Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF)

Abstract

Currently the Protein Data Bank (PDB) contains over 18,000 structures that contain a metal ion including Na, Mg, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, Ag, Cd, Ir, Pt, Au, and Hg. In general, carrying out classical molecular dynamics (MD) simulations of metalloproteins is a convoluted and time consuming process. Herein, we describe MCPB (Metal Center Parameter Builder), which allows one, to conveniently and rapidly incorporate metal ions using the bonded plus electrostatics model (Hoops et al., J. Am. Chem. Soc. 1991, 113, 8262-8270) into the AMBER Force Field (FF). MCPB was used to develop a Zinc FF, ZAFF, which is compatible with the existing AMBER FFs. The PDB was mined for all Zn containing structures with most being tetrahedrally bound. The most abundant primary shell ligand combinations were extracted and FFs were created. These include Zn bound to CCCC, CCCH, CCHH, CHHH, HHHH, HHHO, HHOO, HOOO, HHHD, and HHDD (O = water and the remaining are 1 letter amino acid codes). Bond and angle force constants and RESP charges were obtained from B3LYP/6-31G* calculations of model structures from the various primary shell combinations. MCPB and ZAFF can be used to create FFs for MD simulations of metalloproteins to study enzyme catalysis, drug design and metalloprotein crystal refinement.

Figure 1

Three Approaches to Incorporate Metal Atoms into Molecular Mechanics Force Fields. The bonded model (left) defines bonds, angles, and dihedrals between the metal and ligands, while the non-bonded model (middle) does not and uses electrostatics and van der Waals to model the interactions. The cationic dummy atom model (right) is a derivative of the non-bonded model where cations are placed near the metal center to mimic valence electrons around the metal.

Figure 2

MCPB Flow Diagram.

Figure 3

Metal Ligand Geometries Perceived Using Harding's Rules.

Figure 4

Zinc Coordination Geometry Distribution from the PDB.

Figure 5

The Most Common Tetrahedral Zinc Coordinating ligands Combination Distribution. Three lettered environments also contain a secondary ligand not shown.

Figure 6

Zn-S Bond Length distributions in CCCC (top left), CCCH (top right), CCHH (middle left), and CHHH (middle right) Tetrahedral Environments and a Box Plot summarizing all four environments (bottom).

Figure 7

ZAFF Flow Diagram. This illustration demonstrates when a metalloprotein structure is downloaded from the PDB and an equivalent metal site is stored the MTK++ package has the ability to assign parameters to carry out MD simulations.

Figure 8

Zn-CCCC Cluster Models (PDB ID: 1A5T).

Figure 9

The Correlation between (top) Zn-Cys@S and (bottom) Zn-His@N Bond Lengths and Calculated Force Constants through the Series CCCC, CCCH, CCHH, CHHH, and HHHH using the “Traditional” and Seminario methods.

Figure 10

Cartoon Representation (left) of the dizinc Protein (PDB ID 1AMP) and its metal sites (right).

Figure 11

Correlation from 1A5T normal mode calculation with parameters built from the Seminario model to the B3LYP/6-31G* computed frequencies (R²=0.99).

Figure 12

RMSD (in Å) of the 1AMP backbone heavy atoms (above) and the RMSD of the zinc complex (bottom) over the final 2 nanoseconds.

Figure 13

Fitting results from 1AMP normal mode calculation with parameters built from Seminario model coupled with restraint scheme 1 to B3LYP/6-31G* computed frequencies (R²=0.99).