NMR paper An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: applicati

		BioNMR > Educational resources > Journal club
[NMR paper] An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: applicati

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

11-19-2010, 08:44 PM

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

An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: applicati

An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: application to the 26-kDa dead ringer-DNA complex.

Related Articles An efficient NMR experiment for analyzing sugar-puckering in unlabeled DNA: application to the 26-kDa dead ringer-DNA complex.

J Magn Reson. 2001 Dec;153(2):262-6

Authors: Iwahara J, Wojciak JM, Clubb RT

We present a new NMR experiment for estimating the type and degree of sugar-puckering in high-molecular-weight unlabeled DNA molecules. The experiment consists of a NOESY sequence preceded by a constant-time scalar coupling period. Two subexperiments are compared, each differing in the amount of time the (3)J(H3'H2') and (3)J(H3'H2") couplings are active on the H3' magnetization. The resultant data are easy to analyze, since a comparison of the signal intensities of any resolved NOE cross peak originating from H3' atoms of the duplex can be used to estimate the sum of the (3)J(H3'H2') and (3)J(H3'H2") couplings and thus the puckering type of the deoxyribose ring. Isotope filters to eliminate signals of the (13)C-labeled component in the F1-dimension are implemented, facilitating analyses of high-molecular-weight protein-DNA complexes containing (13)C-labeled protein and unlabeled DNA. The utility of the experiment is demonstrated on the 26-kDa Dead Ringer protein-DNA complex and reveals that the DNA uniformly adopts the S-type configuration when bound to protein.

PMID: 11740904 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Bruker and Berkeley Lab Combine NMR with SAXS for Analyzing Large Protein ... - Genetic Engineering News http://nt1.ggpht.com/news/tbn/pbujffOLTN-5EM/6.jpg SunHerald.com <img alt="" height="1" width="1" /> Bruker and Berkeley Lab Combine NMR with SAXS for Analyzing Large Protein ... Genetic Engineering News Bruker and Lawrence Berkeley National Laboratory are collaborating to develop structural biology methods and tools that integrate small-angle x-ray scattering (SAXS) technology with nuclear magnetic resonance (NMR). The aim is to generate a set of data ... Bruker and Lawrence Berkeley National Laboratory Collaborate on Novel ...MarketWatch (press release) all 14 news articles »	nmrlearner	Online News	0	11-11-2011 08:26 AM
Bruker and Berkeley Lab Combine NMR with SAXS for Analyzing Large Protein ... - Genetic Engineering News Bruker and Berkeley Lab Combine NMR with SAXS for Analyzing Large Protein ... - Genetic Engineering News http://nt1.ggpht.com/news/tbn/pbujffOLTN-5EM/6.jpg SunHerald.com <img alt="" height="1" width="1" /> Bruker and Berkeley Lab Combine NMR with SAXS for Analyzing Large Protein ... Genetic Engineering News The aim is to generate a set of data analysis algorithms for determining the structures of larger, multi-domain proteins and protein complexes with DNA, RNA or other proteins. The organizations claim that combining the NMR-derived 3-dimensional atomic ... Bruker and Lawrence...	nmrlearner	Online News	0	11-10-2011 08:09 PM
[NMR paper] Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically l Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Related Articles Intein-based biosynthetic incorporation of unlabeled protein tags into isotopically labeled proteins for NMR studies. Nat Biotechnol. 2005 Jun;23(6):736-40 Authors: Züger S, Iwai H Segmental isotopic labeling of proteins using protein ligation is a recently established in vitro method for incorporating isotopes into one domain or region of a protein to reduce the complexity of NMR spectra, thereby facilitating...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Applicati High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Application to the study of trypsin-inhibitor complexes and trypsinogen activation by NMR spectroscopy. Related Articles High-level bacterial expression and 15N-alanine-labeling of bovine trypsin. Application to the study of trypsin-inhibitor complexes and trypsinogen activation by NMR spectroscopy. Biochemistry. 2001 May 29;40(21):6275-83 Authors: Peterson FC, Gordon NC, Gettins PG We describe here the high-level expression of bovine trypsinogen in E. coli, its...	nmrlearner	Journal club	0	11-19-2010 08:32 PM
[NMR paper] A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation da A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. Related Articles A simple approach to analyzing protein side-chain dynamics from 13C NMR relaxation data. J Magn Reson. 1998 Feb;130(2):329-34 Authors: Daragan VA, Mayo KH A simple approach to deriving motional dynamics information of protein and peptide side chains by using 13C NMR relaxation data is presented. By using linear approximation of internal rotational correlation functions, simple equations for relating side-chain conformation, bond rotational...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
[NMR software blog] Oh, Sugar Oh, Sugar I have good news! With a minimal simplification of my INADEQUATE filter I have been able to rescue the last cross-peak of cholesterol. It had been rejected because too near to the diagonal. I changed the code saying: "if it's on the diagonal, it is bad; if it's just near, let's accept it". So it is possible to have the perfect INADEQUATE of cholesterol, with all the expected cross-peaks IN and everything else OUT. Yesterday I received another INADEQUATE spectrum, this time of sucrose. The S/N is still high enough to make my filter unnecessary. If I play with the contour plot all...	nmrlearner	News from NMR blogs	0	09-03-2010 04:16 PM
[NMR paper] Defining the precision with which a protein structure is determined by NMR. Applicati Defining the precision with which a protein structure is determined by NMR. Application to motilin. Related Articles Defining the precision with which a protein structure is determined by NMR. Application to motilin. Biochemistry. 1993 Feb 16;32(6):1610-7 Authors: Shriver J, Edmondson S A simple procedure is introduced for accurately defining the precision with which the Cartesian coordinates of any macromolecular structure are determined by nuclear Overhauser data. The method utilizes an ensemble of structures obtained from an array of...	nmrlearner	Journal club	0	08-21-2010 11:53 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