NMR paper Refinement of the protein backbone angle psi in NMR structure calculations.

		BioNMR > Educational resources > Journal club
[NMR paper] Refinement of the protein backbone angle psi in NMR structure calculations.

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

11-18-2010, 09:15 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

Refinement of the protein backbone angle psi in NMR structure calculations.

Refinement of the protein backbone angle psi in NMR structure calculations.

Related Articles Refinement of the protein backbone angle psi in NMR structure calculations.

J Biomol NMR. 2000 Jan;16(1):47-58

Authors: Sprangers R, Bottomley MJ, Linge JP, Schultz J, Nilges M, Sattler M

Cross-correlated relaxation rates involving the Calpha-Halpha dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle psi can be directly refined against such cross-correlated relaxation rates (gammaHalphaCalpha,C') and the three-bond H/D isotope effect on the Calpha chemical shifts (3 deltaCalpha(ND)). By simultaneously using both experimental parameters as restraints during NMR structure calculations, a unique value for the backbone angle psi is defined. We have applied the new refinement method to the alpha-Spectrin SH3 domain (a beta-sheet protein) and to the Sgs1p HRDC domain (an alpha-helical protein) and show that the quality of the NMR structures is substantially improved, judging from the atomic coordinate precision and the Ramachandran map. In addition, the psi-refined NMR structures of the SH3 domain deviate less from the 1.8 A crystal structure, suggesting an improved accuracy. The proposed refinement method can be used to significantly improve the quality of NMR structures and will be applicable to larger proteins.

PMID: 10718612 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside...	nmrlearner	Journal club	0	09-26-2011 06:42 AM
High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data. J Biomol NMR. 2011 Sep 22; Authors: Tang M, Sperling LJ, Berthold DA, Schwieters CD, Nesbitt AE, Nieuwkoop AJ, Gennis RB, Rienstra CM Abstract X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular...	nmrlearner	Journal club	0	09-23-2011 05:30 PM
Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G Density functional calculations of backbone 15N shielding tensors in beta-sheet and turn residues of protein G Abstract We performed density functional calculations of backbone 15N shielding tensors in the regions of beta-sheet and turns of protein G. The calculations were carried out for all twenty-four beta-sheet residues and eight beta-turn residues in the protein GB3 and the results were compared with the available experimental data from solid-state and solution NMR measurements. Together with the alpha-helix data, our calculations cover 39 out of the 55 residues (or 71%) in GB3....	nmrlearner	Journal club	0	02-11-2011 08:36 PM
[NMR paper] A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations. Related Articles A protein backbone psi and phi angle dependence of 2J(N(i),C alpha(i-1)): the new NMR experiment and quantum chemical calculations. J Biomol NMR. 2005 Feb;31(2):87-95 Authors: Ko?mi?ski W, Zhukov I, Pecul M, Sadlej J A new pulse sequence exploiting double- and zero-quantum evolution of two-spin 15N-13C' coherence is proposed for the accurate measurements of 2J(N(i),C alpha(i-1)) coupling...	nmrlearner	Journal club	0	11-24-2010 11:14 PM
[NMR paper] Carbonyl CSA restraints from solution NMR for protein structure refinement. Carbonyl CSA restraints from solution NMR for protein structure refinement. Related Articles Carbonyl CSA restraints from solution NMR for protein structure refinement. J Am Chem Soc. 2001 Nov 7;123(44):11065-6 Authors: Lipsitz RS, Tjandra N	nmrlearner	Journal club	0	11-19-2010 08:44 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR. 1991 Nov;1(4):447-56 Authors: GÃ¼ntert P, WÃ¼thrich K A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...	nmrlearner	Journal club	0	08-21-2010 11:12 PM
[NMR paper] Improved efficiency of protein structure calculations from NMR data using the program Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. Related Articles Improved efficiency of protein structure calculations from NMR data using the program DIANA with redundant dihedral angle constraints. J Biomol NMR. 1991 Nov;1(4):447-56 Authors: GÃ¼ntert P, WÃ¼thrich K A new strategy for NMR structure calculations of proteins with the variable target function method (Braun, W. and Go, N. (1985) J. Mol. Biol., 186, 611) is described, which makes use of...	nmrlearner	Journal club	0	08-21-2010 11:12 PM
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints F. Gabel, B. Simon, M. Nilges, M. Petoukhov, D. Svergun and M. Sattler Journal of Biomolecular NMR; 2008; 41(4); pp 199-208 Abstract: We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313–327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC)...	Abe	Journal club	0	09-21-2008 11:30 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