Journal
JOURNAL OF BIOMOLECULAR NMR
Volume 56, Issue 1, Pages 51-63Publisher
SPRINGER
DOI: 10.1007/s10858-013-9734-x
Keywords
Complexes; Interface; Water; Protein; DNA
Categories
Funding
- Dutch Foundation for Scientific Research (NWO) through a VICI Grant [700.56.442]
- WeNMR project (European FP7 e-Infrastructure grant) [261572]
- European Grid Initiative
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Interfacial water molecules play an important role in many aspects of protein-DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein-DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein-DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein-DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein-DNA complexes.
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