Computational Analysis of the Steric Gate Region in the Y-Family DNA Polymerases



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Background: The Y-family DNA polymerases specialize in translesion synthesis. This is ascribed to steric clashes with a residue near the active site, the steric gate and 2′-OH (hydroxyl) group. The steric gate provides by steric and physical constraints an effective mechanism for most DNA polymerases to selectively insert deoxyribonucleotides. Deoxyribonucleotides synthesis into DNA leads to replication stress and genomic instability. Defective replication leads to mutation in the protein sequences which can prevent the drug from binding to the target and consequently blocking treatment of disease. The aim of this research study was to determine the effectiveness of sequence pattern recognition to provide better insights into the Y-family DNA polymerases structure-function relationships. Methods and Materials: A combination of methods of computational structure analysis, correlated mutations, and sequence pattern recognition were used. Multiple Sequence Alignments (MSA) of the UmuC domain from PFAM were used to identify critical residues in the steric gate position. The Consurf database was used to calculate conservation score and COUSCOus was used to calculate correlated mutations of the conserved regions. Residue pair scores were used as an amino acid pair position comparison analysis in order to assess the predicted residue-residue interactions. Results: 17,662 aligned sequences (as of April 11th, 2020) from PFAM of the UmuC domain were used; of these, 13,768 sequences (78.0%) had phenylalanine (F) or tyrosine (Y) at the steric gate position, 369 sequences (2.1%) had another residue at steric gate position and 3,525 sequences (20.0%) had no known steric gate. 150 (4.3%) of these were found to be fragments and were not considered for the analysis. An example of the structure 5KFZ from the human DNA polymerase eta retrieved from PFAM yielded conservation scores from the consurf database that were plotted against the correlation values from COUSCOus in r. An intersection showed that residues that were highly conserved were similarly correlated. Conclusions: The steric gate of approximately 90% of organisms is as expected with tyrosine (Y) and phenylalanine (F) in this position. However, a small number of organisms have been known to have been a different residue at the position. Understanding how these organisms discriminate against deoxyribonucleotides will give insight on how are they able to function. Specific human DNA repair and lesion bypass polymerases have been proposed to be anticancer drug targets. For instance, Pol η (eta) appears to be specialized in bypass of cyclobutane pyrimidine dimers, a UV- induced lesion.