Access Type

Open Access Dissertation

Date of Award

January 2015

Degree Type


Degree Name




First Advisor

Andres Cisneros


This thesis describes analyses performed on three enzyme systems. Chapter 2, 3, and 4 involve studies carried out on the GatCAB enzyme of H. pylori and S. aureus. Since information at the electronic level was not required for these studies, sampling of the configuration space carried out at the molecular mechanics level was adequate. In Chapter 2, the snapshots sampled using MD were used as input for average correlation difference calculations and average RMSD difference calculations to ascertain the existence of a communication pathway between two subunits of GatCAB. Experimental and computational results obtained, suggest the existence of a communication pathway between the GatA and GatB subunits of H. pylori GatCAB. In Chapter 3, the snapshots sampled using MD were used as input for average correlation difference calculations and pKa calculations to analyze the possibility of an amino acid residue acting as a possible catalytic acid/base at the entrance of an intramolecular tunnel that transfers ammonia from one active site to another. Experimental results that compare glutaminase, kinase, and transamidase activity for wild-type H. pylori GatCAB with the mutants D185(A)E, D185(A)A, and D185(A)N as well as our computational results support the possibility of D185(A) in H. pylori GatCAB acting as a catalytic acid/base in protonation/deprotonation of ammonia. In Chapter 4, MD snapshots were used to calculate intramolecular tunnels inside S. aureus GatCAB along which the free energy for the transfer of ammonia was calculated using the WHAM method to identify the tunnel that was thermodynamically more favorable. EDA and APBS analyses were utilized for further characterization of the tunnels in terms of non-bonded interactions between the ammonia molecule and the surrounding amino acids lining the tunnel. The results of the free energy calculations using WHAM as well as the energy differences calculated using EDA showed that tunnel1 (proposed in 2006 by Nakamura et al.) is thermodynamically more favorable for transfer of ammonia compared to tunnel2 (proposed in 2012 by Kang et al.)

Chapter 5 discusses the inorganic pyrophosphatase (PPase) mechanism in M. tuberculosis which requires information at the electronic level. The QM/MM hybrid method was used in which the reactive moieties were included in the QM subsystem to achieve accuracy at the electronic level while the rest of the system was treated at the molecular mechanics level. Based on a set of newly isolated crystal structures and the results of the QM/MM calculations, a new mechanism for the PPase catalyzed PPi hydrolysis was proposed and an energy barrier of 6.6 kcal/mol was calculated at the B3LYP/6-31G(d,p) level of theory.

In Chapter 6, molecular docking was used to dock a set of novel substrates that are being experimentally tested as potential radiotracers, onto HDAC4 and HDAC8 enzymes to calculate/compare their relative binding affinities. The trends in the increase in affinity, of the novel substrates for HDAC4 and HDAC8 active sites calculated by molecular docking, agreed with the experimentally shown trends.