The overall goal of our research is to achieve a detailed mechanistic understanding of signal transduction processes triggered by molecular recognition by means of computational methodologies that range from bioinformatics to modeling and simulation. The strength of our research relies on the deliberate integration of these computational methodologies with collaborative experimental approaches to provide valuable mechanistic interpretations at the molecular level of the ligand-induced transmission of the signal to the inner side of the cell membrane. While our research is driven by the exploration and improvement of computational methods to characterize generalizable mechanisms of molecular recognition and signal transduction, we are excited by the contributions that our computational and modeling efforts make to the experimental field through the generation of new testable hypotheses.

Current Research

1. Prediction and Validation of Opioid Receptor Oligomerization
   The recent discoveries that opioid receptors, which are members of the G-protein coupled receptor (GPCR) family, can exist as heteromers in live cells, and that delta-mu and delta-kappa opioid receptor complexes are distinct functional signaling units, have added a new dimension of complexity to the opioid research field. Structural and mechanistic information about opioid receptor dimeric/oligomeric complexes has therefore become of major importance for understanding the mechanisms of action of opiates. We plan to identify the molecular determinants responsible for the oligomerization of delta- and mu-opioid receptors (both homo- and heteromers) in a structural context of receptor models, using an iterative combined computational and experimental approach. In preliminary studies, inferences from our correlated mutation analysis methods were used to construct several putative configurations of interacting transmembrane regions of opioid receptor dimers. These first-generation models provided specific hypotheses of interaction between TM regions of monomeric entities, which helped prioritize cysteine cross-linking experiments designed to map the dimerization/oligomerization interfaces of opioid receptors. These experiments are currently ongoing in the laboratory of our collaborator at Columbia University, Dr. Jonathan Javitch. In an iterative fashion, our computational studies will then use the detailed information obtained from the experimental studies on wild-type, agonist-bound, and inverse-agonist bound states of opioid receptors to develop more refined molecular models of the interfaces of active and inactive delta- and mu-opioid receptor homo- and heteromers; in turn, these models will suggest dimerization-disrupting mutants. The role of these dimerization-disrupting mutations will first be evaluated computationally and then tested experimentally using both cysteine cross-linking and time resolved fluorescence energy transfer (TR-FRET) techniques. Inferences from these studies are expected to provide new insights into conformational and structural details in the activation mechanisms of opioid receptor subtypes. In particular, an important goal of these studies is to identify negative and/or positive modulators of GPCR dimerization/oligomerization, and thus affect receptor function in a manner that will reveal physiologically relevant mechanisms that depend and/or ensue from these phenomena.
2. Construction of an Information Management System to store computational and experimental information about GPCR dimers/oligomers
   This project involves the bioinformatics infrastructure for our research on GPCR dimerization. We plan to develop, interpret and disseminate to the scientific community detailed information about the structural context of GPCR oligomerization. The work involves fundamental concepts and constructs in bioinformatics. We have recently finalized the development of an appropriate ontology for an information management system (GPCR-Oligomerization Knowledge Base; GPCR-OKB) that will store, allow structured queries, browsing and visualization of the structural features at the interface of GPCR dimers/oligomers in a manner that will facilitate the design and interpretation of pointed physiological and pharmacological experiments. While the planned studies of this project do not explicitly involve experimental work, they do rely on the expertise of experimental collaborators (Drs. Michel Bouvier, Lakshmi Devi, Susan George, Jonathan Javitch, Martin Lohse, Graeme Milligan, Richard Neubig, Krzysztof Palczewski, Marc Parmentier, and Jean Philippe Pin) for the interdisciplinary assessment of the requirements for a user-friendly database containing experimental and computational information about GPCR dimers/oligomers. In addition, this project takes advantage of the expertise in data management and multimedia design in the lab of Dr. Fabien Campagne in the Institute for Computational Biomedicine at Weill Medical College of Cornell University. Last but not the least we rely on the expertise of Dr. Gerrit Vriend (Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, Nijmegen, The Netherlands) in data management of GPCRs.
3. Integrin Allostery and Bidirectional Signaling
   Integrins are hetero-dimeric cell-surface receptors that mediate dynamic adhesive cell-cell and cell-extracellular matrix (ECM) interactions, which are critical for embryonal growth and development, tissue homeostasis, tumor formation, and many other processes in the cell. In addition to connect the cell to its neighborhood, integrins also function as signal transducers, activating various intracellular signaling pathways either through interactions of the short cytoplasmic integrin tails with intracellular proteins (inside-out signaling) or through interaction of their ectodomain with ECM components (outside-in signaling). Both these mechanisms involve long-range conformational changes that still need to be elucidated at the molecular level. The recently published crystal structures of integrin alphaVbeta3 and alphaIIbbeta3 provide the structural basis for the application of computational methodologies to help understand the dynamics of integrin structures, and the allosteric changes that guide their diverse functions. A close and productive collaboration with the laboratory of Dr. Barry Coller at Rockefeller University has strengthened our interest in the study of structure-function relationships of the so-called beta3 integrin receptors, and the role of their dynamic behavior in bidirectional signaling. We are currently using both atomistic and coarse-grained approximations to define the correlation between global dynamics and molecular mechanisms of function of beta3 integrins, and help provide a coherent structural context to ongoing experimental studies in Dr. Coller's lab.