Electrostatics and packing in biomolecules : accounting for conformational change in protein folding and binding

The role of electrostatics and packing in protein folding and molecular association was assessed in different biomolecular systems. A continuum electrostatic model was applied to long-range electrostatic effects in the binding of human carbonic anhydrase II to a sulfonamide inhibitor. The effect of chemically modifying lysine -amino groups was computed, and the average calculated value showed good agreement with experimental results determined by capillary electrophoresis. In a second study, the continuum model was used to analyze all the electrostatic interactions in the Zif268 protein–DNA complex. The net electrostatic effect was unfavorable to binding, although many individual groups or group pairs had a favorable effect, and the residues most unfavorable to binding correspond to those thought to be important for specificity. Also, a measure of electrostatic complementarity was developed and applied to myoglobin—both to known sequences and to hypothetical chimeric myoglobin sequences. The complementarity measure rated the correct myoglobins higher than chimeric myoglobins when crystal structures were used, and performed better than other readily available measures of complementarity when myoglobin homology models were evaluated. In the second part of the thesis, methods for repacking proteins were presented and applied to Arc repressor. Sequence variants that are predicted to fold as heterodimers preferentially and variants that favor a switch-Arc structure over wild-type were found. In a final set of calculations, the search algorithms for repacking were combined with electrostatic effects predicted from an approximate continuum model. The structure of Zif268 zinc finger 1 complexed to DNA was predicted when limited docking and side chain flexibility were allowed. The predicted structure shows good agreement with the x-ray crystal structure. A second repacked structure provides insight into how sequence changes affect structure and hence binding specificity in the zinc finger protein. Thesis Supervisor: Bruce Tidor Title: Associate Professor of Bioengineering and Computer Science