Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns.
Cobalt and potassium are biologically important metal elements that are present in a large array of proteins. Cobalt is mostly found in vivo associated with a corrin ring, which represents the core of the vitamin B12 molecule. Potassium is the most abundant metal in the cytosol, and it plays a crucial role in maintaining membrane potential as well as correct protein function. Here, we report a thorough analysis of the geometric properties of cobalt and potassium coordination spheres that was performed with high resolution on a representative set of structures from the Protein Data Bank and complemented by quantum mechanical calculations realized at the DFT level of theory (B3LYP/ SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of both Co and K centers, and to evaluate the importance of effects such as their association energies and intrinsic thermodynamic stabilities. Overall, the results obtained provide useful data for enhancing the atomic models normally applied in theoretical and computational studies of Co or K proteins performed at the quantum mechanical level, and for developing molecular mechanical parameters for treating Co or K coordination spheres in molecular mechanics or molecular dynamics studies.
REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
Natércia F
NF
Brás
António J M
AJ
Ribeiro
Marina
M
Oliveira
Nathália M
NM
Paixão
Juan A
JA
Tamames
Pedro A
PA
Fernandes
Maria J
MJ
Ramos
D003035:Cobalt / Q000737:chemistry*; D003198:Computer Simulation; D030562:Databases, Protein; D004735:Energy Transfer; D004795:Enzyme Stability; D004798:Enzymes / Q000737:chemistry*; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D011188:Potassium / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D011789:Quantum Theory; D013329:Structure-Activity Relationship; D013696:Temperature
D004798:Enzymes; D008024:Ligands; D008667:Metalloproteins; D003035:Cobalt; D011188:Potassium