Molecular dynamics simulations of metalloproteins

Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations

“…As expected and as already discussed elsewhere (Banci, 2003), a sizeable amount of charge is redistributed from the metal to the ligand shell. In this study we investigate proteins containing Zn, Mn, and Mg ions.…”

“…Classical force field molecular dynamics (MD) can be extremely helpful in shedding light at the molecular role of metal ions in membrane translocation, protein structural flexibility, functional activation, and ligand binding (Baik et al, 2003;Banci, 2003;Nordlund et al, 1995). They can also provide an efficient tool to further relax frustrations in NMR structures of metalloproteins (where metals are silent).…”

“…Furthermore, a non-bonded approach is needed for de novo designed bioinorganic protein complexes. Although MD has been a powerful tool for exploring the dynamical properties of protein complexes in the past three decades, the description of the interactions of metal ions with the protein skeleton is still challenging (Banci, 2003).…”

“…(i) A quantum mechanical description provides complete flexibility but is prohibitive for computational tasks such as calculating substrate binding affinities, refining NMR structures, or simulating large-scale motions. Conversely, (ii) bonded models (Banci, 2003)-that preserve the integrity of the active site by treating all metal-ligand interactions as non-dissociable bonds-are computationally efficient, but prevent any ligand insertion, substitution, or permutation. They only allow small deviations from the original coordination structure, and are especially limiting for the flexible catalytic sites of zinc enzymes (Harding, 2000).…”

Computational approaches to structural and functional analysis of plastocyanin and other blue copper proteins

“…The papers related to these topics and published in the period from 2000 to early 2003 are analyzed in detail, but previous works are also briefly reported where relevant. This review is complementary to several recent reviews which deal with electron transfer and association in redox proteins, either by discussing the experimental and theoretical perspectives [1 -3], or by pointing out recent computational developments [4,5]. Redox reactions are amongst the simplest chemical reactions and play a primary role in biology.…”