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Papillomaviruses are small DNA tumor viruses that infect mammalian hosts, with consequences from benign to cancerous lesions. The Early pro-tein 2 is the master regulator for the virus life cycle, participating in gene transcription, DNA replication, and viral episome migration. | ỊFEBS Journal Molecular dynamics of the DNA-binding domain of the papillomavirus E2 transcriptional regulator uncover differential properties for DNA target accommodation M. Falconi1 A. Santolamazza1 T. Eliseo2 G. de Prat-Gay3 D. O. Cicero2 and A. Desideri1 1 Department of Biology and CIBB Centro Interdipartimentale di Biostatistica e Bioinformatica University of Rome Tor Vergata Italy 2 Department of Science and ChemicalTechnologies University of Rome Tor Vergata Italy 3 Instituto de Investigaciones Bioquimicas Fundacion Leloir Facultad de Ciencias Exactas y Naturales and CONICET Universidad de Buenos Aires Argentina Keywords molecular dynamics simulation papillomavirus protein-DNA recognition protein flexibility transcription factor Correspondence A. Desideri Department of Biology University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy Fax 39 06 202279 Tel 39 06 72594376 E-mail desideri@uniroma2.it Received 5 December 2006 revised 5 March 2007 accepted 7 March 2007 doi 10.1111 j.1742-4658.2007.05773.x Papillomaviruses are small DNA tumor viruses that infect mammalian hosts with consequences from benign to cancerous lesions. The Early protein 2 is the master regulator for the virus life cycle participating in gene transcription DNA replication and viral episome migration. All of these functions rely on primary target recognition by its dimeric DNA-binding domain. In this work we performed molecular dynamics simulations in order to gain insights into the structural dynamics of the DNA-binding domains of two prototypic strains human papillomavirus strain 16 and the bovine papillomavirus strain 1. The simulations underline different dynamic features in the two proteins. The human papillomavirus strain 16 domain displays a higher flexibility of the b2-b3 connecting loop in comparison with the bovine papillomavirus strain 1 domain with a consequent effect on the DNA-binding helices and thus on the modulation of DNA recognition. A compact b-barrel
