Dimer properties

It is not clear why some organisms have two 14-3-3 isoforms while others have up to 12. Binding 14-3-3 inhibits the plant enzyme nitrate reductase and there appears to be no selectivity between plant 14-3-3 isoforms in fact yeast and human isoforms appear to work equally as well in vitro. The best example where selectivity has been demonstrated is human 14-3-3o. 14-3-3o Preferential homodimerizes with itself and crystallization revealed a structural basis for this isoform s dimerization properties as well as for its specific selectivity for target binding proteins. Here partner specificity is the result of amino acid differences outside of the phosphopeptide-binding cleft. 

Table 4.3. Water dimer properties the interaction energy (Ei t) in kcal/mol, the intermolecular distance (R00) in A, and the dipole moment p. in Debye, calculated using the B88/P86 exchange-correlation functional and different basis sets.

Laasonen, K., F. Csajka, and M. Parrinello. 1992. Water dimer properties in the gradient-corrected density functional theory. Chem. Phys. Lett. 194,172. 

Ottilie S, Diaz JL, Horne W, Chang J, Wang Y, Wilson G, Chang S, Weeks S, Fritz LC, Oltersdorf T (1997), Dimerization properties of human BAD. Identification of a BH-3 domain and analysis of its binding to mutant BCL-2 and BCL-XL proteins, J. Biol. Chem. 272 30866-30872. 

Most nonpolarizable water models are actually fragile in this regard they are not transferable to temperatures or densities far from where they were parameterized. Because of the emphasis on transferability, polarizable models are typically held to a higher standard and are expected to reproduce monomer and dimer properties for which nonpolarizable liquid-state models are known to fail. Consequently, several of the early attempts at polarizable models were in fact less successful at ambient conditions than the benchmark nonpolarizable models, (simple point charge) and TIP4P (transfer-... 

The potentials discussed above are pairwise or two-body potentials (i.e., potentials describing dimers). Yet, in many cases such potentials are fitted to thermodynamics data for liquids and solids. In such media the pairwise nonadditive effects are usually quite important. Therefore, potentials of this type are called effective two-body potentials since they approximate the many-body effects by an unphysical distortion of the two-body potential relative to the exact two-body potential. As a consequence, the effective two-body potentials perform poorly in predicting pure dimer properties such as dimer spectra or second virial coefficients. In fact, the effective two-body potentials perform poorly also in predicting trimer properties (although the three-body component dominates the nonadditive effects, cf. section III.C). 

A partial solution to the problem is offered by the so-called polarizable potentials. As discussed in section III.C, the major component of the three-body nonadditivity for hydrogen-bonded systems are the induction effects. These effects can be modeled by computing the electric field on a given monomer due to other monomers and finding the dipole moments induced by this field. The polarizable water potentials are able to predict the dimer properties much... 

Although QM calculations can be expected to be more useful to determine single-molecule, or dimer, properties (since they usually involve one or two molecules, treated in vacuum), Lucas and co-workers" have been able to develop a successful framework to determine multipole moments and dispersion interactions from QM. Using a fairly rigorous level of theory (MP2/ aug-cc-Pvdz/B3LYP/TZVP) dipole and quadrupole moments, dipole polarizability and dispersion coefficients were determined and subsequently used with the PCP-SAFT approach to study a number of pure fluids and their binary mixtures (see section 8.4.2)." " ... 

Dimer properties derived from the different types of potential discussed earlier in the section on parameter fitting differ from each other depending on their type of parameterization. In Table 3 we can see that an empirical liquid water potential tends to overestimate the binding energy, whereas the geometry is more akin to typical dimer configurations in a liquid environment. Grafting a... 

Table 3 Computed Water Dimer Properties Using Different Types of Models...

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