NMR paper Correlation between 2H NMR side-chain order parameters and sequence conservation in g

		BioNMR > Educational resources > Journal club
[NMR paper] Correlation between 2H NMR side-chain order parameters and sequence conservation in g

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

11-24-2010, 09:16 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,733

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

Correlation between 2H NMR side-chain order parameters and sequence conservation in g

Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins.

Related Articles Correlation between 2H NMR side-chain order parameters and sequence conservation in globular proteins.

J Am Chem Soc. 2003 Jul 30;125(30):9004-5

Authors: Mittermaier A, Davidson AR, Kay LE

Side-chain 2H NMR relaxation data have been collected for the SH3 domain from the Fyn tyrosine kinase and analyzed with respect to sequence preference and per-residue solvent accessibility. Residues that are highly preferred at a given position show a tendency to be less mobile than average with a coefficient of correlation that is greater than that obtained when side-chain flexibility and solvent accessibility are compared. The same trend is observed for five of six additional proteins considered. This provides evidence for the existence of conserved structural features other than hydrophobic burial that govern side-chain motions. Through examination of an SH3 domain structural alignment, we identify side-chain hydrogen bonding of threonine residues and a specific secondary structural element as potential determinants of protein internal dynamics.

PMID: 15369343 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy Estimating side-chain order in methyl-protonated, perdeuterated proteins via multiple-quantum relaxation violated coherence transfer NMR spectroscopy Abstract Relaxation violated coherence transfer NMR spectroscopy (Tugarinov et al. in J Am Chem Soc 129:1743â??1750, 2007) is an established experimental tool for quantitative estimation of the amplitudes of side-chain motions in methyl-protonated, highly deuterated proteins. Relaxation violated coherence transfer experiments monitor the build-up of methyl proton multiple-quantum coherences that can be created in magnetically equivalent...	nmrlearner	Journal club	0	02-11-2012 10:31 AM
[NMR paper] Determination of protein structures consistent with NMR order parameters. Determination of protein structures consistent with NMR order parameters. Related Articles Determination of protein structures consistent with NMR order parameters. J Am Chem Soc. 2004 Jul 7;126(26):8090-1 Authors: Best RB, Vendruscolo M Order parameters obtained from NMR experiments characterize distributions of bond vector orientations. Their interpretation, however, usually requires the assumption of a particular motional model. We propose a multiple-copy simulation method in which the experimental order parameters are used as restraints in...	nmrlearner	Journal club	0	11-24-2010 09:51 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] Contact model for the prediction of NMR N-H order parameters in globular proteins. Contact model for the prediction of NMR N-H order parameters in globular proteins. Related Articles Contact model for the prediction of NMR N-H order parameters in globular proteins. J Am Chem Soc. 2002 Oct 30;124(43):12654-5 Authors: Zhang F, Brüschweiler R An analytical relationship is presented for the estimation of NMR S2 order parameters of N-HN vectors of the protein backbone from high-resolution protein structures. The relationship solely depends on close contacts of the peptide plane to the rest of the protein. Application of the...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-label NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-labeled proteins. Related Articles NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-labeled proteins. J Biomol NMR. 2000 Aug;17(4):305-10 Authors: Liu A, Hu W, Majumdar A, Rosen MK, Patel DJ We describe the direct observation of side chain-side chain hydrogen bonding interactions in proteins with sensitivity-enhanced NMR spectroscopy. Specifically, the remote correlation between the guanidinium nitrogen 15Nepsilon of arginine 71,...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-cor A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk. Related Articles A study of protein side-chain dynamics from new 2H auto-correlation and 13C cross-correlation NMR experiments: application to the N-terminal SH3 domain from drk. J Mol Biol. 1998 Mar 13;276(5):939-54 Authors: Yang D, Mittermaier A, Mok YK, Kay LE Two new NMR experiments are presented for measuring side-chain dynamics in proteins. The first method, requiring 15N, 13C,...	nmrlearner	Journal club	0	11-17-2010 11:06 PM
[NMR paper] Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy. Protein Sci. 1995 May;4(5):936-44 Authors: Hammen PK, Scholtz...	nmrlearner	Journal club	0	08-22-2010 03:41 AM
Script to obtain order parameters from a structure A Python script for prediction of order paramter from a structure is available from this website. The script is based on the following paper F. Zhang and R. Brüschweiler (2002) "Contact Model for the Prediction of NMR N-H Order Parameters in Globular Proteins" J. Am. Chem. Soc. 124(43), 12654-12655.	nmrlearner	NMR dynamics	0	05-07-2005 09:21 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