About SAAP force field
Importance of the single amino acid potentials
Polypeptide is a copolymer molecule comprising a number of amino acids. The principle idea of the SAAP force field stems from cutting a polypeptide into the individual amino acids. Let us consider that we have those amino-acid fragments in hands. What structure does each amino-acid fragment tend to have by itself? To get the answer, we carried out high-level ab initio molecular orbital calculation that is based on quantum mechanics and obtained the precise potential energy surfaces (Ramachandran maps) for the single amino acid fragments. The two-dimensional potential surface obtained for alanine in water is shown below in the left-hand side. It should be noted that the deep blue regions, which correspond to the energetically stable structures, are located in the regions of alpha helix and beta sheet. Furthermore, when the obtained potential surface was compared with the Ramachandran plots of alanine residues in proteins, it was found that the single amino acid potential of alanine calculated in water is perfectly consistent with the statistical structures of alanine residues in proteins. The Boltzmann plot shown below in the right-hand side shows a linear correlation when the single amino acid potential in water is applied, suggesting the random (or statistical) distribution of the amino acid structures in proteins. This notable property would have significant implications for understanding evolution and folding of proteins.
What is SAAP force field?
If the potential energies of single amino acids in water strongly correlate with the structures of proteins, it would be possible to simulate the protein or polypeptide structures more accurately and effectively by using the single amino acid potentials. On the basis of this idea, the SAAP force field project was started. SAAP is a short word of the Single Amino Acid Potential. The fundamental energetic formula is shown below. In the SAAP force field, each amino acid residue is considered as the principle unit of a polypeptide, whereas in the conventional force fields the principle unit is each atom. Thus, the SAAP is a unique all-atom force field based on a novel concept. Since the force field parameters involve solvent effects implicitly, rapid simulation for a polypeptide is possible in water.
Cross terms, which are important but were neglected in Lifson formula, are included within the single amino acid units.
Solvent effects are involved in the force field parameters implicitly, allowing high-speed simulation in water.
Polypeptide structures are defined simply by the main-chain and side-chain dihedral angles.
The force field parameters are determined by ab initio molecular orbital calculation.
The total energy of a peptide molecule can be decomposed to three components: SAAP, electrostatic interactions, and van der Waals (Lennard-Jones) interactions.
Side-chain separation approximation
Except for glycine and alanine, many amino acids have a long side chain. In these cases, rotational freedoms of the side chain have to be considered to define the single amino acid potential parameters. However, it is practically impossible to obtain the single amino acid potentials with four or more dimensions of dihedral angles by ab initio calculation because of a limit of computer resources. Therefore, in the SAAP force field the structure of the amino acid with a long side chain is divided into the main-chain and side-chain parts, and the multi-dimensional potential energy surface is calculated separately for each part. The single amino acid potential is then calculated by combination of the main-chain and side-chain parameters. This approximation is called the side-chain separation approximation. In the renovated SAAP (SAAP3D) force field, the amino acid units are separated between the C(beta) and C(gamma) atoms so that the main chain part has three dimensions of rotation (i.e., phi, psi, and chi1).
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