NMR paper Studying DNA-protein interactions using NMR.

		BioNMR > Educational resources > Journal club
[NMR paper] Studying DNA-protein interactions using 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

08-21-2010, 11:16 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

Studying DNA-protein interactions using NMR.

Studying DNA-protein interactions using NMR.

Related Articles Studying DNA-protein interactions using NMR.

Trends Biotechnol. 1991 Mar;9(3):96-104

Authors: Russu IM

NMR spectroscopy is emerging as a powerful tool in molecular biology and biotechnology; one aspect of which is the use of one- and two-dimensional NMR methodologies to investigate the interactions of proteins with DNA. The dynamic and structural information which NMR can provide, on the changes in conformation and molecular flexibility, complements X-ray crystallography data and enables mechanistic models of DNA-protein interactions to be formulated.

PMID: 1367095 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMR thesis] NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions Sun, Yun (1992) NMR Studies of Protein-DNA Interactions : Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions. Dissertation (Ph.D.), California Institute of Technology. http://resolver.caltech.edu/CaltechTHESIS:09132011-160134197 More...	nmrlearner	NMR theses	0	09-16-2011 10:02 PM
[NMR paper] Photo-CIDNP NMR methods for studying protein folding. Photo-CIDNP NMR methods for studying protein folding. Related Articles Photo-CIDNP NMR methods for studying protein folding. Methods. 2004 Sep;34(1):75-87 Authors: Mok KH, Hore PJ Chemically induced dynamic nuclear polarization (CIDNP) is a nuclear magnetic resonance phenomenon that can be used to probe the solvent-accessibility of tryptophan, tyrosine, and histidine residues in proteins by means of laser-induced photochemical reactions, resulting in significant enhancement of NMR signals. CIDNP offers good sensitivity as a surface probe of...	nmrlearner	Journal club	0	11-24-2010 10:01 PM
[NMR paper] NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabili NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes. Related Articles NMR structure of Desulfovibrio gigas rubredoxin: a model for studying protein stabilization by compatible solutes. Extremophiles. 2001 Oct;5(5):303-11 Authors: Lamosa P, Brennan L, Vis H, Turner DL, Santos H Rubredoxins are small, soluble proteins that display a wide variation in thermostability, despite having a high degree of sequence similarity They also vary in the extent to which they are stabilized by...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
Ph.D. student in solid-state NMR: Studying protein folding and assembly at atomic sca Ph.D. student in solid-state NMR: Studying protein folding and assembly at atomic scale Description of the Faculty / Research group The Faculty of Science consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Mathematics and Chemistry. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The NMR Research Group is part of the Chemistry Department (Universiteit Utrecht fac. Scheikunde) and belongs to the Bijvoet Center for Biomolecular...	markber	Job marketplace	0	09-11-2010 07:15 PM
The STINT-NMR Method for Studying In-cell Protein-Protein Interactions. The STINT-NMR Method for Studying In-cell Protein-Protein Interactions. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles The STINT-NMR Method for Studying In-cell Protein-Protein Interactions. Curr Protoc Protein Sci. 2010 Aug;Chapter 17:Unit17.11 Authors: Burz DS, Shekhtman A This unit describes critical components and considerations required to study protein-protein structural interactions inside a living cell by using NMR...	nmrlearner	Journal club	0	09-05-2010 05:53 AM
[NMR paper] Solid-state NMR approaches for studying membrane protein structure. Solid-state NMR approaches for studying membrane protein structure. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--arjournals.annualreviews.org-images-AnnualReviews100x25.gif Related Articles Solid-state NMR approaches for studying membrane protein structure. Annu Rev Biophys Biomol Struct. 1992;21:25-47 Authors: Smith SO, Peersen OB	nmrlearner	Journal club	0	08-21-2010 11:41 PM
Application of the random coil index to studying protein flexibility Application of the random coil index to studying protein flexibility Mark V. Berjanskii and David S. Wishart Journal of Biomolecular NMR; 2008; 40(1); pp 31-48 Abstract: Protein flexibility lies at the heart of many protein–ligand binding events and enzymatic activities. However, the experimental measurement of protein motions is often difficult, tedious and error-prone. As a result, there is a considerable interest in developing simpler and faster ways of quantifying protein flexibility. Recently, we described a method, called Random Coil Index (RCI), which appears to be able to...	matthias	Journal club	0	08-14-2008 01:03 AM
Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR/x-ray crystallography Spincore.com are advertising a postdoc NMR position. It sounds pretty interesting. """ Postdoctoral position to study Protein-Protein Interactions and their role in Mechanisms of Signal Transduction using protein solution NMR /x-ray crystallography Case Medical School, Cleveland, Ohio, USA How are signaling events transmitted from one protein to another? To answer this question we are looking to add a postdoctoral co-workers to our interdisciplinary team. Our interest is to understand protein-protein interactions, protein structure and dynamics in the context of cell signaling...	steveUK	Job marketplace	0	08-10-2008 02:37 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