NMR paper NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by

		BioNMR > Educational resources > Journal club
[NMR paper] NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by

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

11-17-2010, 11:15 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

NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by

NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy.

Related Articles NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy.

Proc Natl Acad Sci U S A. 1998 Nov 24;95(24):14147-51

Authors: Pervushin K, Ono A, Fernández C, Szyperski T, Kainosho M, Wüthrich K

This paper describes the NMR observation of 15N---15N and 1H---15N scalar couplings across the hydrogen bonds in Watson-Crick base pairs in a DNA duplex, hJNN and hJHN. These couplings represent new parameters of interest for both structural studies of DNA and theoretical investigations into the nature of the hydrogen bonds. Two dimensional [15N,1H]-transverse relaxation-optimized spectroscopy (TROSY) with a 15N-labeled 14-mer DNA duplex was used to measure hJNN, which is in the range 6-7 Hz, and the two-dimensional hJNN-correlation-[15N,1H]-TROSY experiment was used to correlate the chemical shifts of pairs of hydrogen bond-related 15N spins and to observe, for the first time, hJHN scalar couplings, with values in the range 2-3.6 Hz. TROSY-based studies of scalar couplings across hydrogen bonds should be applicable for large molecular sizes, including protein-bound nucleic acids.

PMID: 9826668 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR paper] Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Related Articles Direct identification of NH...N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Nucleic Acids Res. 1999 Aug 1;27(15):3104-10 Authors: Wöhnert J, Dingley AJ, Stoldt M, Görlach M, Grzesiek S, Brown LR It is shown that the recently developed quantitative J(NN)HNN-COSY experiment can be used for the direct identification of hydrogen bonds in non-canonical base pairs in RNA. Scalar(2h)J(NN)couplings across...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
[NMR paper] Solution NMR characterization of hydrogen bonds in a protein by indirect measurement Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. J Magn Reson. 1997 Jul;127(1):54-64 Authors: Liwang AC, Bax A Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for...	nmrlearner	Journal club	0	08-22-2010 03:31 PM
[NMR paper] Solution NMR characterization of hydrogen bonds in a protein by indirect measurement Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Solution NMR characterization of hydrogen bonds in a protein by indirect measurement of deuterium quadrupole couplings. J Magn Reson. 1997 Jul;127(1):54-64 Authors: Liwang AC, Bax A Hydrogen bonds stabilize protein and nucleic acid structure, but little direct spectroscopic data have been available for...	nmrlearner	Journal club	0	08-22-2010 03:03 PM
[NMR paper] H NMR probes for inter-segmental hydrogen bonds in myoglobins. H NMR probes for inter-segmental hydrogen bonds in myoglobins. Related Articles H NMR probes for inter-segmental hydrogen bonds in myoglobins. J Biochem. 1996 Jul;120(1):126-32 Authors: Yamamoto Y NMR signals arising from the HisB5 N delta H and HisEF5 N epsilon H protons in sperm whale skeletal and horse heart myoglobins have been located for the first time in the downfield shifted portion of the spectra. The shifts and hydrogen exchange rates indicate that these His imidazole ring NH protons are involved in the inter-segmental hydrogen bonds...	nmrlearner	Journal club	0	08-22-2010 02:27 PM
[NMR paper] Transient hydrogen bonds identified on the surface of the NMR solution structure of H Transient hydrogen bonds identified on the surface of the NMR solution structure of Hirudin. Related Articles Transient hydrogen bonds identified on the surface of the NMR solution structure of Hirudin. Biochemistry. 1994 Aug 9;33(31):9303-10 Authors: Szyperski T, Antuch W, Schick M, Betz A, Stone SR, WÃ¼thrich K Recombinant desulfatohirudin retains largely the thrombin-inhibitory activity of natural hirudin from Hirudo medicinalis and causes at most minimal immune response in humans. With regard to potential pharmaceutical applications it is...	nmrlearner	Journal club	0	08-22-2010 03:29 AM
[NMR paper] Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Decreased imino proton exchange and base-pair opening in the IHF-DNA complex measured by NMR. J Mol Biol. 1999 May 14;288(4):659-71 Authors: Dhavan GM, Lapham J, Yang S, Crothers DM Integration Host Factor, IHF, is an E. coli DNA binding protein that imposes a substantial bend on DNA. Previous footprinting studies and bending...	nmrlearner	Journal club	0	08-21-2010 04:03 PM
MQ-HNCO-TROSY for the measurement of scalar and residual dipolar couplings in larger Abstract We describe a novel pulse sequence, MQ-HNCO-TROSY, for the measurement of scalar and residual dipolar couplings between amide proton and nitrogen in larger proteins. The experiment utilizes the whole 2TN polarization transfer delay for labeling of 15N chemical shift in a constant time manner, which efficiently doubles the attainable resolution in 15N dimension with respect to the conventional HNCO-TROSY experiment. In addition, the accordion principle is employed for measuring (J + D)NHs, and the multiplet components are selected with the generalized version of the TROSY scheme...	nmrlearner	Journal club	0	08-14-2010 04:19 AM
S3EPY: a Sparky extension for determination of small scalar couplings from spin-state Abstract S3EPY is a Python extension to the program Sparky written to facilitate the assessment of coupling constants from in-phase/antiphase and spin-state-selective excitation (S3E) experiments. It enables the routine use of small scalar couplings by automating the coupling evaluation procedure. S3EPY provides an integrated graphical user interface to programs which outputs graphs and the table of determined couplings. Content Type Journal Article DOI 10.1007/s10858-009-9392-1 Authors Petr NovÃ¡k, Masaryk University National Centre for Biomolecular Research, Faculty of Science...	nmrlearner	Journal club	0	08-14-2010 04:19 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