Protein-protein interactions are central to life. Nearly all cellular processes depend critically on proteins forming specific complexes. Many human diseases are a result of proteins from microbes interacting with host proteins, or mutations in human proteins, that dysregulate signaling pathways.
Research in our laboratory focuses on understanding protein-protein interactions, both to define the molecular basis of and to develop novel therapeutics against particular diseases, as well as to define the fundamental driving forces that govern specificity and affinity in protein-protein interactions universally. To do so, we combine the tools of protein engineering (e.g., directed evolution), structural biology (e.g., X-ray crystallography) and molecular biophysics (e.g., surface plasmon resonance and isothermal titration calorimetry). Current projects in our laboratory include:
Our research group currently conducts several HIV-related projects. The first of two projects related to characterizing natural immunity to HIV exhibited by some individuals is an investigation of the molecular basis of antibody-dependent cellular cytotoxicity in elite controller or natural virus suppressor populations versus individuals with progressive disease. The second project concerning natural immunity to HIV is aimed at understanding the role of single-nucleotide polymorphisms in the human leukocyte antigen locus that strongly correlated with natural HIV control. These studies could lead to the development of novel HIV/AIDS vaccines in pre-exposed populations or adaptive T cell therapies in HIV-infected individuals. Our third HIV-related project focuses on determining the molecular basis of myelomonocytic receptor interactions with cytotoxic T lymphocyte escape variants of HIV antigens displayed by MHC class I molecules, a novel immune escape mechanism utilized by HIV. Again, these studies are poised to lead to novel protein-based therapeutics against HIV infection.
Since its inception, the Sundberg laboratory has been studying the molecular basis of toxic shock syndrome and other human diseases caused by the overstimulation of the immune system by a family of bacterial protein toxins, superantigens, secreted by Staphylococcus aureus and Streptococcus pyogenes. We continue our studies to fully define the molecular basis of T cell activation by superantigens, as well as the engineering of T cell receptor-based protein therapeutics against superantigen-related disease, which we have shown to be completely protective against a particular superantigen in animal models of superantigen-mediated lethality.
A protein virulence factor from Helicobacter pylori, CagA, causes gastric adenocarcinoma through its ability to alter cell signaling pathways in human gastric epithelial cells. CagA is a polymorphic protein, and the genetic differences between distinct strains of H. pylori correlate with the risk of developing cancer. The molecular basis of how CagA polymorphisms result in differential interactions with host cell proteins, subsequent changes in cell signaling, and the development of gastric cancer is poorly understood. We are currently working towards determining the X-ray crystal structure of CagA, alone and in complex with its molecular chaperone within the bacterium, CagF. We are also defining the stoichiometric, kinetic and thermodynamic parameters of CagA/CagF binding. We are extending these studies to investigate the molecular basis of CagA complex formation with human host cell proteins known to be important in the dysregulation of cellular signaling associated with gastric cancer.
Due to the importance of protein-protein interactions in nearly all aspects of biology, efforts to decipher the rules that govern these associations have been underway for decades. In order to better quantify the various effects that contribute to protein molecular recognition, model protein-protein interaction systems are often generated that can be perturbed in a controllable manner to alter one factor that affects binding in isolation, and subsequently assessed for structural and energetic changes resulting from that perturbation. Altering these model systems is commonly achieved by mutating individual amino acid residues and measuring the effects of each individual mutation. However, many properties of proteins that affect binding are not restricted to the effects of a single amino acid residue but instead are dependent on the coordinated behavior of numerous residues within an interface. Indeed, there exists a significant degree of networked communication between interface residues that serves as a significant energetic driver for interaction. To address this key issue in protein molecular recognition, we have pioneered the use of directed evolution to develop model protein-protein interaction systems from which the networked energetics within protein interfaces can be quantified. We are currently defining the roles of energetic cooperativity and of disordered protein regions in protein complex formation.
Sangwoo Cho, Chittoor P. Swaminathan, Daniel A. Bonsor, Jianying Yang, Melissa C. Kerzic, Michele C. Kieke, Peter S. Andersen, David M. Kranz, Roy A. Mariuzza, and Eric J. Sundberg (2010). Assessing the energetic contributions to binding from a disordered region in a protein-protein interaction, Biochemistry 49(43), 9256-9268.
Mathias Lichterfeld, Daniel G. Kavanagh, Katie L. Williams, Beenu Moza, Stanley K. Mui, Toshiyuki Miura, RohiniSivamurhty, Rachel Allgaier, Florencia Pereyra, Alicja Trocha, Danlei Mou, Margaret Feeney, Huabiao Chen, Rajesh T. Gandhi, Marcus Altfeld, Eric S. Rosenberg, Todd M. Allen, Rachel Allen, Bruce D. Walker, Eric J. Sundberg and Xu G. Yu (2007). A viral CTL escape mutation leading to immunoglobulin-like transcript 4 (ILT4)-mediated functional inhibition of myelomonocytic cells, Journal of Experimental Medicine 204(12), 2813-2824.
Beenu Moza, Ashok K. Varma, Rebecca A. Buonpane, Penny Zhu, Christine A. Herfst, Melissa J. Nicholson, Anne-Kathrin Wilbuer, Kai W. Wucherpfennig, John K. McCormick, David M. Kranz, and Eric J. Sundberg (2007). Structural basis and T cell specificity and activation by the bacterial superantigen TSST-1, EMBO Journal 26(4), 1187-1197.
Beenu Moza, Rebecca A. Buonpane, Penny Zhu, Christine A. Herfst, John K. McCormick, David M. Kranz, and Eric J. Sundberg (2006). Long-range cooperative binding effects in a T cell receptor variable domain, Proceedings of the National Academy of Sciences of the United States of America, 103(26), 9867-9872.