Proteins are biological polymers that fold into specific three-dimensional structures. They are the molecular workhorses of life and are involved in a wide variety of functions such as increasing the rates of chemical reactions, storing and transporting small molecules such as oxygen, mediating the propagation of signals or "instructions" within the cell and much more. Most protein function involves binding to a small molecule or another protein through special features on the surface within so-called binding sites. Dr. Mattos and members of her group are interested in understanding the features that distinguish binding sites on proteins from other areas on the protein surface. This project aims to do this by observing how a variety of small molecules bind to a set of well-studied proteins using a method called X-ray crystallography that allows visualization of the three-dimensional structure of proteins and the associated small molecules at near atomic resolution. The Mattos lab has collected the experimental data sets necessary for this type of analysis and is now using computational methods to mine the data sets for fundamental properties of protein surfaces in general and binding sites in particular. The quantitative methods will be used to validate the correspondence between protein surface properties obtained in the small molecule solvent environment and those observed in the more natural aqueous environment. Once the validation is complete the fundamental protein binding site properties will be directly obtained from experimental data sets acquired in the non-natural solvent environment. Understanding the properties of protein binding sites is critical to understanding of how proteins work and therefore a very important step in making sense of the complicated processes of life.
Broader impact Dr. Mattos has developed this project in such a way that research is an integral part of teaching undergraduates. The research will build on the thriving and diverse educational environment that she has already created in her group. Ten undergraduates from her classes each year will be invited to work with graduate students and the more senior members of the laboratory. The team will participate in an international collaboration with Prof. Janet Thornton's group at the European Bioinformatics Institute (EBI) in England, which is at the forefront of computational analysis of protein experimental databases. Dr. Mattos has recently returned from a sabbatical at the EBI, during which both a graduate and an undergraduate student also participated. She plans to continue to engage students in this international collaboration. In addition, Dr. Mattos is involved in mentoring minority junior faculty members at various universities in the United States and is working to encourage minority undergraduate and graduate students at North Carolina State University to write research proposals for fellowship applications to graduate school.
The intellectual merit of this grant focused on the study of binding sites for ligands on protein surfaces, including analysis of water binding sites that aid in maintaining protein structure, function and completing binding pockets for enzyme substrates and other ligands. We used the Multiple Solvent Crystal Structures method to produce a series of structures of several proteins in different solvent environments. We collected data and solved structures for a diverse group of proteins involved in cancer, digestion, virus integration into host cell DNA and a sugar-binding protein. We developed the analysis software DRoP to mine the protein structures we collected. We not only confirmed what was already known about these proteins through other methods (validation), but discovered a new binding pocket in the active site of the viral protein P22TSP, showed that the protein-DNA interaction in the protein BAF is mediated by water molecules and determined a pathway of communication between the active site of the signal transduction protein Ras and membrane binding sites on the opposite side of the molecule. We recently made our solvent analysis program DRoP available to the public through a webserver at DRoPinTheMattosLab.org and will soon be making the code open source through GitHub. The broader impacts of the grant were many. This funding supported two graduate students, Bradley M. Kearney and Mychal Smith (African American), each of whom worked on a project with international collaborations. Brad went with me to England to visit our collaborator Janet Thornton in 2009 and Mychal met with our German collaborator Stephanie Barbirz during her visit to our laboratory in 2010. Both students presented their work in several conferences and recently finished their Ph.D. thesis. Brad defended in October 2012 and is currently doing postdoctoral work with Jack Johnson at The Scripps Research Insitute in La Jolla, CA and Mychal defended his thesis October 2013 and is currently interviewing for postdoctoral positions. During the funding period both Brad and Mychal helped mentor undergraduates from underrepresented groups in the sciences. I have continued to work toward my commitments to increase diversity in my laboratory, at Northeastern University and at the national level in general. I am the PI on a recently funded REU site in Chemistry and will reach out to minority students at universities that are not heavily focused on research. At Northeastern I have started the Northeastern faculty seminar program where the College of Science funds faculty to give research talks at institutions that graduate large numbers of minority students in sciences and at the national level I have continued to work with QEM on several grant-writing workshops for faculty at HBCUs, HSIs and other minority-serving institutions.
