NMR paper Protein structural motif recognition via NMR residual dipolar couplings.

		BioNMR > Educational resources > Journal club
[NMR paper] Protein structural motif recognition via NMR residual dipolar couplings.

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, 08:32 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

Protein structural motif recognition via NMR residual dipolar couplings.

Protein structural motif recognition via NMR residual dipolar couplings.

Related Articles Protein structural motif recognition via NMR residual dipolar couplings.

J Am Chem Soc. 2001 Feb 14;123(6):1222-9

Authors: Andrec M, Du P, Levy RM

NMR residual dipolar couplings have great potential to provide rapid structural information for proteins in the solution state. This information even at low resolution may be used to advantage in proteomics projects that seek to annotate large numbers of gene products for entire genomes. In this paper, we describe a novel approach to the structural interpretation of dipolar couplings which is based on structural motif pattern recognition, where a predefined gapless structural template for a motif is used to search a set of residual dipolar couplings for good matches. We demonstrate the applicability of the method using synthetic and experimental data. We also provide an analysis of the statistical power of the method and the effects of order tensor frame orientation, motif size, and structural complexity on motif detection. Finally, we discuss remaining problems that must be overcome before the method can be used routinely to identify protein homologies.

PMID: 11456677 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings. J Am Chem Soc. 2011 Apr 5; Authors: Sgourakis NG, Lange OF, Dimaio F, Andre? I, Fitzkee NC, Rossi P, Montelione GT, Bax A, Baker D Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR...	nmrlearner	Journal club	0	04-07-2011 09:54 PM
Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings Determination of the Structures of Symmetric Protein Oligomers from NMR Chemical Shifts and Residual Dipolar Couplings Nikolaos G. Sgourakis, Oliver F. Lange, Frank DiMaio, Ingemar Andre?, Nicholas C. Fitzkee, Paolo Rossi, Gaetano T. Montelione, Ad Bax and David Baker http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja111318m/aop/images/medium/ja-2010-11318m_0008.gif Journal of the American Chemical Society DOI: 10.1021/ja111318m http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA...	nmrlearner	Journal club	0	04-06-2011 10:54 AM
Residual dipolar couplings: are multiple independent alignments always possible? Residual dipolar couplings: are multiple independent alignments always possible? Abstract RDCs for the 14 kDa protein hen egg-white lysozyme (HEWL) have been measured in eight different alignment media. The elongated shape and strongly positively charged surface of HEWL appear to limit the protein to four main alignment orientations. Furthermore, low levels of alignment and the proteinâ??s interaction with some alignment media increases the experimental error. Together with heterogeneity across the alignment media arising from constraints on temperature, pH and ionic strength for some...	nmrlearner	Journal club	0	12-26-2010 04:43 AM
[NMR paper] Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Related Articles Various strategies of using residual dipolar couplings in NMR-driven protein docking: application to Lys48-linked di-ubiquitin and validation against 15N-relaxation data. Proteins. 2005 Aug 15;60(3):367-81 Authors: van Dijk AD, Fushman D, Bonvin AM When classical, Nuclear Overhauser Effect (NOE)-based approaches fail, it is possible, given high-resolution...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: ne Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. Related Articles Protein Backbone 1H(N)-13Calpha and 15N-13Calpha residual dipolar and J couplings: new constraints for NMR structure determination. J Am Chem Soc. 2004 May 26;126(20):6232-3 Authors: Ding K, Gronenborn AM A simple, sensitivity-enhanced experiment was devised for accurate measurement of backbone 15N-13Calpha and 1HN-13Calpha couplings in proteins. The measured residual dipolar couplings 2DHCA,...	nmrlearner	Journal club	0	11-24-2010 09:51 PM
[NMR paper] Residual dipolar couplings in NMR structure analysis. Residual dipolar couplings in NMR structure analysis. Related Articles Residual dipolar couplings in NMR structure analysis. Annu Rev Biophys Biomol Struct. 2004;33:387-413 Authors: Lipsitz RS, Tjandra N Residual dipolar couplings (RDCs) have recently emerged as a new tool in nuclear magnetic resonance (NMR) with which to study macromolecular structure and function in a solution environment. RDCs are complementary to the more conventional use of NOEs to provide structural information. While NOEs are local-distance restraints, RDCs provide...	nmrlearner	Journal club	0	11-24-2010 09:25 PM
[NMR paper] Detecting protein kinase recognition modes of calmodulin by residual dipolar coupling Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR. Related Articles Detecting protein kinase recognition modes of calmodulin by residual dipolar couplings in solution NMR. Biochemistry. 2002 Oct 29;41(43):12899-906 Authors: Mal TK, Skrynnikov NR, Yap KL, Kay LE, Ikura M Calmodulin-regulated serine/threonine kinases (CaM kinases) play crucial roles in Ca2+-dependent signaling transduction pathways in eukaryotes. Despite having a similar overall molecular architecture of catalytic and...	nmrlearner	Journal club	0	11-24-2010 08:58 PM
[NMR paper] Residual dipolar couplings: synergy between NMR and structural genomics. Residual dipolar couplings: synergy between NMR and structural genomics. Related Articles Residual dipolar couplings: synergy between NMR and structural genomics. J Biomol NMR. 2002 Jan;22(1):1-8 Authors: Al-Hashimi HM, Patel DJ Structural genomics is on a quest for the structure and function of a significant fraction of gene products. Current efforts are focusing on structure determination of single-domain proteins, which can readily be targeted by X-ray crystallography, NMR spectroscopy and computational homology modeling. However,...	nmrlearner	Journal club	0	11-24-2010 08:49 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