NMR paper Temperature as an extra dimension in multidimensional protein NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Temperature as an extra dimension in multidimensional protein 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

09-29-2020, 07:53 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,734

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

Temperature as an extra dimension in multidimensional protein NMR.

Temperature as an extra dimension in multidimensional protein NMR.

Related Articles Temperature as an extra dimension in multidimensional protein NMR.

Chemistry. 2020 Sep 28;:

Authors: Shchukina A, Ma?ecki P, Mateos B, Nowakowski M, Urba?czyk M, Kontaxis G, Kasprzak P, Conrad-Billroth C, Konrat R, Kazimierczuk K

Abstract
Nuclear magnetic resonance spectroscopy (NMR) is a particularly informative method for studying protein structure and dynamics in solution; however, it is also one of the most time-consuming. Modern approaches to biomolecular NMR are based on lengthy multidimensional (ND) experiments whose duration grows exponentially with the number of dimensions. The experimental time may even be several days in the case of 3D and 4D spectra. Moreover, the experiment often has to be repeated in several different conditions, for example in order to measure the temperature-dependent effects in a spectrum (temperature coefficients, TCs). In this paper we propose a new approach that involves joint sampling of indirect evolution times and temperature. This allows us to measure TCs with 3D spectra in even less time than is needed to acquire a single spectrum using the conventional approach. We propose two signal processing methods that are complementary in terms of sensitivity and resolution: a) dividing the data into overlapping subsets followed by compressed sensing reconstruction, and b) treating the complete data set with a variant of the Radon transform. The temperature-swept 3D HNCO spectra of two intrinsically disordered proteins---osteopontin and CD44 cytoplasmic tail---show that our new approach makes it possible to determine TCs and their non-linearities effectively. Non-linearities, which indicate the presence of a compact state, are particularly interesting. We provide the complete package of data acquisition and processing software for this new approach.

PMID: 32985764 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Journal Highlight: Extra-large NMR spectroscopy (XLSY) Journal Highlight: Extra-large NMR spectroscopy (XLSY) http://www.spectroscopynow.com/common/images/thumbnails/166119fe47b.jpgeXtra Large NMR SpectroscopY (XLSY) has been developed for experimental data collection, reconstruction and handling of very large NMR spectra by a combination of radial and non-uniform sampling, a new processing algorithm and rigorous statistical validation. Read the rest at Spectroscopynow.com	nmrlearner	General	0	11-25-2018 06:02 AM
Protein Crystallization & Crystallography Market Industry Growth, Drivers and Forecast by 2024 - Technology News Extra Protein Crystallization & Crystallography Market Industry Growth, Drivers and Forecast by 2024 - Technology News Extra http://www.bionmr.com//t2.gstatic.com/images?q=tbn:ANd9GcR4vJVO1a_RbefhgyTqFj9BeUMDv3U05lAyZVC_2i9Ucufx5MITigvkgBy5MypLkFdt8iDXjsBz Technology News Extra <img alt="" height="1" width="1"> Protein Crystallization & Crystallography Market Industry Growth, Drivers and Forecast by 2024 Technology News Extra Proteins are the natural macromolecules that are made of long chain of amino-acids. Crystallography and protein crystallization is the method for the making of small...	nmrlearner	Online News	0	02-20-2018 10:04 AM
Terrestrial NMR: Extra Terrestrial NMR: Extra http://www.spectroscopynow.com/common/images/thumbnails/14816471e2b.jpgThe Earth's magnetic field is strong enough for experiments in low-field NMR spectroscopy according to a research team from Lawrence Berkeley National Laboratory, which is developing the technique for analysis of fluids in situ in their native environments. Read the rest at Spectroscopynow.com	nmrlearner	General	0	09-01-2014 06:09 AM
Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control From The DNP-NMR Blog: Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control Sakaguchi, S., et al., Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2013. 317(0): p. 679-684. http://www.sciencedirect.com/science/article/pii/S0168583X13008872	nmrlearner	News from NMR blogs	0	01-23-2014 01:37 AM
Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control From The DNP-NMR Blog: Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control Sakaguchi, S., et al., Proton polarization in photo-excited aromatic molecule at room temperature enhanced by intense optical source and temperature control. Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, 2013(0). http://www.sciencedirect.com/science/article/pii/S0168583X13008872	nmrlearner	News from NMR blogs	0	11-21-2013 01:14 AM
Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins Werner Kremer, Martin Arnold, Claudia Elisabeth Munte, Rainer Hartl, Markus Beck Erlach, Joerg Koehler, Alexander Meier and Hans Robert Kalbitzer http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja2050698/aop/images/medium/ja-2011-050698_0003.gif Journal of the American Chemical Society DOI: 10.1021/ja2050698 http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/zlQj5rBkfDs	nmrlearner	Journal club	0	08-11-2011 02:24 AM
Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins. Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins. Pulsed Pressure Perturbations, an Extra Dimension in NMR Spectroscopy of Proteins. J Am Chem Soc. 2011 Jul 21; Authors: Kremer W, Arnold M, Munte CE, Hartl R, Beck Erlach M, Koehler J, Meier A, Kalbitzer HR The introduction of the multidimensional NMR spectroscopy was a breakthrough in biological NMR me-thodology since it allowed the unequivocal correlation of different spin states of the system. The introduction of large pressure perturbations in the corresponding...	nmrlearner	Journal club	0	07-23-2011 08:54 AM
[NMR paper] The detection of proline isomerase activity in FK506-binding protein by two-dimension The detection of proline isomerase activity in FK506-binding protein by two-dimensional 1H NMR exchange spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles The detection of proline isomerase activity in FK506-binding protein by two-dimensional 1H NMR exchange spectroscopy. Biochem Biophys Res Commun. 1990 Aug 31;171(1):445-50 Authors: Justice RM, Kline AD, Sluka JP, Roeder WD, Rodgers GH, Roehm N, Mynderse JS 1H NMR assignments of the trans and cis isomers of...	nmrlearner	Journal club	0	08-21-2010 11:04 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