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 12-08-2010, 06:21 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 20,040
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 Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.

Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.

Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction.

Structure. 2010 Dec 8;18(12):1678-1687

Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ

Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the structure of biomineral-associated proteins cannot be determined by X-ray crystallography or solution nuclear magnetic resonance (NMR). Here we report a method for determining the structure of biomineral-associated proteins. The method combines solid-state NMR (ssNMR) and ssNMR-biased computational structure prediction. In addition, the algorithm is able to identify lattice geometries most compatible with ssNMR constraints, representing a quantitative, novel method for investigating crystal-face binding specificity. We use this method to determine most of the structure of human salivary statherin interacting with the mineral phase of tooth enamel. Computation and experiment converge on an ensemble of related structures and identify preferential binding at three crystal surfaces. The work represents a significant advance toward determining structure of biomineral-adsorbed protein using experimentally biased structure prediction. This method is generally applicable to proteins that can be chemically synthesized.

PMID: 21134646 [PubMed - as supplied by publisher]



Source: PubMed
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Structure Determination in “Shiftless” Solid State NMR of Oriented Protein Samples
Structure Determination in “Shiftless” Solid State NMR of Oriented Protein Samples Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 20 June 2011</br> Yuanyuan, Yin , Alexander A., Nevzorov</br> An efficient formalism for calculating protein structures from oriented-sample NMR data in the torsion-angle space is presented. Angular anisotropies of the NMR observables are treated by utilizing an irreducible spherical basis of rotations. An intermediate rotational transformation is introduced that greatly speeds up structural...
nmrlearner Journal club 0 06-21-2011 03:40 PM
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination.
A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination. A Proton-Detected 4D Solid-State NMR Experiment for Protein Structure Determination. Chemphyschem. 2011 Apr 4;12(5):915-8 Authors: Huber M, Hiller S, Schanda P, Ernst M, Böckmann A, Verel R, Meier BH
nmrlearner Journal club 0 03-29-2011 07:04 PM
[NMR paper] Protein structure determination by high-resolution solid-state NMR spectroscopy: appl
Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. Related Articles Protein structure determination by high-resolution solid-state NMR spectroscopy: application to microcrystalline ubiquitin. J Am Chem Soc. 2005 Jun 22;127(24):8618-26 Authors: Zech SG, Wand AJ, McDermott AE High-resolution solid-state NMR spectroscopy has become a promising method for the determination of three-dimensional protein structures for systems which are difficult to crystallize or exhibit low...
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] A concept for rapid protein-structure determination by solid-state NMR spectroscopy.
A concept for rapid protein-structure determination by solid-state NMR spectroscopy. Related Articles A concept for rapid protein-structure determination by solid-state NMR spectroscopy. Angew Chem Int Ed Engl. 2005 Mar 29;44(14):2089-92 Authors: Lange A, Becker S, Seidel K, Giller K, Pongs O, Baldus M
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Membrane protein structure determination using solid-state NMR.
Membrane protein structure determination using solid-state NMR. Related Articles Membrane protein structure determination using solid-state NMR. Methods Mol Biol. 2004;278:403-73 Authors: Watts A, Straus SK, Grage SL, Kamihira M, Lam YH, Zhao X Solid-state NMR is emerging as a method for resolving structural information for large biomolecular complexes, such as membrane-embedded proteins. In principle, there is no molecular weight limit to the use of the approach, although the complexity and volume of data is still outside complete assignment...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] Membrane protein structure determination by solid state NMR.
Membrane protein structure determination by solid state NMR. Related Articles Membrane protein structure determination by solid state NMR. Nat Prod Rep. 1999 Aug;16(4):419-23 Authors: Watts A, Burnett IJ, Glaubitz C, Gröbner G, Middleton DA, Spooner PJ, Watts JA, Williamson PT
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Ribosomal protein L9: a structure determination by the combined use of X-ray crystall
Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Ribosomal protein L9: a structure determination by the combined use of X-ray crystallography and NMR spectroscopy. J Mol Biol. 1996 Dec 20;264(5):1058-71 Authors: Hoffman DW, Cameron CS, Davies C, White SW, Ramakrishnan V The structure of protein L9 from the Bacillus stearothernophilus ribosome has been...
nmrlearner Journal club 0 08-22-2010 02:20 PM
Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff
Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff, Microsoft Research Summer School , Cambridge , July 2008
MCGowan Educational web pages 0 09-16-2008 02:10 AM


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 08:34 AM.


Map