Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.
Parameters for the zinc ion have been developed in the self-consistent charge density functional tight-binding (SCC-DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC-DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc-assisted proton transfers), as compared with B3LYP/6-311+G** or MP2/6-311+G** calculations.
Elstner
Marcus
M
Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
Cui
Qiang
Q
Munih
Petra
P
Kaxiras
Efthimios
E
Frauenheim
Thomas
T
Karplus
Martin
M
D000426:Alcohol Dehydrogenase / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D000626:Aminopeptidases / Q000737:chemistry* / Q000378:metabolism; D001224:Aspartic Acid / Q000737:chemistry / Q000378:metabolism; D001426:Bacterial Proteins; D001665:Binding Sites; D002256:Carbonic Anhydrases / Q000737:chemistry / Q000378:metabolism; D003545:Cysteine / Q000737:chemistry / Q000378:metabolism; D018698:Glutamic Acid / Q000737:chemistry / Q000378:metabolism; D006639:Histidine / Q000737:chemistry / Q000378:metabolism; D008099:Liver / Q000201:enzymology; D008958:Models, Molecular; D008968:Molecular Conformation; D011485:Protein Binding; D011487:Protein Conformation; D014867:Water / Q000737:chemistry; D015032:Zinc / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D014867:Water; D001224:Aspartic Acid; D018698:Glutamic Acid; D006639:Histidine; D000426:Alcohol Dehydrogenase; D000626:Aminopeptidases; C038222:bacterial leucyl aminopeptidase; D002256:Carbonic Anhydrases; D015032:Zinc; D003545:Cysteine