Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation

Chagas' disease, caused by the protozoan parasite Trypanosoma cruzi (T. cruzi), is a life-threatening illness affecting 11–18 million people. Currently available treatments are limited, with unacceptable efficacy and safety profiles. Recent studies have revealed an essential T. cruzi proline racemase enzyme (TcPR) as an attractive candidate for improved chemotherapeutic intervention. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and immune system evasion. Characterization of the conformational states of TcPR requires access to long-time-scale motions that are currently inaccessible by standard molecular dynamics simulations. Here we describe advanced accelerated molecular dynamics that extend the effective simulation time and capture large-scale motions of functional relevance. Conservation and fragment mapping analyses identified potential conformational epitopes located in the vicinity of newly identified transient binding pockets. The newly identified open TcPR conformations revealed by this study along with knowledge of the closed to open interconversion mechanism advances our understanding of TcPR function. The results and the strategy adopted in this work constitute an important step toward the rationalization of the molecular basis behind the mitogenic B-cell response of TcPR and provide new insights for future structure-based drug discovery. Author Summary: There is an urgent need for the development of better drug therapies for tropical diseases, including Chagas' disease, sleeping sickness and leishmaniasis. Known collectively as the human trypanosomiases, these traditionally neglected diseases are responsible for substantial human suffering and death in Latin America and sub-Saharan Africa. Current chemotherapy for Chagas' disease is particularly unsatisfactory, with available drug treatments displaying poor efficacy and undesirable toxic side effects. Recent developments in the study of the basic biochemistry of the causative Trypanosoma cruzi parasite and its host infection mechanism have identified an essential proline racemase enzyme (TcPR) as a novel target for chemotherapeutic intervention for Chagas' disease. Conformational changes associated with substrate binding to TcPR are believed to expose critical residues that elicit a host mitogenic B-cell response, a process contributing to parasite persistence and the undermining of host immunity against T. cruzi. Here we describe advanced accelerated molecular dynamics simulations that capture previously uncharacterized large-scale motions of TcPR. These motions reveal new conformational epitopes of potential importance for the mitogenic B-cell response. Furthermore, knowledge of the conformational interconversion mechanism and corresponding transient binding pockets will greatly aid future structure-based drug discovery efforts.