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 > Protein-ligand interactions
Advanced Search



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  
Unread 09-28-2006, 06:37 AM
administrator's Avatar
Junior Member
 
Join Date: Sep 2006
Posts: 11
Points: 172, Level: 3
Points: 172, Level: 3 Points: 172, Level: 3 Points: 172, Level: 3
Level up: 44%, 28 Points needed
Level up: 44% Level up: 44% Level up: 44%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 172
Downloads: 0
Uploads: 0
Default Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts

Structure Determination of Protein-Ligand Complexes by Transferred Paramagnetic Shifts
Michael John, Guido Pintacuda, Ah Young Park, Nicholas E. Dixon, and Gottfried Otting
J. Am. Chem. Soc.; 2006; 128(39) pp 12910 - 12916; (Article)


Abstract:

Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent 1H and 13C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit , and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.
Attached Images
File Type: gif ja063584zn00001.gif (25.5 KB, 50 views)
Reply With Quote

  #2  
Unread 03-30-2007, 03:03 PM
premprakash's Avatar
Junior Member
 
Join Date: Mar 2007
Posts: 7
Points: 24, Level: 1
Points: 24, Level: 1 Points: 24, Level: 1 Points: 24, Level: 1
Level up: 47%, 26 Points needed
Level up: 47% Level up: 47% Level up: 47%
Activity: 0%
Activity: 0% Activity: 0% Activity: 0%
NMR Credits: 0
NMR Points: 24
Downloads: 0
Uploads: 0
Default Re:

Hi!
Interesting work!
cheers
Prem Prakash Pathak
Reply With Quote
Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach. Methods Enzymol. 2011;493:241-75 Authors: Ziarek JJ, Peterson FC, Lytle BL, Volkman BF Over the last 15years, the role of NMR spectroscopy in the lead identification and optimization stages of pharmaceutical drug discovery has steadily increased. NMR occupies a unique niche in the biophysical analysis of drug-like...
nmrlearner Journal club 0 03-05-2011 01:02 PM
[NMR paper] Structure determination of protein/RNA complexes by NMR.
Structure determination of protein/RNA complexes by NMR. Related Articles Structure determination of protein/RNA complexes by NMR. Methods Enzymol. 2005;394:525-45 Authors: Wu H, Finger LD, Feigon J Structure determination of protein?RNA complexes in solution provides unique insights into factors that are involved in protein/RNA recognition. Here, we review the methodology used in our laboratory to overcome the challenges of protein?RNA structure determination by nuclear magnetic resonance (NMR). We use as two examples complexes recently...
nmrlearner Journal club 0 11-24-2010 11:14 PM
[NMR paper] Determination of the electron relaxation rates in paramagnetic metal complexes: appli
Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods. Related Articles Determination of the electron relaxation rates in paramagnetic metal complexes: applicability of available NMR methods. J Magn Reson. 2004 Apr;167(2):169-77 Authors: Jensen MR, Led JJ Four different approaches for determining the electron relaxation rates in paramagnetic metallo-proteins are investigated, using a paramagnetic Ni2+ complex of a protein as an example. All four approaches rely on the...
nmrlearner Journal club 0 11-24-2010 09:51 PM
[NMR paper] Structure determination of protein complexes by NMR.
Structure determination of protein complexes by NMR. Related Articles Structure determination of protein complexes by NMR. Methods Mol Biol. 2004;278:255-88 Authors: Nietlispach D, Mott HR, Stott KM, Nielsen PR, Thiru A, Laue ED This chapter describes nuclear magnetic resonance (NMR) methods that can be used to determine the structures of protein complexes. Many of these techniques are also applicable to other systems (e.g., protein-nucleic acid complexes). In the first section, we discuss methodologies for optimizing the sample conditions for...
nmrlearner Journal club 0 11-24-2010 09:25 PM
[NMR paper] NMR structure determination of proteins and protein complexes larger than 20 kDa.
NMR structure determination of proteins and protein complexes larger than 20 kDa. Related Articles NMR structure determination of proteins and protein complexes larger than 20 kDa. Curr Opin Chem Biol. 1998 Oct;2(5):564-70 Authors: Clore GM, Gronenborn AM Recent advances in multidimensional nuclear magnetic resonance methodology to obtain 1H, 15N and 13C resonance assignments, interproton distance and torsion angle restraints, and restraints that characterize long-range order, coupled with new methods of structure refinement and novel methods...
nmrlearner Journal club 0 11-17-2010 11:15 PM
[NMR paper] Protein structure refinement based on paramagnetic NMR shifts: applications to wild-t
Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c. 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 Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c. Protein Sci. 1995 Feb;4(2):296-305 ...
nmrlearner Journal club 0 08-22-2010 03:41 AM
PCS-based structure determination of protein‚??protein complexes
Abstract A simple and fast nuclear magnetic resonance method for docking proteins using pseudo-contact shift (PCS) and 1HN/15N chemical shift perturbation is presented. PCS is induced by a paramagnetic lanthanide ion that is attached to a target protein using a lanthanide binding peptide tag anchored at two points. PCS provides long-range (~40 √?) distance and angular restraints between the lanthanide ion and the observed nuclei, while the 1HN/15N chemical shift perturbation data provide loose contact-surface information. The usefulness of this method was demonstrated through the structure...
nmrlearner Journal club 0 08-14-2010 04:19 AM
Structure Determination of Protein Complexes by NMR
Structure Determination of Protein Complexes by NMR D. Nietlispach, H.R. Mott, K.M. Stott, P.R. Nielsen, A. Thiru & E.D. Laue The Department of Biochemistry, University of Cambridge Introduction As the structures of more proteins and domains are solved by structural genomics projects, the future of structural biology will be oriented more toward the study of macromolecular complexes. Since so many biological processes are mediated by interactions between proteins, it is important to study them at a molecular level. The study of protein-protein interactions also has applications in a...
timbo Educational web pages 0 08-29-2008 02:43 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This 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



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



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2017, 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 01:38 PM.


Map