NMR paper Protein structural class identification directly from NMR spectra using averaged chem

		BioNMR > Educational resources > Journal club
[NMR paper] Protein structural class identification directly from NMR spectra using averaged chem

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: 23,732

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 class identification directly from NMR spectra using averaged chem

Protein structural class identification directly from NMR spectra using averaged chemical shifts.

Related Articles Protein structural class identification directly from NMR spectra using averaged chemical shifts.

Bioinformatics. 2003 Nov 1;19(16):2054-64

Authors: Mielke SP, Krishnan VV

Knowledge of the three-dimensional structure of proteins is integral to understanding their functions, and a necessity in the era of proteomics. A wide range of computational methods is employed to estimate the secondary, tertiary, and quaternary structures of proteins. Comprehensive experimental methods, on the other hand, are limited to nuclear magnetic resonance (NMR) and X-ray crystallography. The full characterization of individual structures, using either of these techniques, is extremely time intensive. The demands of high throughput proteomics necessitate the development of new, faster experimental methods for providing structural information. As a first step toward such a method, we explore the possibility of determining the structural classes of proteins directly from their NMR spectra, prior to resonance assignment, using averaged chemical shifts. This is achieved by correlating NMR-based information with empirical structure-based information available in widely used electronic databases. The results are analyzed statistically for their significance. The robustness of the method as a structure predictor is probed by applying it to a set of proteins of unknown structure. Our results show that this NMR-based method can be used as a low-resolution tool for protein structural class identification.

PMID: 14594710 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
[NMRpipe Yahoo group] Re: Baseline issues in directly detected proton dimension of 13C-HSQ Re: Baseline issues in directly detected proton dimension of 13C-HSQ Hi Justin, This sensitivity enhanced experiment usually achieves good water suppression, but you could try removing some of the water with a polynomial solvent More...	NMRpipe Yahoo group news	News from other NMR forums	0	07-13-2011 08:31 PM
Affymetrix launches NG Class detergents for better protein analysis - Pharmaceutical Business Review <img alt="" height="1" width="1" /> Affymetrix launches NG Class detergents for better protein analysis Pharmaceutical Business Review Affymetrix chief commercial officer Andy Last said the new NG Class Detergents give biologists enhanced tools to solve the structure of membrane proteins using advanced techniques, such as nuclear magnetic resonance and X-ray diffraction. ... and more » Affymetrix launches NG Class detergents for better protein analysis - Pharmaceutical Business Review More...	nmrlearner	Online News	0	02-15-2011 09:29 PM
[NMR paper] Signal identification in NMR spectra with coupled evolution periods. Signal identification in NMR spectra with coupled evolution periods. Related Articles Signal identification in NMR spectra with coupled evolution periods. J Magn Reson. 2005 Sep;176(1):47-53 Authors: Malmodin D, Billeter M Novel multidimensional NMR experiments rely on modified time-domain sampling schemes to provide significant savings of experimental time. Several approaches are based on the coupling of evolution times resulting in a reduction of the dimensionality of the recorded spectra, and a concomitant saving of experimental time. We...	nmrlearner	Journal club	0	12-01-2010 06:56 PM
[NMR paper] NMR identification of local structural preferences in HIV-1 protease tethered heterod NMR identification of local structural preferences in HIV-1 protease tethered heterodimer in 6 M guanidine hydrochloride. Related Articles NMR identification of local structural preferences in HIV-1 protease tethered heterodimer in 6 M guanidine hydrochloride. FEBS Lett. 2001 Dec 7;509(2):218-24 Authors: Bhavesh NS, Panchal SC, Mittal R, Hosur RV Understanding protein folding requires complete characterization of all the states of the protein present along the folding pathways. For this purpose nuclear magnetic resonance (NMR) has proved to be...	nmrlearner	Journal club	0	11-19-2010 08:44 PM
[NMR paper] NMR study on the interaction between MHC class I protein and its antigen peptide. NMR study on the interaction between MHC class I protein and its antigen peptide. Related Articles NMR study on the interaction between MHC class I protein and its antigen peptide. Biochem Biophys Res Commun. 2000 Nov 30;278(3):609-13 Authors: Nakagawa M, Chiba-Kamoshida K, Udaka K, Nakanishi H A major histcompatibility complex (MHC) class I protein H-2K(b) was expressed in a large scale as a fusion protein with thioredoxin and hexahistidine at the N-terminus to analyze the interaction with the antigen peptide SIYRYYGL. NMR spectra of the...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] Solid-state (13)C CP MAS NMR spectroscopy of mushrooms gives directly the ratio betwe Solid-state (13)C CP MAS NMR spectroscopy of mushrooms gives directly the ratio between proteins and polysaccharides. Related Articles Solid-state (13)C CP MAS NMR spectroscopy of mushrooms gives directly the ratio between proteins and polysaccharides. J Agric Food Chem. 2000 Nov;48(11):5484-8 Authors: Pizzoferrato L, Manzi P, Bertocchi F, Fanelli C, Rotilio G, Paci M The solid-state (13)C CP MAS NMR technique has the potential of monitoring the chemical composition in the solid state of an intact food sample. This property has been utilized...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles The CD4 determinant for downregulation by HIV-1 Nef directly binds to Nef. Mapping of the Nef binding surface by NMR. Biochemistry. 1996 Aug 13;35(32):10256-61 Authors: Grzesiek S, Stahl SJ, Wingfield PT, Bax A Using heteronuclear NMR spectroscopy, we demonstrate that a 13-residue peptide (MS-QIKRLLSEKKT) from the...	nmrlearner	Journal club	0	08-22-2010 02:20 PM
[NMR paper] 1H NMR sequential assignments and identification of secondary structural elements in 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Related Articles 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Biochemistry. 1992 Feb 25;31(7):1961-8 Authors: Ye XM, Pochapsky TC, Pochapsky SS Sequential 1H resonance assignments and secondary structural features of putidaredoxin (Pdx), a 106-residue globular protein consisting of...	nmrlearner	Journal club	0	08-21-2010 11:41 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