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Protein Science (2001), 10:2131-2137.
Copyright © 2001 The Protein Society

FOR THE RECORD

A novel approach for assesing macromolecular complexes combining soft-docking calculations with NMR data

Xavier J. Morelli1, P. Nuno Palma2,3, Françoise Guerlesquin4 and Alan C. Rigby1

1 Division of Hemostasis and Thrombosis Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115, USA
2 Departamento de Quimica, Centro Quimica Fina e Biotecnologia, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2825–114 Monte de Caparica, Portugal
3 Instituto Superior de Ciências da Saúde-Sul, 2829–511 Monte de Caparica, Portugal
4 Laboratoire de Bioenergetique et Ingenierie des Proteines, Institut de Biologie Structurale et Microbiologie/CNRS, Marseille Cedex 20, France

Reprint requests to: Xavier J. Morelli, Beth Israel Deaconess Medical Center/Research East, P.O. 15732, Boston, MA 02215, USA; e-mail: xmorelli{at}caregroup.harvard.edu; fax: (617) 975-5505.

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.

Keywords: NMR; BiGGER; soft docking; protein complex; structure


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