NMR paper] Characterization of water in hydrated Bombyx mori silk fibroin fiber and films by (2)H NMR relaxation and (13)C solid state NMR.
Characterization of water in hydrated Bombyx mori silk fibroin fiber and films by (2)H NMR relaxation and (13)C solid state NMR. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Characterization of water in hydrated Bombyx mori silk fibroin fiber and films by (2)H NMR relaxation and (13)C solid state NMR. Acta Biomater. 2017 Mar 01;50:322-333 Authors: Asakura T, Isobe K, Kametani S, Ukpebor OT, Silverstein MC, Boutis GS Abstract The...
nmrlearner Journal club 0 11-08-2017 02:52 PM
(13) C Solid state NMR study of the (13) C-labeled peptide, (E)(8) GGLGGQGAG(A)(6) GGAGQGGYGG as a model for the local structure of Nephila clavipes dragline silk (MaSp1) before and after spinning.
(13) C Solid state NMR study of the (13) C-labeled peptide, (E)(8) GGLGGQGAG(A)(6) GGAGQGGYGG as a model for the local structure of Nephila clavipes dragline silk (MaSp1) before and after spinning. (13) C Solid state NMR study of the (13) C-labeled peptide, (E)(8) GGLGGQGAG(A)(6) GGAGQGGYGG as a model for the local structure of Nephila clavipes dragline silk (MaSp1) before and after spinning. Biopolymers. 2011 Sep 12; Authors: Yazawa K, Yamaguchi E, Knight D, Asakura T Abstract We prepared the water soluble model peptide, (E)(8)...
nmrlearner Journal club 0 09-14-2011 08:07 PM
[NMR paper] Effect of pH and copper(II) on the conformation transitions of silk fibroin based on
Effect of pH and copper(II) on the conformation transitions of silk fibroin based on EPR, NMR, and Raman spectroscopy. Related Articles Effect of pH and copper(II) on the conformation transitions of silk fibroin based on EPR, NMR, and Raman spectroscopy. Biochemistry. 2004 Sep 28;43(38):11932-41 Authors: Zong XH, Zhou P, Shao ZZ, Chen SM, Chen X, Hu BW, Deng F, Yao WH Much attention has been paid to the natural mechanism of silkworm spinning due to the impressive mechanical properties of the natural fibers. Our results in the present work show...
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Structural analysis of Bombyx mori silk fibroin peptides with formic acid treatment u
Structural analysis of Bombyx mori silk fibroin peptides with formic acid treatment using high-resolution solid-state 13C NMR spectroscopy. Related Articles Structural analysis of Bombyx mori silk fibroin peptides with formic acid treatment using high-resolution solid-state 13C NMR spectroscopy. Biomacromolecules. 2004 Sep-Oct;5(5):1763-9 Authors: Yao J, Ohgo K, Sugino R, Kishore R, Asakura T Bombyx mori silk fibroin fiber is a fibrous protein produced by the silkworm at room temperature and from an aqueous solution whose primary structure is...
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Structure of the model peptides of Bombyx mori silk-elastin like protein studied with
Structure of the model peptides of Bombyx mori silk-elastin like protein studied with solid state NMR. Related Articles Structure of the model peptides of Bombyx mori silk-elastin like protein studied with solid state NMR. Biomacromolecules. 2004 May-Jun;5(3):744-50 Authors: Ohgo K, Kurano TL, Kumashiro KK, Asakura T The peptides (AG)(6)(VPGVG)(AG)(7) and (AG)(5)(VPGVG)(2)(AG)(5) are models for a new type of protein with both composition and properties such as Bombyx mori silk and elastin. In this paper, we report the solid-state NMR results...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR a
Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II. Related Articles Structural role of tyrosine in Bombyx mori silk fibroin, studied by solid-state NMR and molecular mechanics on a model peptide prepared as silk I and II. Magn Reson Chem. 2004 Feb;42(2):258-66 Authors: Asakura T, Suita K, Kameda T, Afonin S, Ulrich AS The influence of the bulky and H-bonding Tyr side-chain on its Ala- and Gly-rich environment in Bombyx mori silk fibroin was...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Solid-state NMR determination of the secondary structure of Samia cynthia ricini silk
Solid-state NMR determination of the secondary structure of Samia cynthia ricini silk. Related Articles Solid-state NMR determination of the secondary structure of Samia cynthia ricini silk. Nature. 2000 Jun 29;405(6790):1077-9 Authors: van Beek JD, Beaulieu L, Schäfer H, Demura M, Asakura T, Meier BH Silks are fibrous proteins that form heterogeneous, semi-crystalline solids. Silk proteins have a variety of physical properties reflecting their range of functions. Spider dragline silk, for example, has high tensile strength and elasticity,...
nmrlearner Journal club 0 11-18-2010 09:15 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 11:13 AM.


Map