Christopher Negron, Christian Fufezan, and Ronald Koder. The City College of New York, New York, NY
De novo protein design stands to usher in an era of extremely promising biomedical procedures. One of the current hurdles hindering the development of de novo protein based therapies is the implantation of high affinity cofactor binding sites, where there is particular interest in developing heme binding. The method suggested for the construction of strong porphyrin binding sites is through consensus analysis of natural occurring non-homologous porphyrin binding sites, which are related by secondary structure, and most importantly subdivided by the various rotamers of the ligated amino acid. Determination of the rotameric distribution of heme ligated helical histidines was carried out by in lab PERL scripts that analyze Protein Data Bank structures. Sequence preferences, not subdivided by rotamer, yielded very small percentages, which are in sync with previous observations. Yet, sequence preferences subdivided by rotamer yielded strikingly high percentages, with particular residues, such as a glycine in position 4 of the t73 rotamer, reaching preferences of nearly 50%. Computational modeling illuminates the structural basis for some of these findings. Molecular simulation conducted with a single histidine residue placed in the center of an all-alanine helix, agreed with the natural rotameric distribution, with very important exceptions that demonstrate the importance of complimentary residues in the heme histidine ligation, and reinforcing the structural claims of the computational model. These preferences have allowed the derivation of helical consensus for each rotamer. These findings thus promise to guide the creation of higher affinity heme and porphyrin binding sites.
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