Probing an Ancient Protein's Dynamics with NMR

		BioNMR > Educational resources > Journal club
Probing an Ancient Protein's Dynamics with NMR

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

01-29-2014, 12:50 AM

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

Probing an Ancient Protein's Dynamics with NMR

Probing an Ancient Protein's Dynamics with NMR

Publication date: 28 January 2014
Source:Biophysical Journal, Volume 106, Issue 2, Supplement 1

Author(s): Marc S. Hoemberger , Christopher G. Wilson , Dorothee Kern

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Probing Arginine Side-Chains and Their Dynamics with Carbon-Detected NMR Spectroscopy: Application to the 42 kDa Human Histone Deacetylase 8 at High pH From Mendeley Biomolecular NMR group: Probing Arginine Side-Chains and Their Dynamics with Carbon-Detected NMR Spectroscopy: Application to the 42 kDa Human Histone Deacetylase 8 at High pH Angewandte Chemie International Edition (2013). Pages: n/a-n/a. Nicolas D. Werbeck, John Kirkpatrick, D. Flemming Hansen et al. Published using Mendeley: The library management tool for researchers	nmrlearner	Journal club	0	04-11-2013 03:08 PM
[NMR paper] Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy. Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy. Probing Structure and Dynamics of Protein Assemblies by Magic Angle Spinning NMR Spectroscopy. Acc Chem Res. 2013 Feb 13; Authors: Yan S, Suiter CL, Hou G, Zhang H, Polenova T Abstract In living organisms, biological molecules often organize into multicomponent complexes. Such assemblies consist of various proteins and carry out essential functions, ranging from cell division, transport, and energy transduction to catalysis, signaling, and viral...	nmrlearner	Journal club	0	02-14-2013 02:37 PM
Probing Protein Side Chain Dynamics via (13)C NMR Relaxation. Probing Protein Side Chain Dynamics via (13)C NMR Relaxation. Probing Protein Side Chain Dynamics via (13)C NMR Relaxation. Protein Pept Lett. 2011 Jan 11; Authors: Yang D Protein side chain dynamics is associated with protein stability, folding, and intermolecular interactions. Detailed dynamics information is crucial for the understanding of protein function and biochemical and biophysical properties, which can be obtained using NMR relaxation techniques. In this review, (13)C relaxation of methine, methylene and methyl groups with and without...	nmrlearner	Journal club	0	01-13-2011 12:00 PM
[NMR paper] Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Related Articles Probing conformational disorder in neurotensin by two-dimensional solid-state NMR and comparison to molecular dynamics simulations. Biophys J. 2005 Sep;89(3):2113-20 Authors: Heise H, Luca S, de Groot BL, Grubmüller H, Baldus M An approach is introduced to characterize conformational ensembles of intrinsically unstructured peptides on the atomic level using two-dimensional solid-state NMR data and...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Probing side-chain dynamics in high molecular weight proteins by deuterium NMR spin r Probing side-chain dynamics in high molecular weight proteins by deuterium NMR spin relaxation: an application to an 82-kDa enzyme. Related Articles Probing side-chain dynamics in high molecular weight proteins by deuterium NMR spin relaxation: an application to an 82-kDa enzyme. J Am Chem Soc. 2005 Jun 8;127(22):8214-25 Authors: Tugarinov V, Ollerenshaw JE, Kay LE New NMR experiments for the measurement of side-chain dynamics in high molecular weight ( approximately 100 kDa) proteins are presented. The experiments quantify (2)H spin...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Probing the backbone dynamics of oxidized and reduced rat microsomal cytochrome b5 vi Probing the backbone dynamics of oxidized and reduced rat microsomal cytochrome b5 via 15N rotating frame NMR relaxation measurements: biological implications. Related Articles Probing the backbone dynamics of oxidized and reduced rat microsomal cytochrome b5 via 15N rotating frame NMR relaxation measurements: biological implications. Biochemistry. 1998 Sep 1;37(35):12320-30 Authors: Banci L, Bertini I, Cavazza C, Felli IC, Koulougliotis D Rotating frame 15N relaxation NMR experiments have been performed to study the local mobility of the...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
Probing Microsecond Time Scale Dynamics in Proteins by Methyl 1H Carr-Purcell-Meiboom Probing Microsecond Time Scale Dynamics in Proteins by Methyl 1H Carr-Purcell-Meiboom-Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrCr Renee Otten, Janice Villali, Dorothee Kern and Frans A. A. Mulder http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja107410x/aop/images/medium/ja-2010-07410x_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja107410x http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/aNQDkVtDj-4	nmrlearner	Journal club	0	11-17-2010 06:08 PM
Probing Microsecond Time Scale Dynamics in Proteins by Methyl (1)H Carr-Purcell-Meibo Probing Microsecond Time Scale Dynamics in Proteins by Methyl (1)H Carr-Purcell-Meiboom-Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrC(r). Probing Microsecond Time Scale Dynamics in Proteins by Methyl (1)H Carr-Purcell-Meiboom-Gill Relaxation Dispersion NMR Measurements. Application to Activation of the Signaling Protein NtrC(r). J Am Chem Soc. 2010 Nov 8; Authors: Otten R, Villali J, Kern D, Mulder FA To study microsecond processes by relaxation dispersion NMR spectroscopy, low power...	nmrlearner	Journal club	0	11-10-2010 02:29 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