NMR paper Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

		BioNMR > Educational resources > Journal club
[NMR paper] Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

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:

View First Unread

Thread Tools

Search this Thread

Rate Thread

Display Modes

12-01-2010, 06:56 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,187

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 spectroscopy: folding and aggregation of domains in p53.

Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

Related Articles Diffusion NMR spectroscopy: folding and aggregation of domains in p53.

Chembiochem. 2005 Sep;6(9):1550-65

Authors: Dehner A, Kessler H

Protein interactions and aggregation phenomena are probably amongst the most ubiquitous types of interactions in biological systems; they play a key role in many cellular processes. The ability to identify weak intermolecular interactions is a unique feature of NMR spectroscopy. In recent years, pulsed-field gradient NMR spectroscopy has become a convenient method to study molecular diffusion in solution. Since the diffusion coefficient of a certain molecule under given conditions correlates with its effective molecular weight, size, and shape, it is evident that diffusion can be used to map intermolecular interactions or aggregation events. Complex models can be derived from comparison of experimental diffusion data with those predicted by hydrodynamic simulations. In this review, we will give an introduction to pulsed-field gradient NMR spectroscopy and the hydrodynamic properties of proteins and peptides. Furthermore, we show examples for applying these techniques to a helical peptide and its hydrophobic oligomerization, as well as to the dimerization behavior and folding of p53.

PMID: 16138303 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry Li Ion Diffusion in the Anode Material Li12Si7: Ultrafast Quasi-1D Diffusion and Two Distinct Fast 3D Jump Processes Separately Revealed by 7Li NMR Relaxometry Alexander Kuhn, Puravankara Sreeraj, Rainer Po?ttgen, Hans-Dieter Wiemho?fer, Martin Wilkening and Paul Heitjans http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2020108/aop/images/medium/ja-2011-020108_0005.gif Journal of the American Chemical Society DOI: 10.1021/ja2020108 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...	nmrlearner	Journal club	0	06-28-2011 04:32 AM
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy Abstract It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all detectable species. The analysis was carried out using experimental data obtained during aggregation of the 10.4 kDa Crh protein, which has been shown to involve a partially unfolded intermediate...	nmrlearner	Journal club	0	01-27-2011 04:31 AM
Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy. Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy. Kinetic analysis of protein aggregation monitored by real-time 2D solid-state NMR spectroscopy. J Biomol NMR. 2011 Jan 21; Authors: Etzkorn M, Böckmann A, Baldus M It is shown that real-time 2D solid-state NMR can be used to obtain kinetic and structural information about the process of protein aggregation. In addition to the incorporation of kinetic information involving intermediate states, this approach can offer atom-specific resolution for all...	nmrlearner	Journal club	0	01-22-2011 01:52 PM
Probing the micelle-bound aggregation-prone state of ?-synuclein with (19)F NMR spectroscopy. Probing the micelle-bound aggregation-prone state of ?-synuclein with (19)F NMR spectroscopy. Probing the micelle-bound aggregation-prone state of ?-synuclein with (19)F NMR spectroscopy. Chembiochem. 2010 Sep 24;11(14):1993-6 Authors: Wang GF, Li C, Pielak GJ	nmrlearner	Journal club	0	01-21-2011 01:22 AM
Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy. Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy. Observing selected domains in multi-domain proteins via sortase-mediated ligation and NMR spectroscopy. J Biomol NMR. 2010 Dec 29; Authors: Refaei MA, Combs A, Kojetin DJ, Cavanagh J, Caperelli C, Rance M, Sapitro J, Tsang P NMR spectroscopy has distinct advantages for providing insight into protein structures, but faces significant resolution challenges as protein size increases. To alleviate such resonance overlap issues, the ability to...	nmrlearner	Journal club	0	12-29-2010 04:04 PM
[NMR paper] (1)H/(15)N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamba (1)H/(15)N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamban reconstituted in dodecylphosphocholine micelles. Related Articles (1)H/(15)N heteronuclear NMR spectroscopy shows four dynamic domains for phospholamban reconstituted in dodecylphosphocholine micelles. Biophys J. 2004 Aug;87(2):1205-14 Authors: Metcalfe EE, Zamoon J, Thomas DD, Veglia G We report the backbone dynamics of monomeric phospholamban in dodecylphosphocholine micelles using (1)H/(15)N heteronuclear NMR spectroscopy. Phospholamban is a 52-amino acid...	nmrlearner	Journal club	0	11-24-2010 10:01 PM
[NMR paper] NMR spectroscopy reveals the solution dimerization interface of p53 core domains boun NMR spectroscopy reveals the solution dimerization interface of p53 core domains bound to their consensus DNA. Related Articles NMR spectroscopy reveals the solution dimerization interface of p53 core domains bound to their consensus DNA. J Biol Chem. 2001 Dec 28;276(52):49020-7 Authors: Klein C, Planker E, Diercks T, Kessler H, Künkele KP, Lang K, Hansen S, Schwaiger M The p53 protein is a transcription factor that acts as the major tumor suppressor in mammals. The core DNA-binding domain is mutated in about 50% of all human tumors. The...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
[NMR paper] Demonstration by NMR of folding domains in lysozyme. Demonstration by NMR of folding domains in lysozyme. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_nature.gif Related Articles Demonstration by NMR of folding domains in lysozyme. Nature. 1991 Feb 14;349(6310):633-6 Authors: Miranker A, Radford SE, Karplus M, Dobson CM Although there has been much speculation on the pathways of protein folding, only recently have experimental data on the topic been available. The study of proteins under conditions where species intermediate between the fully folded and...	nmrlearner	Journal club	0	08-21-2010 11:16 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