BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search
Home Forums Wiki NMR feeds Downloads Register Today's Posts



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
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:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
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:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
 
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Old 12-31-2010, 08:38 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,697
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default RDC derived protein backbone resonance assignment using fragment assembly

RDC derived protein backbone resonance assignment using fragment assembly


Abstract Experimental residual dipolar couplings (RDCs) in combination with structural models have the potential for accelerating the protein backbone resonance assignment process because RDCs can be measured accurately and interpreted quantitatively. However, this application has been limited due to the need for very high-resolution structural templates. Here, we introduce a new approach to resonance assignment based on optimal agreement between the experimental and calculated RDCs from a structural template that contains all assignable residues. To overcome the inherent computational complexity of such a global search, we have adopted an efficient two-stage search algorithm and included connectivity data from conventional assignment experiments. In the first stage, a list of strings of resonances (CA-links) is generated via exhaustive searches for short segments of sequentially connected residues in a protein (local templates), and then ranked by the agreement of the experimental 13Cα chemical shifts and 15N-1H RDCs to the predicted values for each local template. In the second stage, the top CA-links for different local templates in stage I are combinatorially connected to produce CA-links for all assignable residues. The resulting CA-links are ranked for resonance assignment according to their measured RDCs and predicted values from a tertiary structure. Since the final RDC ranking of CA-links includes all assignable residues and the assignment is derived from a â??global minimumâ??, our approach is far less reliant on the quality of experimental data and structural templates. The present approach is validated with the assignments of several proteins, including a 42 kDa maltose binding protein (MBP) using RDCs and structural templates of varying quality. Since backbone resonance assignment is an essential first step for most of biomolecular NMR applications and is often a bottleneck for large systems, we expect that this new approach will improve the efficiency of the assignment process for small and medium size proteins and will extend the size limits assignable by current methods for proteins with structural models.

  • Content Type Journal Article
  • DOI 10.1007/s10858-010-9467-z
  • Authors
    • Xingsheng Wang, Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
    • Brian Tash, Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
    • John M. Flanagan, Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
    • Fang Tian, Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA


Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment
Combinatorial triple-selective labeling as a tool to assist membrane protein backbone resonance assignment Abstract Obtaining NMR assignments for slowly tumbling molecules such as detergent-solubilized membrane proteins is often compromised by low sensitivity as well as spectral overlap. Both problems can be addressed by amino-acid specific isotope labeling in conjunction with 15Nâ??1H correlation experiments. In this work an extended combinatorial selective in vitro labeling scheme is proposed that seeks to reduce the number of samples required for assignment. Including three...
nmrlearner Journal club 0 01-21-2012 06:26 PM
[NMR paper] Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone
Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Related Articles Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angew Chem Int Ed Engl. 2005 May 30;44(22):3394-9 Authors: Lange OF, Grubmüller H, de Groot BL
nmrlearner Journal club 0 11-25-2010 08:21 PM
[NMR paper] GANA--a genetic algorithm for NMR backbone resonance assignment.
GANA--a genetic algorithm for NMR backbone resonance assignment. Related Articles GANA--a genetic algorithm for NMR backbone resonance assignment. Nucleic Acids Res. 2005;33(14):4593-601 Authors: Lin HN, Wu KP, Chang JM, Sung TY, Hsu WL NMR data from different experiments often contain errors; thus, automated backbone resonance assignment is a very challenging issue. In this paper, we present a method called GANA that uses a genetic algorithm to automatically perform backbone resonance assignment with a high degree of precision and recall....
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR assignment of the Xenopus laevis prion protein fragment xlPrP (98-226).
NMR assignment of the Xenopus laevis prion protein fragment xlPrP (98-226). Related Articles NMR assignment of the Xenopus laevis prion protein fragment xlPrP (98-226). J Biomol NMR. 2005 Mar;31(3):260 Authors: Pérez DR, Wüthrich K
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] NMR assignment of the turtle prion protein fragment tPrP(121-225).
NMR assignment of the turtle prion protein fragment tPrP(121-225). Related Articles NMR assignment of the turtle prion protein fragment tPrP(121-225). J Biomol NMR. 2004 Sep;30(1):97 Authors: Calzolai L, Lysek DA, Wüthrich K
nmrlearner Journal club 0 11-24-2010 10:01 PM
[NMR paper] Simulated and NMR-derived backbone dynamics of a protein with significant flexibility
Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. Related Articles Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the betaARK1 PH domain. J Am Chem Soc. 2001 Apr 4;123(13):3021-36 Authors: Pfeiffer S, Fushman D, Cowburn D A 7.6 ns molecular dynamics trajectory of the betaARK1 PH domain in explicit water with appropriate ions was calculated at 300 K. Spectral densities...
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics
Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics of protein G B1 domain mutants. Related Articles Comparison of protein backbone entropy and beta-sheet stability: NMR-derived dynamics of protein G B1 domain mutants. J Am Chem Soc. 2001 Jan 10;123(1):185-6 Authors: Stone MJ, Gupta S, Snyder N, Regan L
nmrlearner Journal club 0 11-19-2010 08:32 PM
[NMR paper] Complete resonance assignment for the polypeptide backbone of interleukin 1 beta usin
Complete resonance assignment for the polypeptide backbone of interleukin 1 beta using three-dimensional heteronuclear NMR spectroscopy. Related Articles Complete resonance assignment for the polypeptide backbone of interleukin 1 beta using three-dimensional heteronuclear NMR spectroscopy. Biochemistry. 1990 Apr 10;29(14):3542-56 Authors: Driscoll PC, Clore GM, Marion D, Wingfield PT, Gronenborn AM The complete sequence-specific assignment of the 15N and 1H backbone resonances of the NMR spectrum of recombinant human interleukin 1 beta (153...
nmrlearner Journal club 0 08-21-2010 10:48 PM



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



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 12:17 PM.


Map