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Application of Molecular Dynamics to the Investigation of Metalloproteins Involved in Metal Homeostasis
Author(s) -
Sala Davide,
Musiani Francesco,
Rosato Antonio
Publication year - 2018
Publication title -
european journal of inorganic chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.667
H-Index - 136
eISSN - 1099-0682
pISSN - 1434-1948
DOI - 10.1002/ejic.201800602
Subject(s) - metalloprotein , chemistry , function (biology) , molecular dynamics , nanotechnology , metal , computational biology , biochemical engineering , computational chemistry , biology , microbiology and biotechnology , materials science , organic chemistry , engineering
Available estimates indicate that 30–40 % of all proteins need at least one metal ion to perform their biological function. Therefore, they are called metalloproteins. The correct biosynthesis of metalloproteins requires living organisms to be able to cope with issues such as the limited bioavailability or the potential cytotoxicity of several essential metals. Thus, organisms have developed complex machineries that guarantee the proper intracellular concentration and distribution among compartments of each metal, i.e. metal homeostasis. To understand how the different proteins responsible for metal homeostasis carry out their function, it is necessary to investigate their three‐dimensional (3D) structure and mobility at the atomic level. Nuclear magnetic resonance spectroscopy is one of the main experimental techniques providing this information. Computer simulations of molecular dynamics (MD) complement experimental information by showing how the 3D structure fluctuates over time and as a function of environmental conditions, with the possibility of exploring a wider range of timescales and conditions than usually amenable to experiment. Here we review numerous applications of MD for the investigation of the structure and dynamics of metalloproteins, and we also mention some technical aspects related to the parametrization of metals in commonly used force fields.