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James D. Baleja, Ph.D. Associate Professor, Tufts Department of Biochemistry B.Sc. Biochemistry, University of Manitoba Ph.D. Biochemistry, University of Alberta |
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Links:ResearchLab MembersRecent Publications |
Research Summary:
My laboratory uses nuclear magnetic resonance spectroscopy and other biophysical methods
such as X-ray crystallography, Circular Dichroism spectroscopy, fluorescence spectroscopy,
and isothermal titration calorimetry to gain an understanding of protein-protein interactions.
Although most drugs target proteins with enzymatic activity a few target protein-protein interactions.
We are interested in structure-based approaches to develop inhibitors of protein-protein interactions.
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From a description of the points in space that elicit binding to the HPV E6 protein defined the pharmacophore (left) that was used to select inhibitory compounds (right). The pharmacophore comprises 3 lipophilic points, 2 hydrogen-bonding points (CO2H), and one exclusion sphere. The locations of these points were derived from the three-dimensional structure of a peptide, E6AP, that binds E6. The radii of the location spheres are calculated from a molecular dynamics simulation of the peptide structures. An example of a hit is Aldrich compound r278319. For further information see Baleja et al. (2006). "Identification of inhibitors to papillomavirus type 16 E6 protein based on three-dimensional structures of interacting proteins." Antiviral Res 72: 49-59. |
Design of Papillomavirus Inhibitors
The papillomavirus causes several diseases, ranging from the common wart to a
more virulent strain that produces cervical cancer, a costly and devastating
disease that is the second leading cause of death in women worldwide.
The laboratory is using NMR to analyze the three-dimensional structures of
two viral proteins. The E2 protein takes over the host cell and controls the
growth of the virus by binding to DNA. The E6 protein degrades the p53 tumor
suppressor and has an effect on cell cycle proteins. We have determined the
structures for several cellular proteins that bind E6. Through computer
analysis and modeling, we aim to design drugs that disable the triggering mechanism
of the virus. Some of this work is in collaboration with Elagen, Inc., a biotechnology
company.
Role of the EH domain in Endocytosis and Cellular Proliferation
The movement of molecules to and from the surface of a cell is fundamental
to many biological processes including glucose uptake, fertilization,
cholesterol metabolism, and cellular signaling. These vesicle-mediated sorting
and cellular remodeling mechanisms are mediated by interactions between proteins
containing EH domains and proteins containing asparagine-proline-phenylalanine (NPF)
sequences. The human genome encodes 17 EH domains contained in 11 proteins,
and about twenty proteins contain NPF motifs that are available for interaction.
Although all the EH domain-containing proteins are involved in vesicle trafficking,
the factors that govern selectivity of NPF-containing partners are largely unknown.
The gap in knowledge regarding the most likely EH domain/NPF partners is a problem
as it prevents us from understanding the molecular interactions that guide the
movement of proteins within a cell. For example, the EHD1 protein functions in
the recycling of vesicles and thus plays an important role in cellular physiology
by directing proteins such as the LDL-cholesterol receptor and the epidermal
growth factor (EGF) receptor back to the cell surface as well as controlling
the level of the GLUT4-glucose transporter present on the cell surface.
Therefore, EHD1 affects cholesterol metabolism, cell signaling, and
glucose homeostasis within the cell. The structures of various domains
of EHD1 are being primarily to understand specificity within its EH domain/NPF
interaction pairs. The preliminary data also suggest new protein-protein
partners that can be verified using co-localization, GST-pulldown, and
coimmunoprecipitation experiments. Another example is the EH domain-containing
X-linked Reps2 protein is part of a protein complex that directly interacts
with a GTPase activating protein, RalBP1. Via RalBP1, Reps2 inhibits
growth factor signaling and alters signaling molecules and drug efflux.
Despite the importance of Reps2 in building the networks responsible for
protein trafficking and signaling, we do not know how these proteins assemble.
Such a lack of knowledge is a problem because without it we cannot understand
key features of cellular function that, in the long term,
may be manipulated for therapeutic purposes.
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For more details, please see the publications below.
