A novel approach for assessing macromolecular complexes combining soft-docking calculations with NMR data.
We present a novel and efficient approach for assessing protein-protein complex formation, which combines ab initio docking calculations performed with the protein docking algorithm BiGGER and chemical shift perturbation data collected with heteronuclear single quantum coherence (HSQC) or TROSY nuclear magnetic resonance (NMR) spectroscopy. This method, termed "restrained soft-docking," is validated for several known protein complexes. These data demonstrate that restrained soft-docking extends the size limitations of NMR spectroscopy and provides an alternative method for investigating macromolecular protein complexes that requires less experimental time, effort, and resources. The potential utility of this novel NMR and simulated docking approach in current structural genomic initiatives is discussed.
Morelli
X J
XJ
Division of Hemostasis and Thrombosis Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA. xmorelli@caregroup.harvard.edu
Palma
P N
PN
Guerlesquin
F
F
Rigby
A C
AC
D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System / Q000737:chemistry*; D011487:Protein Conformation; D012260:Ribonucleases / Q000737:chemistry
D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D046911:Macromolecular Substances; D010446:Peptide Fragments; C057438:barstar protein, Bacillus amyloliquefaciens; D010731:Phosphoenolpyruvate Sugar Phosphotransferase System; C030182:phosphocarrier protein HPr; C439615:EIN protein, E coli; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease