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Dean R Madden, Ph.D.

Professor of Biochemistry
Associate Director, Dartmouth Lung Biology Center


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


Contact Information:

Dartmouth Biochemistry
7200 Vail Building
Hanover NH 03755

Office: Vail 408a
Phone: 603-650-1164
Fax: 603-650-1128
Email: drm0001@dartmouth.edu

Professional Interests:

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.

Grant Information:


Courses Taught:

Biochemistry 101: Molecular Information in Biological Systems
Genetics 102: 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 serves 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 lectures and leads small-group discussions in BIOC110 – the Geisel first-term Biochemistry course.

Mentoring Information:

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.

Selected Publications:


Qian Z, Xu X, Amacher JF, Madden DR, Cormet-Boyaka E, Pei D
Intracellular Delivery of Peptidyl Ligands by Reversible Cyclization: Discovery of a PDZ Domain Inhibitor that Rescues CFTR Activity.
Angew Chem Int Ed Engl 2015 Mar 17;
PMID: 25785567

Amacher JF, Zhao R, Spaller MR, Madden DR
Chemically modified peptide scaffolds target the CFTR-associated ligand PDZ domain.
PLoS One 2014; 9(8):e103650
PMID: 25136860

Koeppen K, Coutermarsh BA, Madden DR, Stanton BA
Serum- and glucocorticoid-induced protein kinase 1 (SGK1) increases the cystic fibrosis transmembrane conductance regulator (CFTR) in airway epithelial cells by phosphorylating Shank2E protein.
J Biol Chem 2014 Jun 13; 289(24):17142-50
PMID: 24811177

Bahl CD, Hvorecny KL, Bridges AA, Ballok AE, Bomberger JM, Cady KC, O'Toole GA, Madden DR
Signature motifs identify an Acinetobacter Cif virulence factor with epoxide hydrolase activity.
J Biol Chem 2014 Mar 14; 289(11):7460-9
PMID: 24474692

Amacher JF, Cushing PR, Brooks L 3rd, Boisguerin P, Madden DR
Stereochemical preferences modulate affinity and selectivity among five PDZ domains that bind CFTR: comparative structural and sequence analyses.
Structure 2014 Jan 7; 22(1):82-93
PMID: 24210758

Baranovic J, Ramanujan CS, Kasai N, Midgett CR, Madden DR, Torimitsu K, Ryan JF
Reconstitution of homomeric GluA2(flop) receptors in supported lipid membranes: functional and structural properties.
J Biol Chem 2013 Mar 22; 288(12):8647-57
PMID: 23382380

Amacher JF, Cushing PR, Bahl CD, Beck T, Madden DR
Stereochemical determinants of C-terminal specificity in PDZ peptide-binding domains: a novel contribution of the carboxylate-binding loop.
J Biol Chem 2013 Feb 15; 288(7):5114-26
PMID: 23243314

Madden DR, Swiatecka-Urban A
Tissue-specific control of CFTR endocytosis by Dab2: Cargo recruitment as a therapeutic target.
Commun Integr Biol 2012 Sep 1; 5(5):473-6
PMID: 23181163

Ballok AE, Bahl CD, Dolben EL, Lindsay AK, St Laurent JD, Hogan DA, Madden DR, O'Toole GA
Epoxide-mediated CifR repression of cif gene expression utilizes two binding sites in Pseudomonas aeruginosa.
J Bacteriol 2012 Oct; 194(19):5315-24
PMID: 22843844

Kundu R, Cushing PR, Popp BV, Zhao Y, Madden DR, Ball ZT
Hybrid organic-inorganic inhibitors of a PDZ interaction that regulates the endocytic fate of CFTR.
Angew Chem Int Ed Engl 2012 Jul 16; 51(29):7217-20
PMID: 22700245