title: Differential role of the protein matrix on the binding of a catalytic aspartate to Mg2+ vs Ca2+: application to ribonuclease H.
abstract: Divalent metal cations are essential cofactors for many enzyme functions. Although Mg(2+) is the native cofactor in many enzymes such as ribonuclease H, its competitor Ca(2+) may also bind to the enzyme but inhibit catalysis. Thus, the competition between Mg(2+) and Ca(2+) for a given metal-binding site in an enzyme and their effects on enzyme activity are of great interest. Most studies have focused on the interactions between Mg(2+) or Ca(2+) and the metal ligands in the first and sometimes second coordination shell. However, no study (to our knowledge) has examined the role of the protein architecture and surrounding aqueous environment on the binding of Mg(2+) vs Ca(2+) to a given protein metal-binding site. In this work, the free energy barriers for the binding of a catalytically essential aspartate to Mg(2+) or Ca(2+) in ribonuclease H from two organisms were computed using umbrella sampling with a classical force field ("classical" model). The corresponding free energy barriers in water were computed using the "classical" model as well as density functional theory combined with a self-consistent reaction field. The results reveal that, relative to water, the protein architecture and coupled protein-water interactions raise the free energy barrier for binding of the catalytically essential aspartate to the native Mg(2+) cofactor more than the respective binding to Ca(2+). They also reveal the physical basis for the different observed binding modes of Mg(2+) and Ca(2+) and highlight limitations of simulations with classical force fields that do not explicitly account for charge transfer and polarization effects.
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan. babu@ibms.sinica.edu.tw
authors.forename: C Satheesan
authors.initials: CS
authors.lastname: Babu
authors.forename: Todor
authors.initials: T
authors.lastname: Dudev
authors.forename: Carmay
authors.initials: C
authors.lastname: Lim
mesh_terms: D001224:Aspartic Acid / Q000737:chemistry* / Q000378:metabolism; D002118:Calcium / Q000737:chemistry* / Q000378:metabolism; D002264:Carboxylic Acids / Q000737:chemistry; D002384:Catalysis; D003198:Computer Simulation; D004926:Escherichia coli / Q000201:enzymology; D008274:Magnesium / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011522:Protons; D016914:Ribonuclease H / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D002264:Carboxylic Acids; D011522:Protons; D014867:Water; D001224:Aspartic Acid; D016914:Ribonuclease H; D008274:Magnesium; D002118:Calcium