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Biophysical Journal 84:3883-3893 (2003)
© 2003 The Biophysical Society

Molecular Dynamics Simulations of Lignin Peroxidase in Solution

M. Francesca Gerini *, Danilo Roccatano {dagger}, Enrico Baciocchi * and Alfredo Di Nola *

* Dipartimento di Chimica, Università degli Studi di Roma "La Sapienza," Rome, Italy; and {dagger} Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli Studi, L'Aquila, Italy

Correspondence: Address reprint requests to Danilo Roccatano, Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università degli Studi, v. Vetoio, 67010, L'Aquila, Italy. Fax: 39-086-243-3753; E-mail: roccata{at}caspur.it.

The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.




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