Molecular Biophysics Prof. Thomas Kurtzman, Subdiscipline Chair [email protected] Publications A. Dikiy, I., Edupuganti, U.R., Abzalimov, R.R., Borbat, P.P., Srivastava, M., Freed, J.H., Gardner, K.H. Insights into histidine kinase activation mechanisms from the monomeric blue light sensor EL346. Proceedings of the National Academy of Sciences, USA, 2019, 116, 4963-4972. B. Ben-Shalom, I.Y., Lin, C., Kurtzman, T., Walker, R.C., Gilson, M.K. Simulating Molecular Biophysics seeks to understand essential biological water exchange to buried binding sites. processes in terms of physical chemistry. CUNY has over 30 Journal of Chemical Theory and faculty working in this area. Research interests include the Computation. 2019, 15, 2684-2691. mechanisms of signal transduction in cells, protein dynamics by C. Perea, W., Schroeder, K.T., Bryant, neutron scattering and NMR, experimental and computational A.N., Greenbaum, N.L. Interaction analysis of membrane protein structure and dynamics, and between the Spliceosomal Pre-mRNA protein design. Students are encouraged to contact an Branch Site and U2 snRNP Protein p14 individual faculty member to explore different research Biochemistry, 2016, 55 (4), pp. 629- opportunities. 632. Research Areas • Biophysical mechanisms of ligand binding • Protein NMR • Structural Biology • Computational biophysical chemistry • Neutron scattering • Enzymology • X-ray Crystallography • Biotechnology Dr. Zimei Bu Publications Dr. Bu’s group studies • Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics. Callaway the structure and DJE, Matsui T, Weiss T, Stingaciu LR, Stanley CB, dynamics of protein Heller WT, Bu Z., J Mol Biol. 2017;429(7):987-998. complexes in cell signaling, using neutron • Visualizing the nanoscale: protein internal dynamics and X-ray scattering and neutron spin echo spectroscopy. Callaway DJ, Bu Z., Curr Opin Struct Biol. 2017; 42:1-5. • Phosphatidylinositol 4,5-bisphosphate clusters the cell adhesion molecule CD44 and assembles a Name: Zimei Bu specific CD44-Ezrin heterocomplex, as revealed by small angle neutron scattering. Chen X, Khajeh JA, Ju Position: Professor JH, Gupta YK, Stanley CB, Do C, Heller WT, Affiliation: City College of New York Aggarwal AK, Callaway DJ, Bu Z. J Biol Chem. Address: 160 Convent Avenue 2015;290(10):6639-52. Address: Marshak Science Bldg. Room 1336 New York NY • Molecular conformation of the full-length tumor suppressor NF2/Merlin--a small-angle neutron [email protected] scattering study. Ali Khajeh J, Ju JH, Atchiba M, : http://www.sci.ccny.cuny.edu/~zbu/ Allaire M, Stanley C, Heller WT, Callaway DJ, Bu Z., J Mol Biol. 2014;426(15):2755-68. 2010- current Professor, CCNY 2003-2010 Faculty, Fox Chase Cancer Center • Ligand-induced dynamic changes in extended PDZ domains from NHERF1. Bhattacharya S, Ju JH, 1999-2002 Chemist, NIST Orlova N, Khajeh JA, Cowburn D, Bu Z. J Mol Biol. 1994-1999 Postdoc, Yale University 2013;425(14):2509-28 1994 PhD, Louisiana State University Research Interests •Keywords: Biophysics; Cell Signaling; Structure; Dynamics; Kinetics; Molecular Recognition; X-ray Scattering; Neutron Scattering Our group studies the structure and dynamics of cell signaling proteins and macromolecular complexes that regulate cell adhesion, and the intracellular trafficking of membrane receptors and ion channels. These proteins function as molecular machines and switches that can fail to work properly for various reasons, causing diseases such as cancer. We employ biochemical, biophysical, and structural biology techniques, in particular small angle neutron and x-ray scattering (SAXS and SANS), to study the interactions of these proteins. We also develop methods of utilizing quasielastic neutron scattering, in particular neutron spin echo spectroscopy (NSE) to study protein dynamics and protein domain motions. We have developed a theoretical framework using non-equilibrium statistical mechanics to interpret the NSE data. These methods allow us to see, for the first time, the dynamics of protein complexes on nanometer scales. NSE fills an important information gap in our ability to study protein motion on sub-microsecond time scales and on nanometer length scales. Dr. Junyong Choi Publications Junyong Choi is a JY Choi, et. al., Comparative structural synthetic and computational analysis and molecular design for the medicinal chemist. His development of highly potent and selective research focuses on agents targeting Matrix Metalloproteinase development of therapeutic 13, J. Med. Chem., 2017, 60, 5816-5825 candidates by applying organic synthesis, CM Calvet, JY Choi, et. al., 4-aminopyridyl- computer-aided drug based lead compounds targeting CYP51 design, and chemical prevent spontaneous parasite relapse in a biology. chronic model and improve cardiac pathology in an acute model of Trypanosoma cruzi infection, PLoS Negl. Junyong Choi Trop. Dis., 2017, 11: e0006132 Assistant Professor Department of Chemistry and Biochemistry JY Choi, et. al., Structure Based Design of Queens College of the City University of New York CYP51 Inhibitors, Curr. Top. in Med. 65-30 Kissena Blvd. Chem., 2017, 17, 30-39 Queens, NY [email protected] JY Choi, et. al., Drug strategies targeting CYP51 in neglected tropical diseases, Chem. www.choiresearchlab.com Rev., 2014, 114, 11242-11271 2017- current Assistant Professor, Queens College 2012-2017 Sr. Research Associate, Scripps Florida JY Choi, et. al., The R-Configuration of 4- 2009-2012 Postdoc, Scripps Florida aminopyridyl-based inhibitors of CYP51 2009 PhD, Stony Brook University confers superior efficacy against Trypanosoma cruzi, ACS Med. Chem. Lett., 2014, 5, 434-439 Research Interests Keywords: Medicinal Chemistry, Organic Synthesis, Computer-aided Drug Design, Chemical Biology My scientific objective is to develop specific, target-directed therapeutic candidates for human diseases. My laboratory integrates organic synthesis, medicinal chemistry, computer-aided drug design, and chemical biology to discover bioactive chemical probes. We are particularly interested in discovery of small molecule agents with novel mechanism of action to elucidate specific functions of biological targets. The discovery and techniques established in my laboratory will advance the chemical science in biomedical research for the development of therapeutics Dr. Melissa A. Deri Publications The overarching goal of Deri, M. A.; Mills, P.; McGregor, D. Structure and the Deri Lab is the Evaluation of a Flipped General Chemistry Course integration and application as a Model for both Small and Large Gateway of radiochemistry towards Science Course at an Urban Public Institution. tangible benefits to society. Journal of College Science Teaching: 2018; Vol. 47, We focus on the intersection pp 46-55. of radiochemistry and Deri, M. A.; McGregor, D.; Mills, P., Using biomedical science, more Technology To Flip and Structure General Chemistry specifically in molecular Courses at a Large Public University: Our Approach, imaging and radiotherapy Experience, and Outcomes. In Teaching and the using radioactive metals. Internet: The Application of Web Apps, Networking, and Online Tech for Chemistry Education, American Melissa Deri Chemical Society: 2017; Vol. 1270, pp 75-97. Assistant Professor Lehman College Deri, M. A.; Ponnala, S.; Kozlowski, P.; Burton-Pye, 250 Bedford Park Blvd W B. P.; Cicek, H. T.; Hu, C.; Lewis, J. S.; Francesconi, Bronx, NY 10468 L. C. p-SCN-Bn-HOPO: A Superior Bifunctional [email protected] Chelator for 89Zr ImmunoPET. Bioconjugate Chem http://www.lehman.edu/academics/chemistry/faculty.php 2015; 26(12):2579-2591. PMID: 26550847 Deri, M. A.; Ponnala, S.; Zeglis, B. M.; Pohl, G.; Dannenberg, J. J.; Lewis, J. S.; Francesconi, L. C. 2017- current Assistant Professor, Lehman College An Alternative Chelator for 89Zr 2015-2017 Postdoctoral Fellow, Lehman College Radiopharmaceuticals: Radiolabeling and Evaluation 2015 Postdoctoral Fellow, Memorial Sloan of 3,4,3-(LI-1,2-HOPO). J Med Chem 2014; Kettering Cancer Center 57(11):4849-4860. PMID: 24814511 2010-2015 PhD, Hunter College and The Graduate Center, CUNY Deri, M. A.; Zeglis, B.M.; Francesconi L. C.; Lewis, J. S. PET imaging with 89Zr: From radiochemistry to the clinic. Nucl Med Biol 2013; 40:3-14. PMID: Research Interests 22998840 Keywords: Radiochemistry, Radiopharmaceuticals, Nuclear Medicine, Radiometals, Chelators, Chemical Education, Pedagogy Prof. Deri’s research efforts are focused on addressing the following two questions: How can radioactivity be used to improve human health? Research projects include: Radiometal chelation studies • Bifunctional chelator development • Radiopharmaceutical design How can we get more people interested in chemistry? Teaching practices and strategies studied: Culturally relevant teaching practices • Use of technology in education • Online learning tools • Flipped classroom pedagogy • Active learning strategies Dr. Ruel Desamero Publications Dr. Desamero is a Profit A.A, Desamero R.Z.B. (2018) “Development of spectroscopist by training Peptide-Based Inhibitors of Amylin Aggregation Employing Aromatic and Electrostatic Repulsion. In: currently investigating Mavromoustakos T. Kellici T. (eds) Rational Drug protein-ligand interaction as Design. Methods in Molecular Biology, vol 1824. Human well as protein-protein Press, New York, NY aggregation using various techniques. Lagarias P., Elkhou Y., Vedad J., Konstantinidi A., Profit A.A., Kellici T.F., Kolocouris A., Desamero R.Z.B., Mavromoustakos