Massimiliano Anselmi 1, Maurizio Brunori 1, Beatrice Vallone 1 and Alfredo Di Nola 1*
1 University of Rome
To whom correspondence should
be addressed. E-mail: dinola@caspur.it.
Submitted on October 17, 2006
Revised on November 15, 2006
Accepted
on 26 March 2007
Abstract
Globins are respiratory proteins that reversibly bind dioxygen and other small ligands at the iron of a heme prosthetic group. Hemoglobin (Hb) and myoglobin (Mb) are the most prominent members of this protein family. Unexpectedly few years ago a new member was discovered and called neuroglobin (Ngb) being predominantly expressed in the brain. Ngb is a single polypeptide of 151 amino acids and despite the small sequence similarity with other globins, it displays the typical globin fold. Oxygen, nitric oxide or carbon monoxide can displace the distal histidine which in ferrous Ngb is bound to the iron, yielding a reversible adduct. Recent crystallographic data on carboxy Ngb show that binding of an exogenous ligand (CO) is accompanied by structural changes involving heme sliding and a topological reorganization of the internal cavities; in particular the huge internal tunnel that connects the bulk with the active site (peculiar to Ngb) is heavily reorganized. We report the results of extended (90 ns) molecular dynamics simulations in water of ferrous deoxy and carboxy murine neuroglobin, which are both coordinated on the distal site, in the latter by CO and in the former one by His64(E7). The long time scale of the simulations allowed us to characterize the equilibrated protein dynamics and to compare protein structure and dynamical behaviour coupled to the binding of the exogenous ligand. We have characterized the heme sliding motion, the topological reorganization of the internal cavities, the dynamics of the distal histidine and the CD loop, showing a noticeable change in flexibility of the protein.
Key Words: cavities, hemeproteins, ligand binding, neuroprotection, protein conformation, structure