The contributions of solvent screening and fluctuations to the 23Na+ N M R quadrupolar relaxation rate in a model aqueous ion pair, sodium dimethylphosphate, have been studied using molecular dynamics simulations. Four specific relative interionic geometries are considered, corresponding to models of association of sodium ions with DNA in both inner-sphere and outer-sphere complexes. Analysis of the autocorrelation function of the electric field gradient (efg) at the sodium nucleus indicates correlation times comparable to those for the unpaired ion. The influences of the short-ranged and Coulombic interactions on the efg at the sodium nucleus have been evaluated. It is concluded that the net result for the sodium quadrupolar coupling constant incorporates cancellation between large direct counterion and induced solvent contributions and hence does not sensitively reflect the direct role of Coulombic forces. The quantitative results support the utility of an empirical expression to account for this net contribution for the case of DNA. On the basis of computed average field gradients, we further infer that both contact and solvent-separated ion pairs make potentially important contributions to the N M R observations in DNA solutions.

No abstract

We have analyzed conformational changes that occur at the interface between the light (V(L)) and heavy (V(H)) chains in antibody variable fragments upon binding to antigens. We wrote and applied the Tiny Probe program that computes the buried atomic contact surface area of three-dimensional structures to evaluate changes in compactness of the V(L)-V(H) interface between bound and unbound antibodies. We found three categories of these changes, which correlated with the size of the antigen. Upon binding, medium-sized nonprotein antigens cause an opening of the V(L)-V(H) interface (less compact), small antigens or haptens cause a closure of the interface (more compact), whereas large protein antigens have little effect on the compactness of the V(L)-V(H) interface. The largest changes in the atomic buried contact surface area at the V(L)-V(H) interface occur in residue pairs providing two 'shock absorbers' between the edge beta-strands of the V(L) and V(H) beta-sheets forming the antibody binding site. Importantly, the correlation between the size of antigens and conformational changes indicates that the V(L)-V(H) interface in antibodies plays a significant role in the antigen binding process. Furthermore, as the energy involved in such a motion is significant (up to 3 kcal/mol), these results provide a general mechanism for how residues distant from the combining site can significantly alter the affinity of an antibody for its antigen. Thus, mutations introduced at the V(L)-V(H) interface can be used to change antibody binding affinity with antigens. Due to the tightly packed V(L)-V(H) interface, the introduction of random mutations is not advisable. Rather our analysis suggests that concerted mutations of residues preceding CDRL2 and following CDRH3 or residues preceding CDRH2 and at the end of CDRL3 are most likely to alter or improve antigen binding affinity.