Matthew Junker, Ph.D.

   Associate Professor of Chemistry

   Faculty Advisor, Biochemistry Program

   Department of Physical Sciences Program in Chemistry

   Kutztown University


   314 Boehm Science Center            FAX:  (610) 683-1352

   Phone:  (610) 683-4199                    Email:


Courses Taught:  Biochemistry and Chemistry


   CHM 310, CHM 311        Biochemistry I with laboratory         lecture syllabus     lab syllabus

   CHM 312, CHM 313        Biochemistry II with laboratory        lecture syllabus     lab syllabus

   CHM 215                        Organic Chemistry I laboratory

   CHM 217                        Organic Chemistry II laboratory

   CHM 318                        Advanced Biochemistry

   CHM 370, 371                 Research in Chemistry

   CHM 380                        Senior Seminar in Chemistry

Course materials available online at Desire2Learn


Research: Protein Structure and Function in

Apoptosis, Gene Expression, and Bacteria Pathogenesis

Current student researchers:  Will Blakely, Scott Dougherty, Demetrios Kostomiris, Robert Nwokonko, Tim Trexler     

Prior KU student researchers:  Haley Andersen, James Bowalick, Lindy Carpenter, Ethan Daniels, Marcela Ferreira, Larry Fredericks, Kevin Frey, Stephanie Hoppes, Heather Jones, Patrick McCaffrey, Stephen Pearson, John Ponis, Josh Sabatine, Drew Tietz, Robert Wagner, Kyle Webb, Courtney Young


Many cellular processes are carried out by proteins, tiny machines that catalyze chemical reactions, transport molecules within and between cells, provide cell architecture, and regulate gene expression and cell growth.  The ability of proteins to carry out specific processes depends on their structure and energetics: active site geometries, complementation of recognition surfaces, conformational changes, affinities, stability of folds.  In this laboratory, we investigate the molecular mechanism of proteins that function in programmed cell death, gene expression, and bacterial pathogenesis. 

Experimental approach

All projects generally follow a common set of steps:

   1.  Use recombinant DNA methods (cloning) to insert into bacteria the genes for proteins of interest.

   2.  Grow bacteria to make the proteins of interest.

   3.  Lyse (break open) the bacteria and purify the proteins of interest.

   4.  Carry out complementary functional (biochemical assays) and structural studies of the purified proteins. 


Example: Studies of apoptosis

Apoptosis (programmed cell death) is a process in all animals that eliminates unneeded or unhealthy cells, such as aged cells that need to be regenerated or cells that are at risk for causing cancer.  Dysfunction in apoptosis can lead to cancer or neurodegenerative diseases.  At a biochemical level, apoptosis requires the activation of caspase enzymes.  Caspases are normally held in check by the Inhibitor of Apoptosis (IAP) proteins.  Certain apoptosis stimulators bind to IAPs to de-inhibit (activate) caspases. 

Studies in living cells had shown that alteration of a highly conserved Arg amino acid in IAPs caused dysfunction in apoptosis.  Using purified proteins and a protein binding assay, this laboratory showed that the dysfunction resulted from a loss in the ability of the IAP to bind to apoptosis stimulators (above, right). 


Structure analysis (including CD)  then determined that the impaired binding was caused by an altered conformation of the IAP protein.  Analysis of published IAP structures revealed that the conserved Arg makes several critical interactions (bridging hydrogen bonds, cation-p, helix-capping) that stabilize the IAP tertiary structure.  No other amino acid can make this same set of interactions.  Since the Arg resides on a face of the IAP opposite to where stimulators bind, it may be important for allosterically coupling stimulator binding to other IAP functions. 




Other studies are investigating the mechanism for how IAPs regulate the enzymatic activity of caspases.  One assay measures caspase activity by the increased fluorescence when the capase cleaves a synthetic substrate mimic. 


The information gained from these studies is providing detailed insight into how these proteins regulate apoptosis  in living cells.  It should also aid in developing therapies to treat diseases where apoptosis dysfunction occurs, such as cancer and neurodegeneration.





Recent Funding

   Kutztown University Research Committee                                                             1/13-7/15

   "Substrate recognition and ligation mechanisms of yeast cytochrome c                   $7,662

   heme lyase"                      

   Co-PI's: Dr. Carsten Sanders and Dr. Matt Junker

   Kutztown University Research Committee                                                             1/10-6/11

   "Probing the role of CCHL (cytochrome c heme lyase) in apoptosis"                        $4,360

   Co-PI's: Dr. Carsten Sanders and Dr. Matt Junker

   Kutztown University Research Committee                                                             1/07-6/08

   "Using DNA computing to solve a mathematical problem"                                        $3,550

   Co-PI's: Dr. Fran Vasko and Dr. Matt Junker

   PA State System of Higher Education                                                                   7/06-7/07

   "A new method to control protein-protein interactions for studying apoptosis             $5,800

   (programmed cell death)"

   Kutztown University Research Committee                                                              6/06-6/07

   "Testing a Potential New Mechanism for How Cells Undergo Programmed                $2,500

   Cell Death (Apoptosis)"

   Kutztown Undergraduate Research Committee   (awarded to student)                       2/06-6/06

   "Identifying the binding region for the Cry1A toxin on the BT-R1 receptor protein"       $500

   Student principal investigator: Lindy Carpenter  

   Commonwealth of PA Dept. of Labor & Industry                                                      7/06-7/07

   "Microplate reader technology for preparing students at Kutztown University              $47,600

    for jobs in the bio-medical industry cluster"  

   American Cancer Society Institutional Research Allocation Grant                             1/04-12/04

   "Characterization of Apoptosis Proteins as Therapeutic Targets in Cancer"                $20,000          


Recent Publications


1.   Junker, M. (2010) "A hands-on classroom simulation to demonstrate concepts in enzyme kinetics."

      J. Chem. Ed., 87: 294-295.


2.   Ibrahim, M.A., Griko, N., Junker, M., and Bulla, L.A. (2010) "Bacillus thuringiensis: a genomics

      and proteomics perspective." Bioengineered Bugs, 1: 31-50. 


3.   Griko, N.B., Rose-Young, L., Zhang, X., Candas, M., L. Carpenter, L., Ibrahim, M.A., Junker, M.,

      and Bulla, L.A. (2007)  "Univalent binding of the Cry1Ab toxin of Bacillus thuringiensis to a

      conserved motif in the cadherin receptor BT-R1."  Biochemistry, 46: 10001-10007.


4.   Kou, W., Ortiz-Acevedo, A., Kolla, H.S., Haines, D., Junker, M., and Dieckmann, G.R.(2005)

      "Modulation of zinc- and cobalt-binding affinities through changes in the stability of the

      zinc ribbon protein L36."  J. Biol. Inorg. Chem., 10: 167-180.


5.   Wang, L.L., Denman, I., and Junker, M. (2004)  "Control of HAP1 DNA site recognition

      through the interplay of multiple distinct intermolecular interactions."  Biochemistry,

      43: 13816-13826.


6.   Griko, N., Candas, M., Zhang, X., Junker, M., and Bulla, L.A.  (2004)  "Selective

      antagonism of the cadherin BT-R1 interferes with calcium-induced adhesion of epithelial

      membrane vesicles."  Biochemistry, 43: 1393-1400.


7.   Harrod, C.A., Yang, X., Junker, M., and Reitzer, L.  (2004)  "Evidence for a second

      interaction between the regulatory amino-terminal and central output domains of the response

      regulator NtrC (Nitrogen Regulator I) in Escherichia coli."  J. Biol. Chem. 279: 2350-2359.


8.   Luque, L.E., Grape, K.G., and Junker, M. (2002)  "A highly conserved arginine is critical for

      the functional folding of inhibitor of apoptosis (IAP) protein BIR domains." 

      Biochemistry  41: 13663-13671. 


9.   Upadhyaya, A., Khan, M., Mou, T.-C., Junker, M., Gray, D.M., and DeJong, J.  (2002) 

      "The germ-specific transcription factor ALF: structural properties and stabilization of the

      TBP-DNA complex."   J. Biol. Chem277: 34208-34216.


10.  Junker, M., Rodgers, K.K., and Coleman, J.E. (1998)  "Zinc as a structural and folding

      element of proteins which interact with DNA."  Inorg. Chim. Acta 275-276: 481-492.

Kutztown University of Pennsylvania

A member of the State System of Higher Education

last modified 8/12/15 by M. Junker