NMR paper Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.

		BioNMR > Educational resources > Journal club
[NMR paper] Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

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:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

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:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

05-03-2014, 10:42 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.

Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.

Related Articles Multimodality characterization of microstructure by the combination of diffusion NMR and time-domain diffuse optical data.

Phys Med Biol. 2014 May 1;59(11):2639-2658

Authors: Proverbio A, Siow BM, Lythgoe MF, Alexander DC, Gibson AP

Abstract
Combining datasets with a model of the underlying physics prior to mapping of tissue provides a novel approach improving the estimation of parameters. We demonstrate this approach by merging near infrared diffuse optical signal data with diffusion NMR data to inform a model describing the microstructure of a sample. The study is conducted on a homogeneous emulsion of oil in a dispersion medium of water and proteins. The use of a protein based background, rich in collagen, introduces a similarity to real tissues compared to other models such as intralipids. The sample is investigated with the two modalities separately. Then, the two datasets are used to inform a combined model, and to estimate the size of the microstructural elements and the volume fraction. The combined model fits the microstructural properties by minimizing the difference between experimental and modelled data. The experimental results are validated with confocal laser scanning microscopy. The final results demonstrate that the combined model provides improved estimates of microstructural parameters compared to either individual model alone.

PMID: 24786607 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products December 2012 Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 225</br> </br> Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In this work, Nuclear Magnetic Resonance measurements of relaxation rates and...	nmrlearner	Journal club	0	12-15-2012 09:51 AM
Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products Magnetic resonance diffusion and relaxation characterization of water in the unfrozen vein network in polycrystalline ice and its response to microbial metabolic products December 2012 Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 225</br> </br> Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In this work, Nuclear Magnetic Resonance measurements of relaxation rates and...	nmrlearner	Journal club	0	12-01-2012 06:10 PM
Characterization of the ground state dynamics of proteorhodopsin by NMR and optical spectroscopies Characterization of the ground state dynamics of proteorhodopsin by NMR and optical spectroscopies Abstract We characterized the dynamics of proteorhodopsin (PR), solubilized in diC7PC, a detergent micelle, by liquid-state NMR spectroscopy at T = 323 K. Insights into the dynamics of PR at different time scales could be obtained and dynamic hot spots could be identified at distinct, functionally relevant regions of the protein, including the BC loop, the EF loop, the N-terminal part of helix F and the C-terminal part of helix G. We further characterize the dependence of the photocycle...	nmrlearner	Journal club	0	11-22-2012 05:27 AM
Magnetic Resonance Diffusion and Relaxation Characterization of Water in the Unfrozen Vein Network in Polycrystalline Ice and its Response to Microbial Metabolic Products Magnetic Resonance Diffusion and Relaxation Characterization of Water in the Unfrozen Vein Network in Polycrystalline Ice and its Response to Microbial Metabolic Products Publication year: 2012 Source:Journal of Magnetic Resonance</br> Jennifer R. Brown, Timothy I. Brox, Sarah J. Vogt, Joseph D. Seymour, Mark Skidmore, Sarah L. Codd</br> Polycrystalline ice, as found in glaciers and the ice sheets of Antarctica, is a low porosity porous media consisting of a complicated and dynamic pore structure of liquid-filled intercrystalline veins within a solid ice matrix. In...	nmrlearner	Journal club	0	10-05-2012 09:10 AM
[NMR paper] NMR backbone assignment of a protein kinase catalytic domain by a combination of seve NMR backbone assignment of a protein kinase catalytic domain by a combination of several approaches: application to the catalytic subunit of cAMP-dependent protein kinase. Related Articles NMR backbone assignment of a protein kinase catalytic domain by a combination of several approaches: application to the catalytic subunit of cAMP-dependent protein kinase. Chembiochem. 2004 Nov 5;5(11):1508-16 Authors: Langer T, Vogtherr M, Elshorst B, Betz M, Schieborr U, Saxena K, Schwalbe H Protein phosphorylation is one of the most important mechanisms...	nmrlearner	Journal club	0	11-24-2010 10:03 PM
[NMR paper] Residue-specific real-time NMR diffusion experiments define the association states of Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. Related Articles Residue-specific real-time NMR diffusion experiments define the association states of proteins during folding. J Am Chem Soc. 2002 Jun 19;124(24):7156-62 Authors: Buevich AV, Baum J Characterizing the association states of proteins during folding is critical for understanding the nature of protein-folding intermediates and protein-folding pathways, protein aggregation, and disease-related aggregation. To study the...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Real-time and equilibrium (19)F-NMR studies reveal the role of domain-domain interact Real-time and equilibrium (19)F-NMR studies reveal the role of domain-domain interactions in the folding of the chaperone PapD. Related Articles Real-time and equilibrium (19)F-NMR studies reveal the role of domain-domain interactions in the folding of the chaperone PapD. Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):709-14 Authors: Bann JG, Pinkner J, Hultgren SJ, Frieden C PapD is a periplasmic chaperone essential for P pilus formation in pyelonephritic strains of E. coli. It is composed of two domains, each of which contains a tryptophan...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
NMR Studies on Domain Diffusion and Alignment in Modular GB1 Repeats. NMR Studies on Domain Diffusion and Alignment in Modular GB1 Repeats. Related Articles NMR Studies on Domain Diffusion and Alignment in Modular GB1 Repeats. Biophys J. 2010 Oct 20;99(8):2636-46 Authors: Walsh JD, Meier K, Ishima R, Gronenborn AM Modular proteins contain individual domains that are often connected by flexible, unstructured linkers. Using a model system based on the GB1 domain, we constructed tandem repeat proteins and investigated the rotational diffusion and long-range angular ordering behavior of individual domains by measuring...	nmrlearner	Journal club	0	10-22-2010 06:02 AM

« Previous Thread | Next 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