United-atom protein force

Examples of united-atom protein force-fields for proteins are GROMOS87 and 96,21,48 CHARMM PARAM19,49 OPLS/UA (united atom)50 and the original force fields developed for the AMBER program.51 United atom force fields were developed to reduce the computer time required for molecular dynamics simulations by reducing the number of atoms. They are still... 

The OPLS force field is described in twtt papers, one discussing parameters for proteins W. L. Jorgensen and J. Tirado-Rives,/. Amer. (. hem. Soc., 110, 1557 (iy8K) and on e discii ssin g param eters for n iicleotide bases [J. Pranata, S. Wiersch ke, and W. L. Jorgen sen. , /.. Amer. Chem. Soc.. 117, 281(1 ( 1991)1. The force field uses the united atom concept ftir many, but not all. hydrttgens attached to carbons to allow faster calculation s on macromolecular systems. The amino and nucleic acid residue templates in HyperChein automatically switch to a united atom representation where appropriate when th e OPLS option is selected. 

This force field was developed primarily for protein and nucleic acid applications. It is a united atom force field, and there are many versions. Once again, you might like to see the Abstract of the original Paper. 

Allen and Bevan (80) have applied the SMD technique to the study of reversible inhibitors of monoamine oxidase B, and this paper will be used as an example for discussion of the constant velocity SMD pulling method. They used the Gromacs suite of biomolecular simulation programs (18) with the united-atom Gromos 43al force field to parameterize the lipid bilayer, protein, and small-molecule inhibitors. The protein was inserted into their mixed bilayer composed of phosphatidyl choline (POPC) and phosphatidyl ethanolamine (POPE) lipids in a ratio known to be consistent for a mitochondrial membrane. Each inhibitor-bound system studied was preequilibrated in a periodic box of SPC water (20) with the simulations run using the NPT ensemble at 300 K and 1 atm pressure for 20 ns. Full atomic coordinates and velocities were saved in 200-ps increments giving five replicates for each inhibitor-bound system. A dummy atom was attached to an atom (the SMD atom shown in Fig. 7) of the inhibitor nearest to the... 

Kini RM, Evans HJ (1992) Comparison of protein models minimized by the all-atom and united atom models in the amber force field, J Biomol Structure and Dynamics, 10 265-279... 

Force fields for biological macromolecules fall into two classes united-atom, and all-atom force fields. All-atom force fields, as the name suggests, represent all atoms in a protein explicitly. United-atom force fields, on the other hand, treat only heavy (non-hydrogen) atoms and polar hydrogen atoms explicitly, while nonpolar hydrogen atoms are not represented explicitly, but rather represented as part of the carbon atom to which they are bonded (which will have an enlarged van der Waals radius (Lennard-Jones collision diameter)). 

Within the context of the above, let us try to formulate some necessary requirements for the design of a moderate resolution reduced model (based on united-atom representation and knowledge-based potentials) of real proteins and its force field ... 

All-atom force fields consider every atom as an individual interaction site, while united-atom force fields gather different atoms of a functional group into one interaction site, e.g., as is often done to model methyl or methylene groups. To describe chain-Uke polymers or proteins, coarse grained force fields are also employed, where the interaction sites usually represent a larger number of atoms. 

The optimized potentials for liquid simulations (OPLS) force field can be divided into the OPLS-UA (united-atom) [96, 110-112] and the OPLS-AA (all-atom) [57, 67, 92, 103, 135-139] versions. Among the two, the OPLS-UA force field is predominantly used for engineering applications, mainly because it is computatirMi-ally cheaper than the all-atom version. The OPLS-UA force field is available for hydrocarbons [96], amides [110], peptides [110], alcohols [111], or proteins [112]. The OPLS-AA force field was parameterized for small organic molecules and is intended for biochemical applications. The parameters of the OPLS-AA force field are available for a broader range of functional groups and molecules. Thus, besides hydrocarbons [103] and alcohols [57], parameters can be found for thiols [57], sulfides [57], ketones [57], amides [57], amines [139], pyrrole [138], furan [138], diazoles [138], oxazoles [138], proteins [67], and carbohydrates [92], among others. 

The potential function of a particle corresponds to E IQ) in Equation 4.7, which we write as V(R). It consists of binding forces and forces from nonbonded nuclei groups and other nuclei. What is included in the molecular dynamics simulation depends on how detailed we want to be. Usually, it is sufficient to include CH bonds as a united atom and neglect the motion of the hydrogen atoms. In proteins, we may choose to ignore the bond distances and include only the torsion angles... 

---