NMR paper Mapping Molecular Perturbations by a New Form of Two-Dimensional Spectroscopy.

		BioNMR > Educational resources > Journal club
[NMR paper] Mapping Molecular Perturbations by a New Form of Two-Dimensional 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

12-12-2012, 01:44 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

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

Mapping Molecular Perturbations by a New Form of Two-Dimensional Spectroscopy.

From Mendeley Biomolecular NMR group:

Mapping Molecular Perturbations by a New Form of Two-Dimensional Spectroscopy.

Journal of the American Chemical Society (2012). Eriks Kupce, Ray Freeman et al.

We propose a new general form of two-dimensional spectroscopy where the indirect 'evolution' dimension is derived using the Radon transform. This idea is applicable to several types of spectroscopy but is illustrated here for the case of NMR. This 'projection spectroscopy' displays characteristic correlation peaks that highlight perturbations of chemical shifts caused by temperature, pressure, solvent, molecular binding, chemical exchange, hydrogen-bonding, pH variations, conformational changes, or paramagnetic agents. The result is displayed in a convenient format that allows the chemist to see all the chemical shift perturbations at a glance, and assess their rates of change and directions. As proof of principle, two simple practical examples are presented that display two-dimensional representations of the temperature and solvent effects on NMR spectra.

Published using Mendeley: Academic software for researchers

Read comments about this paper at Mendeley Biomolecular NMR group

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Mapping the Landscape of RNA Dynamics with NMR Spectroscopy. Mapping the Landscape of RNA Dynamics with NMR Spectroscopy. Mapping the Landscape of RNA Dynamics with NMR Spectroscopy. Acc Chem Res. 2011 Sep 6; Authors: Rinnenthal J, Buck J, Ferner J, Wacker A, Fu?rtig B, Schwalbe H Abstract Among the three major classes of biomacromolecules (DNA, RNA, and proteins) RNA's pronounced dynamics are the most explicitly linked to its wide variety of functions, which include catalysis and the regulation of transcription, translation, and splicing. These functions are mediated by a range of RNA...	nmrlearner	Journal club	0	09-08-2011 06:50 PM
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] 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] TIMP-1 contact sites and perturbations of stromelysin 1 mapped by NMR and a paramagne TIMP-1 contact sites and perturbations of stromelysin 1 mapped by NMR and a paramagnetic surface probe. Related Articles TIMP-1 contact sites and perturbations of stromelysin 1 mapped by NMR and a paramagnetic surface probe. Biochemistry. 1998 Jul 7;37(27):9650-7 Authors: Arumugam S, Hemme CL, Yoshida N, Suzuki K, Nagase H, Berjanskii M, Wu B, Van Doren SR Surfaces of the 173 residue catalytic domain of human matrix metalloproteinase 3 (MMP-3(DeltaC)) affected by binding of the N-terminal, 126 residue inhibitory domain of human TIMP-1...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy Abstract Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such transient intermediates in a number of protein-protein and protein-DNA complexes. Here we present an analysis of the recently published PRE NMR data for a protein complex of yeast...	nmrlearner	Journal club	0	11-06-2010 01:24 PM
Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. Mapping the encounter state of a transient protein complex by PRE NMR spectroscopy. J Biomol NMR. 2010 Nov 4; Authors: Volkov AN, Ubbink M, van Nuland NA Many biomolecular interactions proceed via a short-lived encounter state, consisting of multiple, lowly-populated species invisible to most experimental techniques. Recent development of paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance (NMR) spectroscopy has allowed to directly visualize such...	nmrlearner	Journal club	0	11-05-2010 10:01 AM
Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR) Mapping structural interactions using in-cell NMR spectroscopy (STINT-NMR) David S Burz, Kaushik Dutta, David Cowburn & Alexander Shekhtman We describe a high-throughput in-cell nuclear magnetic resonance (NMR)-based method for mapping the structural changes that accompany protein-protein interactions (STINT-NMR). The method entails sequentially expressing two (or more) proteins within a single bacterial cell in a time-controlled manner and monitoring the protein interactions using in-cell NMR spectroscopy. The resulting spectra provide a complete titration of the interaction and define...	sivanmr	Journal club	0	01-27-2006 11:26 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