Predicting OppA Protein-Peptide Binding Affinities from X-ray and Docked Structures

Date of Award


Degree Type


Degree Name

Master of Science (MS)



First Advisor

Joseph Audie, Ph.D.


The experiment is aimed at investigating and comparing the accuracy of computational binding affinity predictions using crystal structures and docked structures. The system chosen for analysis was the OppA-peptide binding protein. Findings indicate that the oligopeptide-binding protein (OppA) is a promising system for studying and analyzing the structure-energy relationships. A recent study utilizing isothermal titration calorimetry (ITC) and x-ray crystallography has been completed with the binding of OppA to twenty tripeptides exhibiting the Lys-X-Lys motif sequence, where X is an amino acid occurring naturally. The availability of comprehensive and accurate crystallographic and calorimetric binding data for twenty peptide ligands render the study of molecular recognition using the OppA protein a promising system for study. This paper discusses comparisons between experimentally determined OppA-peptide ITC binding affinities with computational predictions made using the PRODIGY binding affinity method using both x-ray and docked OppA-peptide structures. The results indicate a consistently weak and insignificant correlation between experimental and PRODIGY binding affinities in all cases study. Indeed, correlation analysts after sub-classifying ligands as hydrophobic, polar and chared failed to produce better correlations. It is concluded that the PRODIGY method must be dramatically improved if it is to be used to accurately predict and rigorously explain OppA-peptide binding reactions. The experiment used 20 peptides for the study. The experiment was performed in 50mM sodium phosphate buffer and at temperatures 25̊C. It was observed that the enthalpy changes in the KKK and KWK differed significantly from the values reported by the previous studies. Crystallography and calorimetry have been extensively used to study protein and protein-ligand complex structures. Consequently, the protein is believed to the bond between two to five amino acids in their peptides. Additionally, the protein serves as the basic receptor used to transport peptide across the cell membrane in a gram-negative bacterium. A recent study utilizing isothermal titration calorimetry and crystallography have experimented with the binding of OppA in several tripeptides exhibiting the Lys-X-Lys sequence. X is an amino acid occurring naturally. The tripeptide backbone is responsible for beta-sheet hydrogen bonding interactions with the protein. On the other hand, peptide side chains are contained in large cavities, which are hydrated for affinity. Crystallography and calorimetry render the study of molecular recognition using the protein a success. Additionally, the extensive number of ligands makes the use of crystallography and calorimetry a suitable method of study. Thermodynamics of binding has been rationalized by the study of interactions between natural peptides found in crystal structures and OppA. The process was a success at the use of different conformational preferences hydration of different free peptides. The experiment used program tools to analyse the results. In this study, Vega ZZ program and Prodigy website were utilized. Specifically, Vega ZZ program was used in molecular docking analysis. The x-ray structure was obtained from the PDB website. The program enabled the use of simulation trajectory animation and visualization supported by programs like AutoDock and BioDock amongst others. On the other hand, the Swiss PDB program was used to produce bigger images other than the screen. It was also utilized to change the density of the dots tracing the Van de Waals surf.


Master's thesis submitted to the faculty of Sacred Heart University's Chemistry Program in partial fulfillment of the requirements for the degree of Master of Chemistry.