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 08-22-2010, 05:08 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,700
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 Expression and secondary structure determination by NMR methods of the major house du

Expression and secondary structure determination by NMR methods of the major house dust mite allergen Der p 2.

Related Articles Expression and secondary structure determination by NMR methods of the major house dust mite allergen Der p 2.

J Biol Chem. 1997 Oct 24;272(43):26893-8

Authors: Mueller GA, Smith AM, Williams DC, Hakkaart GA, Aalberse RC, Chapman MD, Rule GS, Benjamin DC

There exists a strong correlation between asthma and sensitization to indoor allergens. This study reports on the secondary structure of the major house dust mite allergen Der p 2, determined using heteronuclear NMR methods. The DNA was subcloned from the yeast expression vector pSAY1 into the high yield bacterial expression vector pET21a, resulting in yields of 50 mg/liter. The recombinant protein was shown to have immunoreactivity comparable with that of the natural mite protein using competitive inhibition enzyme-linked immunosorbent assay (ELISA) and a modified monoclonal radioallergosorbent test (RAST). The secondary structure was determined by examining chemical shifts, short and long range NOESYs, JHN-HA coupling constants, and amide exchange rates. From these data, it is clear that Der p 2 is composed of beta-sheets and random coil. Based on long range distance constraints, a number of beta-strands were aligned into two three-stranded, anti-parallel beta-sheets.

PMID: 9341122 [PubMed - indexed for MEDLINE]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[Optimization of the methods for small peptide solution structure determination by NMR spectroscopy].
. . Mol Biol (Mosk). 2010 Nov-Dec;44(6):1075-85 Authors: NMR spectroscopy was recognized as a method of protein structure determination in solution. However, determination of the conformation of small peptides, which undergo fast molecular motions, remains a challenge. This is mainly caused by impossibility to collect required quantity of the distance and dihedral angle restraints from NMR spectra. At the same time, short charged peptides play an important role in a number of biological processes, in particular in pathogenesis of neurodegenerative...
nmrlearner Journal club 0 02-05-2011 05:28 PM
[NMR paper] Multidimensional NMR methods for protein structure determination.
Multidimensional NMR methods for protein structure determination. Related Articles Multidimensional NMR methods for protein structure determination. IUBMB Life. 2001 Dec;52(6):291-302 Authors: Kanelis V, Forman-Kay JD, Kay LE Structural studies of proteins are critical for understanding biological processes at the molecular level. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for obtaining structural and dynamic information on proteins and protein-ligand complexes. In the present review, methodologies for NMR structure...
nmrlearner Journal club 0 11-19-2010 08:44 PM
[NMR paper] Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domai
Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin. Related Articles Secondary structure determination by NMR spectroscopy of an immunoglobulin-like domain from the giant muscle protein titin. J Biomol NMR. 1995 Jul;6(1):48-58 Authors: Pfuhl M, Gautel M, Politou AS, Joseph C, Pastore A We present the complete 15N and 1H NMR assignment and the secondary structure of an immunoglobulin-like domain from the giant muscle protein titin. The assignment was obtained using...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] An RBD that does not bind RNA: NMR secondary structure determination and biochemical
An RBD that does not bind RNA: NMR secondary structure determination and biochemical properties of the C-terminal RNA binding domain from the human U1A protein. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles An RBD that does not bind RNA: NMR secondary structure determination and biochemical properties of the C-terminal RNA binding domain from the human U1A protein. J Mol Biol. 1995 Apr 7;247(4):739-52 Authors: Lu J, Hall KB We have obtained backbone 1H, 15N, and 13C...
nmrlearner Journal club 0 08-22-2010 03:41 AM
[NMR paper] NMR determination of the secondary structure and the three-dimensional polypeptide ba
NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles NMR determination of the secondary structure and the three-dimensional polypeptide backbone fold of the human sterol carrier protein 2. FEBS Lett. 1993 Nov 29;335(1):18-26 Authors: Szyperski T, Scheek S, Johansson J, Assmann G, Seedorf U, Wüthrich K Nuclear magnetic resonance (NMR)...
nmrlearner Journal club 0 08-22-2010 03:01 AM
[NMR paper] A systematic comparison of three structure determination methods from NMR data: depen
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. Related Articles A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data. J Biomol NMR. 1992 Jul;2(4):373-88 Authors: Liu Y, Zhao D, Altman R, Jardetzky O We have systematically examined how the quality of NMR protein structures depends on (1) the number of NOE distance constraints, (2) their assumed precision, (3) the method of structure calculation...
nmrlearner Journal club 0 08-21-2010 11:41 PM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination.
Combining NMR and EPR Methods for Homodimer Protein Structure Determination. Related Articles Combining NMR and EPR Methods for Homodimer Protein Structure Determination. J Am Chem Soc. 2010 Aug 10; Authors: Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using...
nmrlearner Journal club 0 08-17-2010 03:36 AM
Combining NMR and EPR Methods for Homodimer Protein Structure Determination
http://pubs.acs.org//appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja105080h/aop/images/medium/ja-2010-05080h_0003.gif Combining NMR and EPR Methods for Homodimer Protein Structure Determination There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein ...
nmrlearner Journal club 0 08-14-2010 05:56 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 10:42 AM.


Map