Side chains, computational studies

There are cases in which one is interested in the motion of a biomolecule but wishes also to study the effect of different solvent environments on this motion. In other cases, one may be interested in studying the motion of one part of the protein (e.g., a side chain or a loop) as moving in a solvent bath provided by the remainder of the protein. One way to deal with these issues is, of course, to explicitly include all the additional components in the simulation (explicit water molecules, the whole protein, etc.). This solution is computationally very expensive, because much work is done on parts of the system that are of no direct interest to the study. 

The use of QM-MD as opposed to QM-MM minimization techniques is computationally intensive and thus precluded the use of an ab initio or density functional method for the quantum region. This study was performed with an AMi Hamiltonian, and the first step of the dephosphorylation reaction was studied (see Fig. 4). Because of the important role that phosphorus has in biological systems [62], phosphatase reactions have been studied extensively [63]. From experimental data it is believed that Cys-i2 and Asp-i29 residues are involved in the first step of the dephosphorylation reaction of BPTP [64,65]. Alaliambra et al. [30] included the side chains of the phosphorylated tyrosine, Cys-i2, and Asp-i 29 in the quantum region, with link atoms used at the quantum/classical boundaries. In this study the protein was not truncated and was surrounded with a 24 A radius sphere of water molecules. Stochastic boundary methods were applied [66]. 

Since there is only a small energy difference between the different conformational states depending upon the presence or absence of a Pro, Gly or N-alkylated amino acid residue, and upon the chirality of the constituent amino acid residues and also to a lesser extent upon the side-chain functionalities, it is not possible to unambiguously predict the conformation of a cyclic pentapeptide. These molecules have often been studied in different solvents and solvent effects were neglected, and/or the methodology to handle such conformational equilibrium was not available. It is only recently that modem NMR techniques and computational procedures have become available to treat this complex problem of fast exchanging conformational equilibria. 36,269,270 ... 

Molecular mechanics and more sophisticated computational techniques are being applied extensively to siloxane conformational problems, to study both the chain backbone and the side chains.98... 

---