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Protein Engineering, Vol. 14, No. 4, 233-243, April 2001
© 2001 Oxford University Press

Modeling multi-component protein–DNA complexes: the role of bending and dimerization in the complex of p53 dimers with DNA

Anne Lebrun1,2, Richard Lavery2 and Harel Weinstein1

1 Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA and 2 Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico-Chimique,13 rue Pierre et Marie Curie, 75005 Paris, France

We used molecular modeling to study the optimal conformation of the complex between two p53 DNA-binding domain monomers and a 12 base-pair target DNA sequence. The complex was constructed using experimental data on the monomer binding conformation and a new approach to deform the target DNA sequence. Combined with an internal/helicoidal coordinate model of DNA, this approach enables us to bend the target sequence in a controlled way while respecting the contacts formed with each p53 monomer. The results show that the dimeric complex favors DNA bending towards the major groove at the dimer junction by a value close to experimental findings. In contrast to inferences from earlier models, the calculation of key contributions to the free energy of the complexes indicates a determinant role for DNA in the formation of the complex with the dimer of the p53 DNA-binding domains.


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