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
Home Forums Wiki NMR feeds Downloads Register Today's Posts



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  
Old 08-14-2010, 04:19 AM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,732
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 HA-detected experiments for the backbone assignment of intrinsically disordered prote

Abstract We propose a new alpha proton detection based approach for the sequential assignment of natively unfolded proteins. The proposed protocol superimposes on following features: HA-detection (1) enables assignment of natively unfolded proteins at any pH, i.e., it is not sensitive to rapid chemical exchange undergoing in natively unfolded proteins even at moderately high pH. (2) It allows straightforward assignment of proline-rich polypeptides without additional proline-customized experiments. (3) It offers more streamlined and less ambiguous assignment based on solely intraresidual 15N(i)-13C�(i)-Hα(i) (or 15N(i)-13Cα(i)-Hα(i)) and sequential 15N(i + 1)-13C�(i)-Hα(i) (or 15N(i + 1)-13Cα(i)-Hα(i)) correlation experiments together with efficient use of chemical shifts of 15N and 13C� nuclei, which show smaller dependence on residue type. We have tested the proposed protocol on two proteins, small globular 56-residue GB1, and highly disordered, proline-rich 47-residue fifth repeat of EspFU. Using the proposed approach, we were able to assign 90% of 1Hα, 13Cα, 13C�, 15N chemical shifts in EspFU. We reckon that the HA-detection based strategy will be very useful in the assignment of natively unfolded proline-rich proteins or polypeptide chains.
  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9421-0
  • Authors
    • Sampo Mäntylahti, University of Helsinki Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory P.O. Box 65 00014 Helsinki Finland
    • Olli Aitio, University of Helsinki Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory P.O. Box 65 00014 Helsinki Finland
    • Maarit Hellman, University of Helsinki Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory P.O. Box 65 00014 Helsinki Finland
    • Perttu Permi, University of Helsinki Program in Structural Biology and Biophysics, Institute of Biotechnology/NMR Laboratory P.O. Box 65 00014 Helsinki Finland

Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using δ subunit (20 kDa) of Bacillus subtilis RNA polymerase...
nmrlearner Journal club 0 02-21-2012 03:40 AM
Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3.
Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3. Backbone and side chain NMR assignments for the intrinsically disordered cytoplasmic domain of human neuroligin-3. Biomol NMR Assign. 2011 Jun 7; Authors: Wood K, Paz A, Dijkstra K, Scheek RM, Otten R, Silman I, Sussman JL, Mulder FA Neuroligins act as heterophilic adhesion molecules at neuronal synapses. Their cytoplasmic domains interact with synaptic scaffolding proteins, and have been shown to be intrinsically disordered. Here we...
nmrlearner Journal club 0 06-08-2011 11:30 AM
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins.
Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. Covalent structural changes in unfolded GroES that lead to amyloid fibril formation detected by NMR: Insight into intrinsically disordered proteins. J Biol Chem. 2011 Apr 20; Authors: Iwasa H, Meshitsuka S, Hongo K, Mizobata T, Kawata Y Co-chaperonin GroES from E. coli works with chaperonin GroEL to mediate the folding reactions of various proteins. However, under specific conditions, i. e., the...
nmrlearner Journal club 0 04-22-2011 02:00 PM
5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion
5D 13C-detected experiments for backbone assignment of unstructured proteins with a very low signal dispersion Abstract Two novel 5D NMR experiments (CACONCACO, NCOCANCO) for backbone assignment of disordered proteins are presented. The pulse sequences exploit relaxation properties of the unstructured proteins and combine the advantages of 13C-direct detection, non-uniform sampling, and longitudinal relaxation optimization to maximize the achievable resolution and minimize the experimental time. The pulse sequences were successfully tested on the sample of partially disordered delta...
nmrlearner Journal club 0 03-22-2011 07:32 PM
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins.
ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. ncIDP-assign: A SPARKY extension for the effective NMR assignment of intrinsically disordered proteins. Bioinformatics. 2011 Mar 3; Authors: Tamiola K, Mulder FA SUMMARY: We describe here the ncIDP-assign extension for the popular NMR assignment programme SPARKY, which aids in the sequence-specific resonance assignment of intrinsically disordered proteins (IDPs). The assignment plugin greatly facilitates the effective matching of a set of...
nmrlearner Journal club 0 03-05-2011 01:02 PM
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins
Extension of the HA-detection based approach: (HCA)CON(CA)H and (HCA)NCO(CA)H experiments for the main-chain assignment of intrinsically disordered proteins Abstract Extensive resonance overlap exacerbates assignment of intrinsically disordered proteins (IDPs). This issue can be circumvented by utilizing 15N, 13C� and 1HN spins, where the chemical shift dispersion is mainly dictated by the characteristics of consecutive amino acid residues. Especially 15N and 13C� spins offer superior chemical shift dispersion in comparison to 13Cα and 13Cβ spins. However, HN-detected experiments...
nmrlearner Journal club 0 01-29-2011 05:31 AM
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins
Sparsely-sampled High-resolution 4-D Experiments for Efficient Backbone Resonance Assignment of Disordered Proteins Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 4 January 2011</br> Jie, Wen , Jihui, Wu , Pei, Zhou</br> Intrinsically disordered proteins (IDPs) play important roles in many critical cellular processes. Due to their limited chemical shift dispersion, IDPs often require four pairs of resonance connectivities (H?, C?, C? and CO) for establishing sequential backbone assignment. Because most conventional 4-D...
nmrlearner Journal club 0 01-05-2011 11:03 AM
13C-direct detected NMR experiments for the sequential J-based resonance assignment o
Abstract We present here a set of 13C-direct detected NMR experiments to facilitate the resonance assignment of RNA oligonucleotides. Three experiments have been developed: (1) the (H)CC-TOCSY-experiment utilizing a virtual decoupling scheme to assign the intraresidual ribose 13C-spins, (2) the (H)CPC-experiment that correlates each phosphorus with the C4â?² nuclei of adjacent nucleotides via J(C,P) couplings and (3) the (H)CPC-CCH-TOCSY-experiment that correlates the phosphorus nuclei with the respective C1â?²,H1â?² ribose signals. The experiments were applied to two RNA hairpin structures....
nmrlearner Journal club 0 08-14-2010 04:19 AM



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 - 2024, 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 12:53 AM.


Map