New Protein Structure Prediction Method Using Inter-Residue Distances and a Theoretical Investigation of the Isomerization of Azobenzene and Disubstituted Azobenzenes

It is often claimed that knowing a protein? s structure is important in understanding its function. The experimental structure determination methods presently available can be costly and time-consuming. This dissertation presents an idea for a fast and inexpensive protein structure prediction method that combines modeling with a minimal set of experimental data. Our method involves three steps: (1) building a decoy set (a set of protein-like structures), (2) measuring inter-residue distances, and (3) comparing the measured distances with those calculated in each decoy. We postulate that structures with a small number of similar inter-residue distances will also have similar three-dimensional structure. We further hypothesize that the minimum number of distances needed to determine structure is much less than the total number of inter-residue distances in the protein. To develop our protocol, we searched the decoy set for target proteins whose structures have been solved experimentally but have not been explicitly included in our decoy set. We simulated experimental data by calculating alpha-carbon distances from the experimentally determined structures of our target proteins. We have created a large, generalized decoy set using most of the structures in the Protein Data Bank. This decoy set can be used to study any protein composed of 100 residues or less. Using this decoy set, we attempted to predict structures for several proteins. We also analyzed the RMSD distributions of the decoys using the search proteins as references and found the distributions to be similar for each protein. Of the nearly five thousand alpha-C-alpha-C distances in a 100 residue protein, knowledge of only twenty-five selected distances will usually result in predicting a reliable model. In the second part of our study, results are presented for a series of azobenzenes which were studied using ab initio methods to determine the substituent effects on the isomerization pathways. Energy barriers were determined from three-dimensional potential energy surfaces of the ground and electronically excited states. In the ground state (S0), the inversion pathway was found to be preferred. Results show that electron donating substituents increase the isomerization barrier along the inversion pathway, while electron withdrawing substituents decrease it. The inversion pathway of the first excited state (S1) showed trans to cis barriers with no curve crossing between the S0 and S1. In contrast, a conical intersection was found between the ground and first excited states along the rotation pathway for each of the azobenzenes studied. No barriers were found in this pathway and we therefore postulate that after n to pi* (S0 to S1) excitation, the rotation mechanism dominates. Upon pi to pi* (S0 to S2) excitation, there may be sufficient energy to open an additional pathway (concerted-inversion) as proposed by Diau. This pathway is only accessible for unsubstituted azobenzene and 4,4-dinitroazobenzene. Because of the S0 and S1 curves crossing on the trans side,…