Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

		BioNMR > Educational resources > Journal club
Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

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

03-09-2012, 09:16 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

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Structure determination and dynamics of protein–RNA complexes by NMR spectroscopy

Publication year: 2011
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 58, Issues 1–2

Cyril Dominguez, Mario Schubert, Olivier Duss, Sapna Ravindranathan, Frédéric H.-T. Allain

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc. 2011 Feb;58(1-2):1-61 Authors: Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FH	nmrlearner	Journal club	0	01-19-2011 11:18 AM
[NMR paper] Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. Related Articles Determination of membrane protein structure and dynamics by magic-angle-spinning solid-state NMR spectroscopy. J Am Chem Soc. 2005 Sep 21;127(37):12965-74 Authors: Andronesi OC, Becker S, Seidel K, Heise H, Young HS, Baldus M It is shown that molecular structure and dynamics of a uniformly labeled membrane protein can be studied under magic-angle-spinning conditions. For this purpose, dipolar recoupling experiments...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Structure determination of protein/RNA complexes by NMR. Structure determination of protein/RNA complexes by NMR. Related Articles Structure determination of protein/RNA complexes by NMR. Methods Enzymol. 2005;394:525-45 Authors: Wu H, Finger LD, Feigon J Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Structure determination of protein complexes by NMR. Structure determination of protein complexes by NMR. Related Articles Structure determination of protein complexes by NMR. Methods Mol Biol. 2004;278:255-88 Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] NMR structure determination of proteins and protein complexes larger than 20 kDa. NMR structure determination of proteins and protein complexes larger than 20 kDa. Related Articles NMR structure determination of proteins and protein complexes larger than 20 kDa. Curr Opin Chem Biol. 1998 Oct;2(5):564-70 Authors: Clore GM, Gronenborn AM Recent advances in multidimensional nuclear magnetic resonance methodology to obtain 1H, 15N and 13C resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long-range order, coupled with new methods of structure refinement and novel methods...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy Publication year: 2010 Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 6 October 2010</br> Cyril, Dominguez , Mario, Schubert , Olivier, Duss , Sapna, Ravindranathan , Frédéric H.-T., Allain</br> More...	nmrlearner	Journal club	0	10-07-2010 02:32 PM
PCS-based structure determination of proteinâ??protein complexes Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 Ã?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure...	nmrlearner	Journal club	0	08-14-2010 04:19 AM
Structure Determination of Protein Complexes by NMR Structure Determination of Protein Complexes by NMR D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue The Department of Biochemistry, University of Cambridge Introduction As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...	timbo	Educational web pages	0	08-29-2008 02:43 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