Dean R Madden, PhD
Professor of Biochemistry and Cell Biology
Vice Provost for Research
Director, Dartmouth COBRE Institute for Biomolecular Targeting
Biochemistry and Cell Biology
A.B. Physics, Harvard 1985
Ph.D. Biophysics, Harvard 1992
Academy of Master Faculty Educators
Molecular and Cellular Biology Graduate Programs
Neuroscience Center at Dartmouth
Quantitative Biomedical Sciences
Dartmouth Biochemistry & Cell Biology
7200 Vail Building
Hanover NH 03755
Office: Vail 408a
The goal of our research is to understand the functional characteristics of ion channels and transporters in terms of their molecular structure. Transmembrane electrochemical gradients underpin a wide variety of essential physiological processes, including photosynthesis and respiration, muscle contraction and nerve signalling. Highly specialized ion transporters are responsible for establishing and maintaining these gradients, while ion channels are designed to exploit the gradients by selectively and/or temporarily permeabilizing the membrane in response to external stimuli. Here is an overview of our research projects:
A major focus of our research involves the AMPA-receptor subfamily of glutamate receptor ion channels, which are found in the postsynaptic membrane and are responsible for most fast excitatory cell-to-cell communication in the central nervous system. After binding to neurotransmitter released from the presynaptic membrane, they open to conduct cation fluxes that depolarize the membrane and stimulate the receiving cell to fire. The channels then spontaneously close ("desensitize"). The kinetics and magnitude of the current can be fine-tuned to cellular requirements by controlling the nature and identity of the glutamate receptor subunits expressed. We wish to understand this complicated molecular machine at the atomic level. Research projects include:
Stereochemistry and thermodynamics of ligand binding:
Published crystallographic data from other groups have shown that agonist binding is associated with a Venus-flytrap style cleft closure in the glutamate receptor. How does the interaction and cleft closure proceed? To understand the exact sequence of molecular events, we have combined site-directed mutagenesis with fluorescence spectroscopy to follow the kinetics of agonist association, leading to a model in which rapid docking to one side of the open cleft is followed by cleft closure and trapping of ligand. We also use small-angle X-ray techniques to follow the conformational dynamics of the LBD in solution. Finally, we have crystallized LBD constructs from additional AMPA-R subunits, revealing additional conformational contributions to channel activation.
Molecular Architecture of AMPA-Receptors:
Although conformational changes in the LBD have been studied in great detail, little is known about how the LBD are assembled to form a molecular machine that can activate the associated ion channel. We have developed a robust expression system for the purification of intact AMPA-R and use electron microscopy to study the structure of these channels.
We are also interested in understanding binding interactions of the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel found in the lung and other epithelial tissues. CFTR mutations leading to trafficking and folding defects are the most common source of genetic disease among Caucasians. Our goal is to characterize the interaction of CFTR with binding partners that regulate trafficking and folding processes.
Design of CAL-selective inhibitors:
We have shown that CAL limits the post-maturational stability of the ΔF508-CFTR mutant, which is carried by ~90% of CF patients. Furthermore, this interaction is mediated by the CAL PDZ domain. More recently, we have demonstrated that the CAL:CFTR interaction is potentially susceptible to selective disruption. Current research is focused on the design and identification of inhibitors selective for the CAL PDZ binding site, and the evaluation of their therapeutic potential. Our work involves a combination of X-ray crystallography, NMR, fluorescence spectroscopy, high-throughput screening of small-molecule inhibitors, and electrophysiological studies of polarized epithelial cell monolayers.
Targeting Pseudomonas infections:
Due to impaired mucociliary clearance, chronic infection with Pseudomonas aeruginosa is major cause of CF morbidity. Our collaborators in the O'Toole and Stanton labs have identified Cif (CFTR Inhibitory Factor) as a Pseudomonas protein that further suppresses CFTR expression and may therefore facilitate airway colonization. We are studying the structure and function of Cif, using X-ray crystallography and enzyme-activity assays, in order to identify its physiological substrates and mechanism of action.
Understanding regulators of CFTR endocytic trafficking:
In collaboration with colleagues at the University of Pittsburgh, we are analyzing the role of proteins that interact with CFTR to control its endocytic uptake. Ultimately, these proteins may provide additional therapeutic targets.
Biochemistry 101: Molecular Information in Biological Systems
Biochemistry 110: The Biochemical and Genetic Basis of Medicine
Dean started teaching math at a summer ‘bootcamp’ for MPP students, and has since taught math, biochemistry, and biophysics in Munich, Heidelberg, Cambridge, and Hanover. He served as Chair of the MCB Graduate Program and has participated in Dartmouth’s Strategic Planning for Graduate Education and the Geisel Curriculum Reform initiative, where he served as co-chair of the Biomedical Sciences Working Group and a member of the Master’s Degree Task Force. Dean is currently course director for BIOC101 – the MCB first-term core course – and leads small-group discussions in BIOC110 – the Geisel first-term Biochemistry course.
Dean mentors early-career faculty interested in small-group teaching, graduate education, and research at the interface of medicine, biology, chemistry, and math. He has coordinated junior faculty mentoring in the Dartmouth Lung Biology COBRE and currently serves in the SYNERGY Office of Research Mentoring.
Optimization of the process of inverted peptides (PIPE<sup>PLUS</sup>) to screen PDZ domain ligands.
Active-Site Flexibility and Substrate Specificity in a Bacterial Virulence Factor: Crystallographic Snapshots of an Epoxide Hydrolase.
The CFTR trafficking mutation F508del inhibits the constitutive activity of SLC26A9.
The cif Virulence Factor Gene Is Present in Isolates From Patients With Pseudomonas aeruginosa Keratitis.
Pseudomonas aeruginosa sabotages the generation of host proresolving lipid mediators.
A parallel panning scheme used for selection of a GluA4-specific Fab targeting the ligand-binding domain.
Rational Design of Potent and Selective Inhibitors of an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa.
Visualizing the Mechanism of Epoxide Hydrolysis by the Bacterial Virulence Enzyme Cif.
Inhibiting an Epoxide Hydrolase Virulence Factor from Pseudomonas aeruginosa Protects CFTR.
A Compact Structure of Cytochrome c Trapped in a Lysine-Ligated State: Loop Refolding and Functional Implications of a Conformational Switch.