NMR paper Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials.

		BioNMR > Educational resources > Journal club
[NMR paper] Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials.

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

06-02-2016, 02:54 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials.

Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials.

Related Articles Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials.

Prog Nucl Magn Reson Spectrosc. 2016 May;94-95:1-10

Authors: Barhoum S, Palit S, Yethiraj A

Abstract
Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments - in this article, we feature aqueous systems involving polymers, surfactants and proteins - the link between dynamics and size is harder to unpack due to macromolecular crowding and confinement. In this review, we demonstrate that the pulsed-field gradient NMR technique, with its spectral separation of different chemical components, is ideal for studying the dynamics of the entire system simultaneously and without labelling, in a wide range of systems. The simultaneous measurement of the dynamics of multiple components allows for internal consistency checks and enables quantitative statements about the link between macromolecular dynamics, size, complex formation and crowding in soft materials.

PMID: 27247282 [PubMed - in process]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials Diffusion NMR studies of macromolecular complex formation, crowding and confinement in soft materials Publication date: May 2016 Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volumes 94–95</br> Author(s): Suliman Barhoum, Swomitra Palit, Anand Yethiraj</br> Label-free methods to obtain hydrodynamic size from diffusion measurements are desirable in environments that contain multiple macromolecular species at a high total concentration: one example is the crowded cellular environment. In complex, multi-species macromolecular environments – in this...	nmrlearner	Journal club	0	04-09-2016 03:54 AM
Understanding macromolecular crowding is critical for quantitative cell biology - SPIE Newsroom http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcSFrZf31PUTVUTveakwA0E1nnJQ316UwMtUs4Y6ZDGqaBp0wkfIb8wo1Lsfi2ZHN1FLVa2FPOY SPIE Newsroom <img alt="" height="1" width="1"> Understanding macromolecular crowding is critical for quantitative cell biology SPIE Newsroom In the past, nuclear magnetic resonance (NMR) has been used to study protein-crowded environments and to investigate the translational and rotational diffusion of chymotrypsin inhibitor 2 in crowded environments. It was found that the heterogeneity of ... Understanding macromolecular crowding is critical for...	nmrlearner	Online News	0	12-15-2015 07:47 AM
Understanding macromolecular crowding is critical for quantitative cell biology - SPIE Newsroom http://www.bionmr.com//t1.gstatic.com/images?q=tbn:ANd9GcSFrZf31PUTVUTveakwA0E1nnJQ316UwMtUs4Y6ZDGqaBp0wkfIb8wo1Lsfi2ZHN1FLVa2FPOY SPIE Newsroom <img alt="" height="1" width="1"> Understanding macromolecular crowding is critical for quantitative cell biology SPIE Newsroom In the past, nuclear magnetic resonance (NMR) has been used to study protein-crowded environments and to investigate the translational and rotational diffusion of chymotrypsin inhibitor 2 in crowded environments. It was found that the heterogeneity of ... Understanding macromolecular crowding is critical for...	nmrlearner	Online News	0	12-12-2015 03:39 AM
[NMR paper] Role of hydrophobic interactions in the encounter complex formation of plastocyanin and cytochrome f complex revealed by paramagnetic NMR spectroscopy. Role of hydrophobic interactions in the encounter complex formation of plastocyanin and cytochrome f complex revealed by paramagnetic NMR spectroscopy. Role of hydrophobic interactions in the encounter complex formation of plastocyanin and cytochrome f complex revealed by paramagnetic NMR spectroscopy. J Am Chem Soc. 2013 Apr 29; Authors: Scanu S, Förster J, Ullmann GM, Ubbink M Abstract Protein complex formation is thought to be at least a two-step process, in which the active complex is preceded by the formation of an encounter complex....	nmrlearner	Journal club	0	05-01-2013 11:46 AM
Translational diffusion of macromolecular assemblies measured using transverse relaxation-optimized PFG-NMR. Translational diffusion of macromolecular assemblies measured using transverse relaxation-optimized PFG-NMR. Translational diffusion of macromolecular assemblies measured using transverse relaxation-optimized PFG-NMR. J Am Chem Soc. 2011 Sep 16; Authors: Horst R, Horwich AL, Wüthrich K Abstract ABSTRACT In structural biology, pulsed field gradient (PFG) NMR for characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution...	nmrlearner	Journal club	0	09-17-2011 08:21 PM
A natural and readily available crowding agent: NMR studies of proteins in hen egg white. A natural and readily available crowding agent: NMR studies of proteins in hen egg white. A natural and readily available crowding agent: NMR studies of proteins in hen egg white. Proteins. 2010 Dec 13; Authors: Martorell G, Adrover M, Kelly G, Temussi PA, Pastore A In vitro studies of biological macromolecules are usually performed in dilute, buffered solutions containing one or just a few different biological macromolecules. Under these conditions, the interactions among molecules are diffusion limited. On the contrary, in living systems,...	nmrlearner	Journal club	0	02-22-2011 10:40 PM
[NMR paper] Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method. Related Articles Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method. J Am Chem Soc. 2003 Mar 5;125(9):2541-5 Authors: Ferrage F, Zoonens M, Warschawski DE, Popot JL, Bodenhausen G The translational diffusion coefficient of an integral membrane protein/surfactant complex has been measured using a novel pulsed field gradient NMR method. In this new approach, the information about the localization of the molecules is...	nmrlearner	Journal club	0	11-24-2010 09:01 PM
[NMR paper] A novel approach for assessing macromolecular complexes combining soft-docking calcul A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data. Related Articles A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data. Protein Sci. 2001 Oct;10(10):2131-7 Authors: Morelli XJ, Palma PN, Guerlesquin F, Rigby AC We present a novel and efficient approach for assessing protein-protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data...	nmrlearner	Journal club	0	11-19-2010 08:44 PM

« 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