DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data

		BioNMR > Educational resources > Journal club
DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data

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

08-22-2012, 02:13 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,185

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

DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data

DEER-Stitch: Combining three- and four-pulse DEER measurements for high sensitivity, deadtime free data

Publication year: 2012
Source:Journal of Magnetic Resonance

J.E. Lovett, B.W. Lovett, J. Harmer

Over approximately the last fifteen years the electron paramagnetic resonance (EPR) technique of double electron electron resonance (DEER) has attracted considerable attention since it allows for the precise measurement of the dipole-dipole coupling between radicals and thus can lead to distance information between pairs of radicals separated by up to ca. 8 nm. The “deadtime free” 4-pulse DEER sequence is widely used but can suffer from poor sensitivity if the electron spin-echo decays too quickly to allow collection of a sufficiently long time trace. In this paper we present a method which takes advantage of the much greater sensitivity that the 3-pulse sequence offers over the 4-pulse sequence since the measured electron spin-echo intensity (for equal sequence lengths) is greater. By combining 3- and 4-pulse DEER time traces using a method coined DEER-Stitch (DEERS) accurate dipole-dipole coupling measurements can be made which combine the sensitivity of the 3-pulse DEER sequence with the deadtime free advantage of the 4-pulse DEER sequence. To develop the DEER-Stitch method three systems were measured: a semi-rigid bis-nitroxide labelled nanowire, the bis-nitroxide labelled protein CD55 with a distance between labels of almost 8 nm and a dimeric copper amine oxidase from Arthrobacter globiformis (AGAO).
Graphical abstract

Graphical abstract Highlights

? 2p primary echo in EPR is more intense that 3p refocused echo. ? The echo difference adversely effects 4p DEER compared to 3p DEER. ? 3p and 4p DEER time traces can be combined to give a good-signal-to-noise ratio deadtime free DEERS signal. ? DEERS applied to measure a nanowire, long distances and Cu-Cu coupling.

Source: Journal of Magnetic Resonance

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Orientation selective DEER measurements on vinculin tail at X-band frequencies reveal spin label orientations Orientation selective DEER measurements on vinculin tail at X-band frequencies reveal spin label orientations Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 216</br> Christoph Abé, Daniel Klose, Franziska Dietrich, Wolfgang H. Ziegler, Yevhen Polyhach, Gunnar Jeschke, Heinz-Jürgen Steinhoff</br> Double electron electron resonance (DEER) spectroscopy has been established as a valuable method to determine distances between spin labels bound to protein molecules. Caused by selective excitation of molecular orientations DEER primary data also...	nmrlearner	Journal club	0	03-13-2012 03:33 PM
Effect of freezing conditions on distances and their distributions derived from Double Electron Electron Resonance (DEER): A study of doubly-spin-labeled T4 lysozyme Effect of freezing conditions on distances and their distributions derived from Double Electron Electron Resonance (DEER): A study of doubly-spin-labeled T4 lysozyme Publication year: 2012 Source:Journal of Magnetic Resonance, Volume 216</br> Elka R. Georgieva, Aritro S. Roy, Vladimir M. Grigoryants, Petr P. Borbat, Keith A. Earle, Charles P. Scholes, Jack H. Freed</br> Pulsed dipolar ESR spectroscopy, DEER and DQC, require frozen samples. An important issue in the biological application of this technique is how the freezing rate and concentration of cryoprotectant...	nmrlearner	Journal club	0	03-13-2012 03:33 PM
Practical Aspects of High-Sensitivity MultidimensionalC MAS NMR Spectroscopy of Perdeuterated Proteins Practical Aspects of High-Sensitivity MultidimensionalC MAS NMR Spectroscopy of Perdeuterated Proteins Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 1 March 2012</br> ÜmitAkbey, Barth-Janvan Rossum, Hartmut*Oschkinat</br> Thedouble nucleus enhanced recoupling(DONER) experiment employs simultaneous irradiation of protons and deuterons to promote spin diffusion processes in a perdeuterated protein. This results in 4-5 times higher sensitivity in 2DC-C correlation experiments as compared to PDSD.Here, a quantitative comparison of PDSD,H-DARR,H-DARR,...	nmrlearner	Journal club	0	03-01-2012 11:03 PM
High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins Abstract Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using Î´ subunit (20 kDa) of Bacillus subtilis RNA polymerase...	nmrlearner	Journal club	0	02-21-2012 03:40 AM
Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme Effect of Freezing Conditions on Distances and Their Distributions Derived from Double Electron Electron Resonance (DEER): A Study of Doubly-Spin-Labeled T4 Lysozyme Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 24 January 2012</br> Elka R.Georgieva, Aritro S.Roy, Vladimir M.Grigoryants, Petr P.Borbat, Keith A.*Earle, ...</br> Pulsed dipolar ESR spectroscopy, DEER and DQC, require frozen samples. An important issue in the biological application of this technique is how the freezing rate and concentration of cryoprotectant could possibly affect the...	nmrlearner	Journal club	0	01-25-2012 08:56 AM
Orientation Selective DEER Measurements on Vinculin Tail at X-Band Frequencies Reveal Spin Label Orientations Orientation Selective DEER Measurements on Vinculin Tail at X-Band Frequencies Reveal Spin Label Orientations Publication year: 2012 Source: Journal of Magnetic Resonance, Available online 8 January 2012</br> ChristophAbé, DanielKlose, FranziskaDietrich, Wolfgang H.Ziegler, Yevhen*Polyhach, ...</br> Double electron electron resonance (DEER) spectroscopy has been established as a valuable method to determine distances between spin labels bound to protein molecules. Caused by selective excitation of molecular orientations DEER primary data also depend on the mutual orientation of...	nmrlearner	Journal club	0	01-10-2012 03:38 PM
DEER in Biological Multispin-Systems: A Case Study on the Fatty Acid Binding to Human Serum Albumin DEER in Biological Multispin-Systems: A Case Study on the Fatty Acid Binding to Human Serum Albumin Publication year: 2011 Source: Journal of Magnetic Resonance, In Press, Accepted Manuscript, Available online 10 March 2011</br> Matthias J.N., Junk , Hans W., Spiess , Dariush, Hinderberger</br> In this study, self-assembled systems of human serum albumin (HSA) and spin-labeled fatty acids are characterized by double electron–electron resonance (DEER). HSA, being the most important transport protein of the human blood, is capable to host up to seven paramagnetic fatty acid...	nmrlearner	Journal club	0	03-11-2011 05:00 PM
[NMR paper] High-sensitivity observation of dipolar exchange and NOEs between exchangeable proton High-sensitivity observation of dipolar exchange and NOEs between exchangeable protons in proteins by 3D solid-state NMR spectroscopy. Related Articles High-sensitivity observation of dipolar exchange and NOEs between exchangeable protons in proteins by 3D solid-state NMR spectroscopy. J Am Chem Soc. 2003 Nov 26;125(47):14222-3 Authors: Paulson EK, Morcombe CR, Gaponenko V, Dancheck B, Byrd RA, Zilm KW A highly sensitive new 1H-detected 3D solid-state NMR method is described for characterizing 1H-1H spin exchange in nanocrystalline samples of...	nmrlearner	Journal club	0	11-24-2010 09:16 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