Protein-protein interactions are essential to all cellular processes and the mechanisms of bacterial and viral infection. Often, those interactions trigger conformational changes at locations away from the binding epitopes that modify or elicit new functionalities in one or both proteins. How are these signals transmitted from one point to another in a protein? Can critical points that will disable signal transduction be identified? Can these points be targeted by small molecular weight inhibitors? The answer to these questions will provide a fundamental understanding of protein function and new ways of engineering molecules that can modulate those interactions. Those are the long-range objectives of this project. This project will focus on the HIV protein Nef, a protein known to interact with different cell proteins in a concerted allosteric way. The binding of Nef to different partners is allosterically modulated by the binding to previous ones in a process in which the weakly structured regions play key roles. This research project will provide a new understanding of protein-protein interactions and the effects of those interactions in regions distal from the binding site.
In addition to the intellectual merit, the broader impact resulting from this research includes different fronts. At the practical level, it provides new strategies for designing small molecules that can inhibit protein-protein interactions or block the transmission of allosteric effects through the protein structure. These intellectual advances may eventually lead to important drug design applications. While guidelines for developing enzyme inhibitors are widely available, it must be noted that precise guidelines for the design of small molecules that inhibit protein-protein interactions or disable allosteric effects are non-existent. The broader impact is, however, not limited to the potential applications of the scientific discoveries. Graduate students and undergraduate students have benefited from this project by the incorporation of these state-of-the-art topics in their educational curriculum. Also this project has allowed and will continue to encourage the participation of undergraduates, including female and minorities, in different experimental and computational aspects of the research.
PI: Ernesto Freire Awardee: Johns Hopkins University Award Number: 0641252 Protein/protein interactions are essential to all living organisms as they define one of the major ways by which cells communicate with each other and within themselves. Protein/protein interactions regulate a multitude of metabolic processes that are essential to life. Protein/protein interactions initiate signaling events that control major metabolic pathways. The signaling process involves the protein/protein interaction itself and the subsequent transmission of information throughout the protein structure. Consequently, modulation of these processes can be achieved by interfering with the protein/protein interaction itself or with the signal pathway throughout the protein structure. Development of the ability to modify these processes will result in major scientific breakthroughs in biology. There were three major outcomes of this project in relation to these issues. The first one dealt with the technologies to identify the cooperative path by which the interaction at some specific location in a protein is transmitted to another location (this is analogous to identifying the wiring between the electric switch and the light bulb). The second major outcome deals with the development of different strategies to modulate signal transmission, either by blocking the protein/protein interaction itself (competitive inhibition) or by intervening at some point in the transmission path (allosteric inhibition). The third major outcome is the development of a general model for the inhibition and modulation of protein/protein interactions by small molecules that unifies the competitive and allosteric mechanisms in a single framework. The outcomes of this project provide the background for the engineering of energy efficient modulators of protein/protein interactions and signaling. Two HIV-1 proteins critical for viral infection (Nef and gp120) were utilized in these studies. The development of this technology will have tremendous influence in different areas of biotechnology, synthetic biology and pharmaceutics. In addition to the scientific outcomes published in scientific journals, this research has had a broader impact in different fronts. At the practical level, it provides new strategies for designing molecules that can modulate biological signaling. These intellectual advances may lead to important applications in areas such as synthetic biology, information transfer in biological systems and regulatory networks. It must be noted that the technologies required for engineering inhibitors or activators of signaling triggered by protein/protein interactions are not yet available. The broader impact is, however, not limited to the potential applications of the scientific discoveries. Graduate and undergraduate students have benefited from this project by the incorporation of these subjects in the courses taught by the PI. Also this project has allowed the participation of undergraduate students in a state-of-the-art research project. The PI presents about 20 seminars per year at universities, colleges, research laboratories as well as national and international meetings. The PI has also participated in television, radio and newspaper interviews. These venues have served to expose to the general public the significance of this research. As part of the outreach program, the PI’s laboratory donated a fully functional Isothermal Titration Calorimetry to Brynn Mawr College in Pennsylvania and trained faculty and students. These activities have contributed to the education and training of a new generation of American scientists.
