Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.

		BioNMR > Educational resources > Journal club
Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.

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

03-05-2011, 01:02 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,777

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

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 compounds because of its ability to identify binding sites, affinities, and ligand poses at the level of individual amino acids without necessarily solving the structure of the protein-ligand complex. However, it can also provide structures of flexible proteins and low-affinity (K(d)>10(-6)M) complexes, which often fail to crystallize. This chapter emphasizes a throughput-focused protocol that aims to identify practical aspects of binding site characterization, automated and semiautomated NMR assignment methods, and structure determination of protein-ligand complexes by NMR.

PMID: 21371594 [PubMed - in process]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release) Searching the protein structure database for ligand-binding site similarities ... - 7thSpace Interactive (press release) <img alt="" height="1" width="1" /> Searching the protein structure database for ligand-binding site similarities ... 7thSpace Interactive (press release) CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the ... Read here	nmrlearner	Online News	0	01-27-2011 04:31 AM
Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica. Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica. Site-specific free energy changes in proteins upon ligand binding by NMR: Ca(2+) -displacement by Ln(3+) in a Ca(2+) -binding protein from Entamoeba histolytica. Chem Biol Drug Des. 2011 Jan 14; Authors: Chandra K, Mustafi SM, Muthukumar S, Chary KV The study of protein-ligand interaction has been of a great interest in contemporary structural biology. The understanding of the nature...	nmrlearner	Journal club	0	01-18-2011 10:22 PM
[NMR paper] Determination of protein-ligand binding affinity by NMR: observations from serum albu Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems. Related Articles Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems. Magn Reson Chem. 2005 Jun;43(6):463-70 Authors: Fielding L, Rutherford S, Fletcher D The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the...	nmrlearner	Journal club	0	11-25-2010 08:21 PM
[NMR paper] Docking multiple conformations of a flexible ligand into a protein binding site using Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Related Articles Docking multiple conformations of a flexible ligand into a protein binding site using NMR restraints. Proteins. 2002 Feb 15;46(3):295-307 Authors: Zabell AP, Post CB A method is described for docking a large, flexible ligand using intra-ligand conformational restraints from exchange-transferred NOE (etNOE) data. Numerous conformations of the ligand are generated in isolation, and a subset of representative conformations is...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] Identification of the bile acid-binding site of the ileal lipid-binding protein by ph Identification of the bile acid-binding site of the ileal lipid-binding protein by photoaffinity labeling, matrix-assisted laser desorption ionization-mass spectrometry, and NMR structure. Related Articles Identification of the bile acid-binding site of the ileal lipid-binding protein by photoaffinity labeling, matrix-assisted laser desorption ionization-mass spectrometry, and NMR structure. J Biol Chem. 2001 Mar 9;276(10):7291-301 Authors: Kramer W, Sauber K, Baringhaus KH, Kurz M, Stengelin S, Lange G, Corsiero D, Girbig F, König W, Weyland C ...	nmrlearner	Journal club	0	11-19-2010 08:29 PM
[NMR paper] NMR structure determination of the binding site for ribosomal protein S8 from Escheri NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA. Related Articles NMR structure determination of the binding site for ribosomal protein S8 from Escherichia coli 16 S rRNA. J Mol Biol. 1998 Jul 24;280(4):639-54 Authors: Kalurachchi K, Nikonowicz EP Many cellular processes involve the preferential interaction of an RNA molecule with a specific protein. A detailed analysis of the individual protein and RNA components of these interactions can provide unique insights into the structural...	nmrlearner	Journal club	0	11-17-2010 11:15 PM
[NMR paper] An investigation of the ligand-binding site of the glutamine-binding protein of Esche An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Related Articles An investigation of the ligand-binding site of the glutamine-binding protein of Escherichia coli using rotational-echo double-resonance NMR. Biochemistry. 1994 Jul 26;33(29):8651-61 Authors: Hing AW, Tjandra N, Cottam PF, Schaefer J, Ho C Glutamine-binding protein (GlnBP) is an essential component of the glutamine transport system in Escherichia coli. Rotational-echo double-resonance...	nmrlearner	Journal club	0	08-22-2010 03:29 AM
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...	administrator	Protein-ligand interactions	1	03-30-2007 03:03 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