NMR paper Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

		BioNMR > Educational resources > Journal club
[NMR paper] Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

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

11-28-2014, 11:37 AM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints.

J Biomol NMR. 2014 Nov 27;

Authors: Furuita K, Kataoka S, Sugiki T, Hattori Y, Kobayashi N, Ikegami T, Shiozaki K, Fujiwara T, Kojima C

Abstract
NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based procedures due to an insufficient number of NOE restraints. By using the 867 PRE-derived distance restraints obtained from the NOE-based structure determination procedure, a high-resolution structure of Sin1 could be successfully determined. The convergence and accuracy of the determined structure were improved by increasing the number of PRE-derived distance restraints. This study demonstrates that PRE-derived distance restraints are useful in the determination of a high-resolution structure of a soluble protein when the number of NOE constraints is insufficient.

PMID: 25428765 [PubMed - as supplied by publisher]

More...

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints Abstract NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based...	nmrlearner	Journal club	0	11-26-2014 10:50 PM
[NMR paper] Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. Related Articles Structure determination of protein-protein complexes with long-range anisotropic paramagnetic NMR restraints. Curr Opin Struct Biol. 2014 Feb;24C:45-53 Authors: Hass MA, Ubbink M Abstract Paramagnetic NMR spectroscopy has evolved rapidly in the last decade, and has shown to be a very useful tool for solving structures of protein-protein complexes. A major breakthrough has been the development of...	nmrlearner	Journal club	0	04-12-2014 06:36 PM
Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints Structure determination of protein–protein complexes with long-range anisotropic paramagnetic NMR restraints Publication date: February 2014 Source:Current Opinion in Structural Biology, Volume 24</br> Author(s): Mathias AS Hass , Marcellus Ubbink</br> Paramagnetic NMR spectroscopy has evolved rapidly in the last decade, and has shown to be a very useful tool for solving structures of protein–protein complexes. A major breakthrough has been the development of paramagnetic metal binding tags that can be attached specifically to the protein. These tags have greatly...	nmrlearner	Journal club	0	12-21-2013 03:15 PM
[NMR paper] Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Related Articles Efficient long-distance NMR-PRE and EPR-DEER restraints for two-domain protein structure determination. Protein Cell. 2013 Nov 27; Authors: Wu K, Shi C, Li J, Wang H, Shi P, Chen L, Wu F, Xiong Y, Tian C PMID: 24282082	nmrlearner	Journal club	0	11-28-2013 05:18 PM
Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. Impact of (15)N R(2)/R(1) Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints. J Am Chem Soc. 2011 Apr 4; Authors: Ryabov Y, Schwieters CD, Clore GM (15)N R(2)/R(1) relaxation data contain information on molecular shape and size as well as on bond vector orientations relative to...	nmrlearner	Journal club	0	04-06-2011 10:54 AM
Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Impact of 15N R2/R1 Relaxation Restraints on Molecular Size, Shape, and Bond Vector Orientation for NMR Protein Structure Determination with Sparse Distance Restraints Yaroslav Ryabov, Charles D. Schwieters and G. Marius Clore http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201020c/aop/images/medium/ja-2011-01020c_0002.gif Journal of the American Chemical Society DOI: 10.1021/ja201020c http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/3J1IyCLkQMQ	nmrlearner	Journal club	0	04-05-2011 10:37 AM
Distance restraints for structure determination Distance restraints for structure determination Experimentally derived parameters for protein structure determination, Part 1: nOe distance restraints. Lecture by Dr. Matthew Cordes from University of Arizona. More...	nmrlearner	General	0	08-16-2010 03:50 AM
Tunable paramagnetic relaxation enhancements by [Gd(DPA)3]3â?? for protein structure Abstract Paramagnetic relaxation enhancements (PRE) present a powerful source of structural information in nuclear magnetic resonance (NMR) studies of proteins and proteinâ??ligand complexes. In contrast to conventional PRE reagents that are covalently attached to the protein, the complex between gadolinium and three dipicolinic acid (DPA) molecules, 3â??, can bind to proteins in a non-covalent yet site-specific manner. This offers straightforward access to PREs that can be scaled by using different ratios of 3â?? to protein, allowing quantitative distance measurements for nuclear spins...	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