NMR paper Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

		BioNMR > Educational resources > Journal club
[NMR paper] Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

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

08-28-2016, 11:03 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,715

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

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS.

Proc Natl Acad Sci U S A. 2016 Aug 26;

Authors: Aznauryan M, Delgado L, Soranno A, Nettels D, Huang JR, Labhardt AM, Grzesiek S, Schuler B

Abstract
The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large group of intrinsically disordered proteins. However, the detailed structural and dynamical characterization of these highly dynamic and conformationally heterogeneous ensembles has remained challenging. Here we combine and compare three of the leading techniques for the investigation of unfolded proteins, NMR spectroscopy (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET), with the goal of quantitatively testing their consistency and complementarity and for obtaining a comprehensive view of the unfolded-state ensemble. Using unfolded ubiquitin as a test case, we find that its average dimensions derived from FRET and from structural ensembles calculated using the program X-PLOR-NIH based on NMR and SAXS restraints agree remarkably well; even the shapes of the underlying intramolecular distance distributions are in good agreement, attesting to the reliability of the approaches. The NMR-based results provide a highly sensitive way of quantifying residual structure in the unfolded state. FRET-based nanosecond fluorescence correlation spectroscopy allows long-range distances and chain dynamics to be probed in a time range inaccessible by NMR. The combined techniques thus provide a way of optimally using the complementarity of the available methods for a quantitative structural and dynamical description of unfolded proteins both at the global and the local level.

PMID: 27566405 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Dynamical and Structural Alterations withing Lipid-Protein Assemblies Control Apoptotic Pore Formation - A Solid State NMR Study Dynamical and Structural Alterations withing Lipid-Protein Assemblies Control Apoptotic Pore Formation - A Solid State NMR Study Publication date: 16 February 2016 Source:Biophysical Journal, Volume 110, Issue 3, Supplement 1</br> Author(s): Artur P.G. Dingeldein, Martin Lidman, Tobias Sparrman, Gerhard Gröbner</br> </br></br> </br></br> More...	nmrlearner	Journal club	0	02-17-2016 07:50 PM
[NMR paper] Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.plosone.org-images-pone_120x30.png Related Articles Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. PLoS One. 2015;10(8):e0135455 Authors: Choudhury AR, Sikorska E, van den Boom J, Bayer P, Popenda ?, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novi? M Abstract We present a 3D model of the four...	nmrlearner	Journal club	0	08-22-2015 11:20 AM
[NMR paper] Gradual Disordering of the Native State on a Slow Two-State Folding Protein Monitored by Single-Molecule Fluorescence Spectroscopy and NMR. Gradual Disordering of the Native State on a Slow Two-State Folding Protein Monitored by Single-Molecule Fluorescence Spectroscopy and NMR. Gradual Disordering of the Native State on a Slow Two-State Folding Protein Monitored by Single-Molecule Fluorescence Spectroscopy and NMR. J Phys Chem B. 2013 Jun 24; Authors: Campos LA, Sadqi M, Liu J, Wang X, English DS, Munoz V Abstract Theory predicts that folding free energy landscapes are intrinsically malleable, and as such are expected to respond to perturbations in topographically complex...	nmrlearner	Journal club	0	06-27-2013 01:52 AM
Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly. Sci China Life Sci. 2011 Feb;54(2):101-11 Authors: Feng W, Pan L, Zhang M NMR spectroscopy and X-ray crystallography are two premium methods for determining the atomic structures of macro-biomolecular complexes. Each method has unique strengths and...	nmrlearner	Journal club	0	02-15-2011 07:17 PM
Comprehensive determination of 3JHNHÎ± for unfolded proteins using 13Câ?²-resolved spin-echo difference spectroscopy Comprehensive determination of 3JHNHÎ± for unfolded proteins using 13Câ?²-resolved spin-echo difference spectroscopy Abstract An experiment is presented to determine 3JHNHÎ± coupling constants, with significant advantages for applications to unfolded proteins. The determination of coupling constants for the peptide chain using 1D 1H, or 2D and 3D 1H-15N correlation spectroscopy is often hampered by extensive resonance overlap when dealing with flexible, disordered proteins. In the experiment detailed here, the overlap problem is largely circumvented by recording 1H-13Câ?² correlation...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] Measurement of long-range cross-correlation rates using a combination of single- and Measurement of long-range cross-correlation rates using a combination of single- and multiple-quantum NMR spectroscopy in one experiment. Related Articles Measurement of long-range cross-correlation rates using a combination of single- and multiple-quantum NMR spectroscopy in one experiment. J Am Chem Soc. 2002 Apr 17;124(15):4050-7 Authors: Fruh D, Chiarparin E, Pelupessy P, Bodenhausen G A method is described to determine long-range cross-correlations between the modulations of an anisotropic chemical shift (e.g., of a C' carbonyl carbon in...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR expe Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Structural and dynamical properties of a denatured protein. Heteronuclear 3D NMR experiments and theoretical simulations of lysozyme in 8 M urea. Biochemistry. 1997 Jul 22;36(29):8977-91 Authors: Schwalbe H, Fiebig KM, Buck M, Jones JA, Grimshaw SB, Spencer A, Glaser SJ, Smith LJ, Dobson CM ...	nmrlearner	Journal club	0	08-22-2010 05:08 PM
Solid-State NMR Reveals Structural and Dynamical Properties of a Membrane Protein http://pubs.acs.org/cgi-bin/abstract.cgi/jacsat/2007/129/i21/abs/ja069028m.html Solid-State NMR Reveals Structural and Dynamical Properties of a Membrane-Anchored Electron-Carrier Protein, Cytochrome b<sub>5</sub> <aui auinm="Durr, U. H. N."> <aui auinm="Yamamoto, K."> <aui auinm="Im, S.-C."> <aui auinm="Waskell, L."> <aui auinm="Ramamoorthy, A."> <aug><aul></aul></aug></aui></aui></aui></aui></aui> <au>Ulrich H. N. Dürr,</au> <au>Kazutoshi Yamamoto,</au><au>Sang-Choul Im,</au><au>Lucy Waskell,and </au><au>Ayyalusamy Ramamoorthy</au> ramamoor@umich.edu <aff></aff> ...	sivanmr	Solid-state high-res. NMR	2	05-30-2007 12:54 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