NMR paper Defining long range order in NMR structure determination from the dependence of heter

		BioNMR > Educational resources > Journal club
[NMR paper] Defining long range order in NMR structure determination from the dependence of heter

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

08-22-2010, 03:31 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

Defining long range order in NMR structure determination from the dependence of heter

Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.

Related Articles Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy.

Nat Struct Biol. 1997 Jun;4(6):443-9

Authors: Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM

Structure determination by NMR presently relies on short range restraints between atoms in close spatial proximity, principally in the form of short (< 5 A) interproton distances. In the case of modular or multidomain proteins and linear nucleic acids, the density of short interproton distance contacts between structural elements far apart in the sequence may be insufficient to define their relative orientations. In this paper we show how the dependence of heteronuclear longitudinal and transverse relaxation times on the rotational diffusion anisotropy of non-spherical molecules can be readily used to directly provide restraints for simulated annealing structure refinement that characterize long range order a priori. The method is demonstrated using the N-terminal domain of Enzyme I,a protein of 259 residues comprising two distinct domains with a diffusion anisotropy(Dparallel/Dperpendicular)of approximately 2.

PMID: 9187651 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Backbone assignment of perdeuterated proteins using long-range H/C-dipolar transfers Backbone assignment of perdeuterated proteins using long-range H/C-dipolar transfers Abstract For micro-crystalline proteins, solid-state nuclear magnetic resonance spectroscopy of perdeuterated samples can provide spectra of unprecedented quality. Apart from allowing to detect sparsely introduced protons and thereby increasing the effective resolution for a series of sophisticated techniques, deuteration can provide extraordinary coherence lifetimesâ??obtainable for all involved nuclei virtually without decoupling and enabling the use of scalar magnetization transfers. Unfortunately,...	nmrlearner	Journal club	0	12-17-2011 04:44 AM
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion. J Biomol NMR. 2011 May;50(1):59-70 Authors: Johnson E Abstract NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca(2+)-free) state of calbindin D(9k). Calculations are performed in an expanding reference frame so as to discriminate between the effects of...	nmrlearner	Journal club	0	08-20-2011 03:31 PM
NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion NMR order parameters calculated in an expanding reference frame: identifying sites of short- and long-range motion Abstract NMR order parameters are calculated from molecular dynamics computer simulations of ubiquitin and the apo (Ca2+-free) state of calbindin D9k. Calculations are performed in an expanding reference frame so as to discriminate between the effects of short- and long-range motions. This approach reveals that the dominant contributions to the order parameters are short-range. Longer-range contributions are limited to specific sites, many of which have been recognized in...	nmrlearner	Journal club	0	04-24-2011 03:40 AM
Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. Structure Calculation from Unambiguous Long-Range Amide and Methyl (1)H-(1)H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy. J Am Chem Soc. 2011 Mar 24; Authors: Linser R, Bardiaux B, Higman V, Fink U, Reif B Magic-angle spinning (MAS) solid-state NMR becomes an increasingly important tool for the determination of structures of membrane...	nmrlearner	Journal club	0	03-26-2011 07:00 PM
Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy Structure Calculation from Unambiguous Long-Range Amide and Methyl 1H-1H Distance Restraints for a Microcrystalline Protein with MAS Solid-State NMR Spectroscopy Rasmus Linser, Benjamin Bardiaux, Victoria Higman, Uwe Fink and Bernd Reif http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja110222h/aop/images/medium/ja-2010-10222h_0004.gif Journal of the American Chemical Society DOI: 10.1021/ja110222h http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA http://feeds.feedburner.com/~r/acs/jacsat/~4/Dh0EBf8PwcY	nmrlearner	Journal club	0	03-24-2011 08:02 PM
[NMR paper] Temperature dependence of NMR order parameters and protein dynamics. Temperature dependence of NMR order parameters and protein dynamics. Related Articles Temperature dependence of NMR order parameters and protein dynamics. J Am Chem Soc. 2003 Sep 17;125(37):11158-9 Authors: Massi F, Palmer AG The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
[NMR paper] De novo determination of protein structure by NMR using orientational and long-range De novo determination of protein structure by NMR using orientational and long-range order restraints. Related Articles De novo determination of protein structure by NMR using orientational and long-range order restraints. J Mol Biol. 2000 May 19;298(5):927-36 Authors: Hus JC, Marion D, Blackledge M Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from...	nmrlearner	Journal club	0	11-18-2010 09:15 PM
[NMR paper] Defining long range order in NMR structure determination from the dependence of heter Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Related Articles Defining long range order in NMR structure determination from the dependence of heteronuclear relaxation times on rotational diffusion anisotropy. Nat Struct Biol. 1997 Jun;4(6):443-9 Authors: Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM Structure determination by NMR presently relies on short range restraints between atoms in close spatial proximity, principally in the...	nmrlearner	Journal club	0	08-22-2010 03:03 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