sign in sign up
<<
Home , Molecular biophysics, Molecular physics, Structural biology

Molecular 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 . 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, dynamics by C. Perea, W., Schroeder, K.T., Bryant, neutron and NMR, experimental and computational A.N., Greenbaum, N.L. Interaction analysis of membrane protein and dynamics, and between the Spliceosomal Pre-mRNA . Students are encouraged to contact an Branch Site and U2 snRNP Protein p14 individual faculty member to explore different research , 2016, 55 (4), pp. 629- opportunities. 632.

Research Areas

• Biophysical mechanisms of ligand binding • Protein NMR • Structural • Computational • Neutron scattering • Enzymology • X-ray Crystallography • 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 signaling, using neutron • Visualizing the nanoscale: protein internal dynamics and X-ray scattering and . Callaway DJ, Bu Z., Curr Opin Struct Biol. 2017; 42:1-5.

• Phosphatidylinositol 4,5-bisphosphate clusters the cell adhesion 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 , 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; ; Structure; Dynamics; Kinetics; Molecular Recognition; X-ray Scattering; Neutron Scattering

Our group studies the structure and dynamics of cell signaling and macromolecular complexes that regulate cell adhesion, and the intracellular trafficking of membrane receptors and ion channels. These proteins 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 and motions. We have developed a theoretical framework using non-equilibrium statistical 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 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: , Organic Synthesis, Computer-aided ,

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 , 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 -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 , 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 T. (2018) Simulations on the Bioactive of hIAPP22-29 (NFGAILSS) and Rational Drug Design. In: Mavromoustakos T. Kellici T. (eds) Rational Drug Ruel Z. B. Desamero Design. Methods in Molecular Biology, vol 1824. Human Professor Press, New York, NY York College, the Institute of Macromolecular Vedad, J., Domaradzki, M. E., Mojica, E.-R. E., Chang, Assembly, and the Graduate Center E. J., Profit, A.A., Desamero, R. Z. B.. (2017) 94-20 Guy R. Brewer Blvd. "Conformational Differentiation of alpha- Jamaica, NY 11451 cyanohydroxycinnamic acid isomers: a Raman [email protected] spectroscopic study." Journal of . www.york.cuny.edu/portal_college/rdesamero 48: 1282-1288. 2015 – present Professor, York College - CUNY Deng, H., Vedad, J., Desamero, R. Z. B., Callender R.. (2017) "Difference FTIR Studies of Substrate Distribution 2010 - 2015 Associate Professor, York College - CUNY in Triosephosphate Isomerase." Journal of Physical 2003 - 2010 Assistant Professor, York College - CUNY Chemistry B. 121: 10036-10046. 2000 - 2003 Postdoc, Albert Einstein College of Medicine 1998 - 2000 Postdoc, City College - CUNY Profit, A.A., Vedad, J. and Desamero, R.Z.B.. (2017) 1998 PhD, University of Connecticut "Peptide Conjugates of Benzene Carboxylic Acids as Agonists and Antagonists of Amylin Aggregation." Bioconjugate Chemistry. 28: 666-677. Research Interests

Keywords: vibrational spectroscopy; ; ; temperature-jump techniques; structural biology; protein biochemistry; enzymology

My research is centered on investigating the structural and dynamical aspects of protein-small molecule interactions using techniques such as vibrational spectroscopy and temperature-jump relaxation. One aspect of the work is to understand at the molecular level how protein systems work. -substrate interactions have long been recognized as representing an extreme expression of structural complementarities in biological chemistry. Basic research geared towards understanding the inner workings of an enzyme system is important if cures for the diseases caused by a malfunctioning or deficient enzyme are to be found. We have also started investigating the mechanism behind amyloid formation with the goal of synthesizing peptide inhibitors that diminish protein aggregation. Dr. Amedee des Georges

The des Georges lab is Publications interested in the molecular mechanisms of cell des Georges et al., Structure of mammalian eIF3 regulation. We use cryo- in the context of the 43S preinitiation complex, electron microscopy to , 2015 decipher at the atomic level the function of large R. Zalk, O. B. Clarke, A. des Georges et al., macromolecular complexes Structure of a mammalian ryanodine receptor. involved in calcium signaling Nature, 2014. and in the regulation of protein synthesis. Y. Hashem, A. des Georges et al., Structure of the mammalian ribosomal 43S preinitiation Amedee des Georges complex bound to the scanning factor DHX29. Assistant Professor, ASRC Structural Biology Initiative Cell, 2013, 153, 1108-1119. City College, Dept. of Chemistry and Biochemistry CUNY Advanced Science Center, Room 3.316 des Georges et al., Structure of the mammalian 85 St. Nicholas Terrace ribosomal pre-termination complex associated New York NY 10031 with eRF1• eRF3• GDPNP, Nucleic acids [email protected] research, 2013, gkt1279. structbio.asrc.cuny.edu 2015- current Assistant professor, Structural Biology Initiative, CUNY Advanced Science Research Center Assistant professor, Department of Chemistry and Biochemistry, City College of New York 2008-2015 Postdoc – HHMI / Columbia University – (w/ Dr. ) 2004-2008 PhD – MRC-Laboratory of Molecular Biology, Cambridge, UK – (w/ Drs. Linda Amos & Jan Lowe)

Research Interests

Keywords:

Cell regulation • Cancer • Heart diseases • Biochemistry • Molecular biology • Structural biology • Cryo- electron microscopy • Image analysis • Modeling • Methods development • initiation • Membrane proteins • Calcium signaling Dr. Terry Dowd Publications

Dr. Terry Dowd is involved Chan KL, Dowd TL, Gibney BR., in two areas of research. Characterization of the Zn(II) binding properties One area is the alteration in of the human Wilms' tumor suppressor protein C- bone mineral properties in terminal zinc finger peptide. (2014) Inorg disease. The second project Chem. 53:6309. involves alterations in structure–function Malashkevich, V., Dowd, T.L., "The X-ray Crystal relationships in the gap Structure of Bovine 3 Glu-Osteocalcin. junction molecule Connexin Biochemistry (2013) 52:8387. in deafness, neuropathy and skin disease. B. Kalmatsky, T.L. Dowd, Structural studies of N-terminal mutants of connexin 32 using 1H Terry Dowd NMR spectroscopy. Arch. Biochem. Biophys. Associate Professor (2012) 526: 1-8. Brooklyn College 2847 Old Ingersoll A.U. Monir, T.L. Dowd, The Effect of Lead on 2900 Bedford Ave. Bone Mineral Properties From Female Adult Brooklyn, NY C57/BL6 Mice. Bone 2010 47:888-94. [email protected] http://academic.brooklyn.cuny.edu/chem/howell/facul B. Kalmatsky, T.L. Dowd, Structural studies of the N-terminus of Connexin 32 using 1H NMR tyWebPages/Dowd/Dowd_home.htm spectroscopy. Arch. Biochim. Biophys. 2009 490: 9-16. 2014- current Associate Professor 2005 Assistant Professor 1992-1996 Instructor 1986-1992 Postdoc 1986 Ph.D.

Research Interests

My research involves investigating the role of the bone protein osteocalcin in bone mineral diseases such as Pb2+ toxicity, low Mg2+ diets and diabetes. The research involves multiple techniques such as atomic absorption, FTIR Imaging and microCT to investigate alterations in mouse bone mineral properties. The second project involves NMR structural-functional studies of the gap junction molecule Connexin in health and diseases such as deafness, fatal skin disease and neuropathy. The project uses 2D NMR techniques on a high field magnet and electrophysiological techniques characterizing the mutant gap junction channels. Dr. Emilio Gallicchio Publications

Emilio Gallicchio’s research Emilio Gallicchio, et al. BEDAM Binding Free is in the area of Predictions for the SAMPL4 Octa-Acid computational molecular Host Challenge. J. Comp. Aided Mol. Des. 29, biophysics. He uses 315-325 (2015). advanced computational models to investigate the Emilio Gallicchio, et al. Virtual Screening of dynamics and Integrase Inhibitors by Large Scale Binding Free of biological Energy Calculations: the SAMPL4 Challenge. J systems. Comp Aided Mol Design, 28, 475-490 (2014).

Guohua Yi, Mauro Lapelosa, Emilio Gallicchio, Gail Ferstandig Arnold et al. Chimeric Emilio Gallicchio Rhinoviruses Displaying MPER Epitopes Elicit Assistant Professor Anti-HIV Neutralizing Responses. PLoS ONE Department of Chemistry, Brooklyn College 8(9), e72205 (2013). 2900 Bedford Avenue Brooklyn, NY Gallicchio E. Role of Ligand Reorganization and [email protected] Conformational Restraints on the Binding Free sites.google.com/site/emiliogallicchiolab of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. Computational Molecular Bioscience, 2, 7-22 (2012).

2013- current Asst. Professor, Dept. Chemistry, Brooklyn College 2012-2013 Research Professor, Dept. Chemistry, Rutgers University 2001-2012 Associate Director, BioMaPS Institute, Rutgers University 1997-2000 Postdoctoral, Rutgers University 1991-1996 PhD Columbia University, Chemical

Research Interests

-Thermodynamics of protein-protein and protein-ligand binding - Virtual drug screening - Protein conformational equilibria - Statistical thermodynamics of and misfolding - Thermodynamics of solvation of biological - Force field development and high resolution protein modeling - Design of high performance algorithms - Parallel and distributed computing Dr. Kevin H. Gardner Publications The Gardner lab studies how cells perceive and Y. Guo et al., Coiled-coil coactivators play a respond to changes in the structural role mediating interactions in hypoxia environment around them. inducible factor heterodimerization. J. Biol. Such information provides Chem., 2015, online now. insights into fundamental principles of protein V. Ocasio et al., Ligand-induced folding of a two structure and signaling, component signaling receiver domain. guides the of Biochemistry, 54, 1353-1363. new protein-based tools, and lays the foundation for G. Rivera-Cancel et al., Full-length structure of a new therapeutic strategies. monomeric histidine kinase reveals basis for sensory regulation, Proc. Natl. Acad. Sci USA, Kevin H. Gardner 2014, 111, 17839-17844. Director, Structural Biology Initiative L.B. Motta-Mena et al., An optogenetic gene CUNY Advanced Science Center, Room 3.322 expression system with rapid activation and 85 St. Nicholas Terrace deactivation kinetics. Nat. Chem. Biol., 2014, New York, NY 10031 10, 196-202. [email protected] structbio.asrc.cuny.edu • kglab.org T.H. Scheuermann et al., Allosteric inhibition of Hypoxia Inducible Factor 2 with small molecules. Nat. Chem. Biol., 9, 271-276.

2014- current Director, Structural Biology Initiative, CUNY Advanced Science Research Center Einstein Professor of Chemistry, City College of New York 1998-2014 Professor of Biophysics and Biochemistry, UT Southwestern Medical Center 1995-1998 Postdoc – Biomolecular NMR methods development, University of Toronto (w/ Dr. Lewis E. Kay) 1989-1995 Ph.D. – Molecular Biophysics & Biochemistry, Yale University (w/ Dr. Joseph E. Coleman)

Research Interests

Keywords: environmental sensing • protein/protein interactions • ligand binding • allostery • NMR spectroscopy • X-ray • biochemistry • photosensors • cancer • Dr. Brian R. Gibney Publications

The Gibney Lab uses Alexandratos, S.D. et al. “Sustaining Water metalloprotein design to Resources: Environmental and Economic investigate the fundamental Impact” ACS Sustainable Chemistry & engineering of , 2019, 7, 2879-2888. systems. These studies provide insight into metal- Gibney, B.R. “Equilibrium Studies of Designed induced protein folding, Metalloproteins” Methods in Enzymology, heme electrochemistry, and Peptide, Protein and Enzyme Design, Pecoraro, the role of chemically V.L. Ed., 2016, 580. 417-438. modified hemes in biology. Assignargues, C. et al. “Structure and Function of a Bacterial Microcompartment Shell Protein Brian R. Gibney Engineered to Bind a [4Fe-4S] Cluster”, J. Am. Associate Professor Chem. Soc. . 2016, 138, 5262-5270. Brooklyn College 2900 Bedford Avenue Reddi A.R. et al. “Evaluation of the Intrinsic Zn(II) Brooklyn, NY 11210 Affinity of a Cys3His1 Site in the Absence of [email protected] Protein Folding Effects”, Inorg. Chem. 2015, 54, 5942-5948. http://www.biochemistry.nyc Chan, K.L. et al. Characterization of the Zn(II) 2008- current Associate Professor Brooklyn College Binding Properties of the Wilms’ Tumor 2005-2008 Associate Professor Columbia University Suppressor Protein C-Terminal Zinc Finger 2000-2005 Assistant Professor Columbia University Peptide”, Inorg. Chem. 2014, 53, 6309-6320. 1995-2000 NIH Postdoc University of Pennsylvania 1990-1995 PhD University of Michigan Gibney, B.R. Metallopeptides as Tools to 1986-1990 BS (ACS Certified) Florida State University Understand Metalloprotein Folding and Stability in Protein Folding and Metal Ions – Mechanisms, Biology and Disease, Gomes, C and Wittung- Research Interests Stafshede, P. Eds. 2011, 227-245.

Keywords: De novo metalloprotein design, inorganic coordination chemistry, biophysics, bioenergetics, electrochemistry

Our research focuses on the role of metal ions in biological systems from both an inorganic coordination chemistry and biophysical perspective. We are currently investigating the role of zinc in controlling gene expressions in human cancer, and the role of heme proteins in cardiovascular disease. Dr. Dixie J. Goss Publications

Recruitment of 40S to the 3' Prof. Goss is a professor of Untranslated Region (UTR) of a Viral mRNA, via Chemistry and Biochemistry the eIF4F Complex, Facilitates Cap-independent and Elion Endowed Scholar Translation. Das Sharma S, Kraft JJ, Miller WA, Goss DJ. J Biol Chem. 2015 Mar 19.

Pokeweed antiviral protein, a ribosome inactivating protein: activity, inhibition and prospects. Domashevskiy AV, Goss DJ. Dr. Dixie Goss Toxins (Basel). 2015 Jan 28;7(2):274-98. Hunter College Chemistry Dept. 695 Park Ave Rapid kinetics of iron responsive element (IRE) New York, NY 10065 RNA/iron regulatory protein 1 and IRE-RNA/eIF4F [email protected] complexes respond differently to metal ions. http://www.hunter.cuny.edu/chemistry/faculty/Dixie/gos Khan MA, Ma J, Walden WE, Merrick WC, Theil s-group-1/resume EC, Goss DJ. Nucleic Acids Res. 2014 Jun;42(10):6567-77. 1990- current Professor of Chemistry Eukaryotic initiation factor (eIF) 4F binding to barley 1989-1990 Associate Professor of Chemistry yellow dwarf (BYDV) 3'-untranslated region 1984-1989 Assistant Professor correlates with translation efficiency. Post-Doc. U. of Nebraska and U. of Banerjee B, Goss DJ. Georgia J Biol Chem. 2014 Feb 14;289(7):4286-94. 1975 Ph.D U. of Nebraska Poly(A) binding proteins: are they all created equal? Goss DJ, Kleiman FE. Wiley Interdiscip Rev RNA. 2013 Mar-Apr;4(2):167- 79. Research Interests

Keywords: protein synthesis, virus, protein- interactions

We use biophysical approaches to understand how non-coding regions of mRNA regulate function. Miss regulation of protein synthesis in responsible for many diseases including cancer. We are interested in how unique in viral RNA allow to take over host cell protein synthesis. Dr. Michael Green Publications

Dr. Green is a A. M. Kariev and M. E. Green, "Caution is computational chemist, with required in interpretation of in a principal interest in the voltage sensing domain of voltage biophysical problems, gated channels as evidence for gating especially related to a class mechanisms.," Int'l J. Molec. Sci. (2015) of proteins, ion channels, 16, 1627-1643. responsible for the nerve impulse, among other things. A. M. Kariev and M. E. Green, "Quantum Effects in a Simple Ring with Hydrogen Bonds " J. Phys. Chem. B (2015)119,5962-5969 Michael E Green Professor A. M. Kariev, P. Njau, and M. E. Green, City College of New York "The Open Gate of the Kv1.2 Channel: Dept. of Chemistry Quantum Calculations Show The Key Role 160 Convent Ave Of Hydration," Biophys J. (2014). 106, 548-555 New York NY 10031 [email protected] A. M. Kariev and M. E. Green, "Voltage http://forum.sci.ccny.cuny.edu/people/science- Gated Ion Channel Function: Gating, division-directory/b009 Conduction, and the Role of Water and Protons," Int'l J. Molec. Sci. (2012) 13, Dr. Green has been a faculty member in 1680-1709 Chemistry at CCNY since Sept 1966. S. Liao and M. E. Green, "Quantum calculations on salt bridges with water: Potentials, structure, and properties," Comput. Theo. Chem. (2011) 963, 207- 214. Research Interests

Keywords: Quantum calculations, proteins, water structure, hydrogen bonds, salt bridges, membranes, water transport through membranes

Research Strategy: Primarily we carry out quantum calculations on overlapping sections of proteins, such as voltage sensing domains of ion channels, to determine structure, bonding, energetics, and transitions of protein, water, hydrogen bonds, and salt bridges, leading to mechanisms, for example, of sensing voltage. Dr. Nancy Greenbaum Publications

Prof. Greenbaum is a Riskowski, R.A., Armstrong, R.E., Greenbaum, structural whose N.L, and Strouse, G.F. (2016) Triangulating research addresses the role Nucleic Acid Conformations Using Multicolor of and Surface Energy Transfer (McSET) ACS Nano function in biochemical 10:1926-1938. activity of noncoding RNA molecules. We incorporate Zhao, C, Devany, M, Greenbaum, NL (2014) solution NMR, fluorescence Measurement of Chemical Exchange between techniques, and biochemical RNA Conformers by 19F NMR. Biochem. approaches in our studies. Biophys. Res. Comm. 453,692-695.

Professor Popović, M, Greenbaum, NL (2014) Role of helical constraints of the EBS1-IBS1 duplex of a Hunter College of CUNY group II on demarcation of the 5′ splice Dept. of Chemistry & Biochemistry site. RNA 20, 24-35. 695 Park Avenue New York NY 10065 Zhao, C*, Bachu, R*, Popović, M, Devany, M, [email protected] Brenowitz, M, Schlatterer, JC, Greenbaum, NL www.cuny.edu/chemistry/faculty/nancy/greenbaum (2013) Conformational heterogeneity of the protein-free human spliceosomal U2-U6 snRNA 2007- current Professor, Hunter College complex. RNA 19, 561-573. *these authors 2004-2007 Associate Professor, Florida State Univ. contributed equally to the work. 1997-2004 Assistant Professor, Florida State Univ. 1992-1996 Postdoc, Columbia University Popović, M, Nelson, JD, Schroeder, KT, 1985-1989 Postdoc, Rockefeller University Greenbaum, NL (2012) Impact of base pair 1981-1984 PhD, University of Pennsylvania identity 5¢ to the spliceosomal branch site adenosine on branch site conformation. RNA Research Interests 18, 2093-2103.

Keywords: RNA, , NMR

We a%empt to answer ques0ons about how RNA molecules fold and interact with other RNA, metal ions, and proteins in order to carry out the complex ac0vity of precursor messenger (pre-m)RNA splicing. This process, by which noncoding intron sequences of pre-mRNA molecules are excised and flanking coding exons are ligated together, is an essen0al step in prepara0on of mRNA transcripts prior to transla0on of their message into protein sequences.

Pre-mRNA splicing in eukaryo0c cells is performed by the spliceosome, a dynamic nuclear supramolecular assembly that comprises five recyclable small nuclear (sn)RNA molecules and many proteins. Similari0es between spliceosomal snRNAs of and func0onally analogous regions of Group II , which excise themselves even in the absence of proteins, suggests shared evolu0onary ancestry and the likelihood that the spliceosomal reac0on is also catalyzed by its RNA components. Using a combina0on of biochemistry, biophysical, and spectroscopy techniques, we characterize the molecular basis of recogni0on and conforma0onal dynamic leading RNA splicing in the two systems. Dr. Rupal Gupta Publications Elucidation of transition metal Rupal Gupta, et al.: “Dynamic Nuclear Polarization -mediated processes Enhanced MAS NMR Spectroscopy for Structural undertaken by pathogens and Analysis of HIV-1 Protein Assemblies”, The Journal of the corresponding immune B, 2016, 120, 329-339. response by the human body Rupal Gupta, Taketo Taguchi, Benedikt Lassalle- during infection using Kaiser, Emile Bominaar, Junko Yano, Michael P. bioinorganic, biophysical and Hendrich, A. S. Borovik: “High-Spin Mn-Oxo computational methodologies Complexes and their Relevance to the Oxygen- Evolving Complex within Photosystem II”, Proceedings of the National Academy of Science of the United States of America, 2015, 112, 5319-5324. Rupal Gupta, Guangjin Hou, Rokus Renirie, Tatyana Rupal Gupta Polenova: “51V NMR Crystallography of Vanadium Assistant Professor Chloroperoxidase and its Directed Department of Chemistry P395D/L241V/T343A Mutant: Protonation College of Staten Island Environment of the Active Site”, Journal of the American Chemical Society, 2015, 137, 5618-5628. 2800 Victory Blvd. Rupal Gupta, David C. Lacy, Emile Bominaar, A. S. Staten Island NY Borovik, and Michael P. Hendrich: “Electron [email protected] Paramagnetic and Mössbauer Spectroscopy and Density Functional Theory 2017- current Assistant Professor Analysis of a High-Spin FeIV-oxo Complex”, Journal of 2013-2016 Postdoc, University of Delaware the American Chemical Society, 2012, 134, 9775– 2006-2012 PhD, Carnegie Mellon University 9784. Rupal Gupta, Rong Fu, Aimin Liu and Michael P. Hendrich: “EPR and Mössbauer Spectroscopy Show Inequivalent Hemes in Tryptophan Dioxygenase”, Journal of the American Chemical Society, 2010, 132, Research Interests 1098–1109. Keywords: Bioinorganic Chemistry, Spectroscopy, Biophysical Chemistry, Magnetic Resonance, Quantum Chemical Calculations

Transition metal is one of mechanisms through which the human body combats microbial attack. We are investigating both the processes undertaken by pathogens during invasion of a host cell and the responses executed by the host cell during such an attack. The research projects aim to study the mechanisms of zinc and copper homeostasis, incorporation of native metal ions by metallochaperones, and pathogenic machinery of zinc acquisition. Investigation of these physiological events at the interface of chemistry and biology will provide atomic-level understanding of fundamental processes in the human body during microbial invasion, which will have significant implications for human health and in the design of efficient therapeutics. Dr. David Jeruzalmi Publications

Lu, M., Yang, J., Ren, Z., Sabui, S., Espejo, A., Jeruzalmi’s group applies Bedford, M. T., et al. (2009). Crystal structure of X-ray crystallography, the three tandem FF domains of the supplemented with electron transcription elongation regulator CA150. microscopy, to understand Journal of Molecular Biology, 393(2), 397–408. these long-standing problems in DNA biology. We also use Pakotiprapha, D., & Jeruzalmi, D. (2013). biochemical studies to inform Small-angle X-ray scattering reveals these approaches and follow architecture and A(2) B(2) stoichiometry of the up on the resulting insights. UvrA-UvrB DNA damage sensor. Proteins: Structure, Function, and , 81(1), 132–139. David Jeruzalmi Professor of Chemistry Pakotiprapha, D., Liu, Y., Verdine, G. L., & Marshak 1219 • City College of New York • Graduate Jeruzalmi, D. (2009). A structural model for the Center of the City University of New York damage-sensing complex in bacterial 160 Convent Avenue excision repair. The Journal of New York, NY 10031 Biological Chemistry, 284(19), 12837–12844. [email protected] Pakotiprapha, D., Samuels, M., Shen, K., Hu, J. H., & Jeruzalmi, D. (2012). Structure and 2012- current Professor of Chemistry, CCNY mechanism of the UvrA–UvrB DNA damage 2002-2012 Molecular and Cellular Biology, Harvard sensor. Nature Structural & Molecular 1996-2002 The Rockefeller University Biology, 1–9. 1994 Ph.D., Yale University Samuels, M., Gulati, G., Shin, J.-H., Opara, R., McSweeney, E., Sekedat, M., et al. (2009). A biochemically active MCM-like helicase in Bacillus cereus. Nucleic Acids Research, Research Interests 37(13), 4441–4452.

The faithful transmission of gene1c information is an important biological imperative. To carry out this function, have evolved processes to replicate their and defend them from attack. We study important mechanisms associated with the processes of DNA replica1on and repair. The central challenge in understanding these processes stems from the large size of the involved multi-protein DNA complexes; these entities also populate many conformational states. Together, these complications place limits on insights that can be revealed by static crystallographic structures or solution methods alone; both sources of information are essential for defining underlying mechanisms. To this end, my group applies X-ray crystallography, supplemented with electron microscopy, to understand these long-standing problems in DNA biology. We also use biochemical studies to inform these approaches and follow up on the resulting insights. Dr. Daniel A. Keedy Publications

The Keedy Lab is DA Keedy*, ZB Hill*, et al. “An expanded interested in how atomic allosteric network in PTP1B by multitemperature motions imbue protein crystallography, fragment screening, and molecules with biological covalent tethering.” eLife (2018). functions. We use novel X- ray experiments plus DA Keedy*, LR Kenner*, M Warkentin*, RA computational modeling to Woldeyes*, et al. "Mapping Energy Landscapes explore dynamic processes of Dynamic Proteins by Multitemperature and like ligand binding and XFEL Crystallography." eLife (2015). allostery in proteins. DA Keedy, JS Fraser, H van den Bedem. “Improved automated modeling of alternative Daniel A. Keedy protein backbone conformations in X-ray Assistant Professor crystallography.” PLoS Comp Biol (2015). City College of New York, Chemistry & Biochemistry Advanced Science Research Center, Structural Biology DA Keedy. “Conformational and connotational 85 St. Nicholas Terrace heterogeneity: A surprising relationship between Room 3.314 protein structural flexibility and puns.” Proteins: New York, NY 10031 Struct Funct Bioinf (2015). [email protected] www.keedylab.org

2018-current Assistant Professor, CUNY Advanced Science Research Center , Structural Biology Initiative Assistant Professor, City College of New York, Department of Chemistry and Biochemistry 2012-2018 Postdoctoral Fellow, University of California, San Francisco (with James Fraser) 2006-2012 PhD, Duke University (with David & Jane Richardson)

Research Interests

Keywords: structural biology, X-ray crystallography, allostery, bioinformatics, protein design

The Keedy Lab develops experimental and computational methods to control proteins by biasing toward specific conformations that underlie functions such as allostery, ligand binding, and catalysis. Our work reveals new opportunities to modulate the activities of therapeutic targets such as tyrosine phosphatases with small molecules and protein engineering, and also offers insights into more general evolutionary processes that led to functional diversity in the human . Dr. Reza Khayat Publications

Khayat group studies the Veesler D, Khayat R, Architecture of a dsDNA structure and function of viral capsid in complex with its maturation proteins encoded for and protease. Structure 2014 Feb 4 (22): 1-8 utilized by pathogens to infect and replicate. We use Khayat R, Lee JH, Structural characterization of a combination of X-ray cleaved, soluble human immunodeficiency virus crystallography, cryo- type-1 envelope glycoprotein trimers. J. , electron microscopy, 2013 Sep;87(17):9865-72 biophysics, biochemistry, and cellular biology to Pejchal R, Khayat R, A potent and broad complete these studies. neutralizing antibody recognizes and penetrates the HIV glycan shield, Science 2011 Nov. Reza Khayat 25:334(6059):1097-103 Assistant Professor City College of New York Khayat R, Brunn N, The 2.3-angstrom structure Center for Discovery and Innovation of porcine circovirus 2, 2011 J. Virology Aug; 85 Saint Nicholas Terrace; 12316 85(15):7856-62 New York, NY 10031 [email protected] Khayat R, Lander GC, An automated procedure for detecting protein folds from sub-nanometer www.khayatlab.org resolution electron density, 2010 J. Struct. Bio. 2012- current Current position Jun; 170(3); 513-21 2008-2012 Sr. Research Associate, TSRI 2003-2008 Research Associate, The Scripps Research Institute 1998-2003 PhD, Columbia University

Research Interests

Keywords: cryo-electron microscopy, X-ray crystallography, biophysics, biochemistry, cellular biology We seek to understand the structural and chemical mechanism by which pathogens hijack the cellular machinery of their host for infection and replication. We use a combination of techniques to understand this mechanism at the atomic resolution to relate how chemistry drives biology, and a number of techniques to understand how biology feeds back into chemistry for new pathways to be exploited by the pathogen for infection and replication. We are also interested in developing computational methods to further combine X-ray crystallography with cryo-electron microscopy. Dr. Tom Kurtzman The Kurtzman group focuses Publications on the development of methodologies to characterize the structure and Wickstrom, L. et al. Parameterization of an thermodynamics of water on effective potential for protein-ligand binding from the surface of proteins and host-guest affinity data. J. Mol. Recognit. the exploitation of solvation (Accepted Journal of Molecular Recognition) properties for the discovery Nguyen, C. N., Cruz, A., Gilson, M. K. & and design of new drugs. Kurtzman, T. Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. J. Chem. Theory Comput. (2014). doi:10.1021/ct401110x Thomas Kurtzman Armaiz-Pena, G. N. et al. Src activation by β- Assistant Professor adrenoreceptors is a key switch for tumour Lehman College metastasis. Nat. Commun. 4, 1403 (2013). 250 Bedford Park Boulevard West Nguyen, C. N., Kurtzman Young, T. & Gilson, M. Bronx,10468 NY K. Grid inhomogeneous solvation theory: http://www.lehman.edu/faculty/tkurtzman/ Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J. Chem. Phys. 137, 044101–044101–17 (2012) 2010- Present Assistant Professor, Lehman College-CUNY *Young, T., Abel, R., Kim, B., Berne, B. J. & 2008-2010 AsssistantProfessor, San José State Univ. Friesner, R. A. Motifs for molecular recognition 2007-2008 Visiting Professor, Yeshiva University exploiting hydrophobic enclosure in protein–ligand 2004-2007 Postdoctoral Fellow, Columbia University binding. Proc. Natl. Acad. Sci. 104, 808 –813 2002 Doctorate, Stanford University (2007).

*Formerly published as T. Young Research Interests

Keywords: Solvation Thermodynamics, , Computer Aided Drug Design Research in the Kurtzman lab focuses on the development of computational tools that can aid in the discovery and rational design of new drugs. His approach applies statistical mechanical theory and computer simulations to better understand the physical principles that govern the molecular recognition between proteins and small molecule ligands (drugs). A particular emphasis is placed on the role that water plays in the molecular recognition process. A principal goal of this research is to help design and discover drugs that bind with high affinity and selectivity to given protein targets Dr. Themis Lazaridis Publications The Lazaridis lab works in the area of theoretical and Brice A., Lazaridis T. "Structure and Dynamics of computational Biophysics. In a Fusion Peptide Helical Hairpin on the the past few years we have Membrane Surface: Comparison of Molecular worked on the interaction of Simulations and NMR", J. Phys. Chem. B, proteins with biological 118:4461-70 (2014) membranes. We are especially interested in the Lazaridis T., Versace R. "The treatment of process of pore formation by solvent in multiscale biophysical modeling", Isr. antimicrobial and J. Chem., 54:1074-83 (2014) other toxins. Themis Lazaridis Lazaridis T., Leveritt JM, PeBenito L. "Implicit membrane treatment of buried charged groups. Professor Application to peptide translocation across City College of New York bilayers", BBA Biomembranes, 1838:2149-59 Dept of Chemistry and Biochemistry (2014) 160 Convent Ave New York NY Prieto L., He Y., Lazaridis T. "Protein arcs may [email protected] form stable pores in membranes", Biophys J, http://www.sci.ccny.cuny.edu/~themis/ 106:154-161 (2014)

1998- City College Rahaman A., Lazaridis, T. "A thermodynamic 1992-1998 Postdoc, Harvard University approach to alamethicin pore formation", BBA 1987-1992 PhD, University of Delaware Biomembranes 1838:98 (2014)

Research Interests

My research is in the area of Theoretical and Computational Biophysical Chemistry, which aims to understand how biological systems work in terms of the fundamental laws of Physics and Chemistry. , such as proteins and nucleic acids, have well defined conformations which often change in the course of their function. Our goal is to understand the forces that operate within and between biomolecules and develop quantitative mathematical models for their energy as a function of conformation. Such models are useful in many ways, such as predicting the three-dimensional structure from sequence, characterizing conformational changes involved in biological function, or predicting the binding affinity between two biomolecules. Dr. Sharon Loverde Publications 1. "Molecular Mechanism for the Role of the Dr. Sharon Loverde is an H2A and H2B Histone Tails in Nucleosome Associate Professor of ReposiDoning," Kaushik Chakraborty, Chemistry at College of Myungshim Kang, and Sharon M. Loverde, Staten Island. Her Journal of Physical Chemistry B, 122, 11827- research group is 11840 (2018). interested in the area of 2. "Molecular Dynamics SimulaDons of soft and biological Supramolecular AnDcancer Nanotubes," materials. Myungshim Kang, Kaushik Chakraborty, and Sharon M. Loverde, Journal of Chemical Informa6on and Modeling, 56, 1164-1168 (2018). Prof. Sharon Loverde 3. "NucleoDde State Effect on the Protofilament ConformaDon of Tubulin Octamers," Anjela Associate Professor Manandhar, Myungshim Kang, Kaushik College of Staten Island Chakraborty, and Sharon M. Loverde, Journal of Staten Island NY Physical Chemistry B, 122, 6164-6178, (2018). [email protected] 4. "Glassy Worm-Like Micelles in Solvent and h"ps://sites.google.com/site/loverdelaboratory/ Shear-Mediated Shape TransiDons," Kaushik Chakraborty, Kandaswamy Vijayan, Andre Brown, Dennis E. Discher, Sharon M. Loverde, SoG MaHer, 2018, DOI: 10.1039/C8SM00080H. 2018- current Associate Professor, College of Staetn 5."Isomeric Control of the Mechanical Island ProperDes of Supramolecular Filament 2012-2018 Assistant Professor, College of Staten Hydrogels," Yi-An Lin,Myungshim Kang, Wei- Island Chiang Chen,Yu-Chuan Ou, Andrew G. 2007-2012 NIH NRSA Postdoctoral Fellow, UPenn Cheetham, Pei-Hsun Wu, Denis Wirtz, Sharon 2001-2007 PhD, and Engineering, M. Loverde and Honggang Cui, Biomaterials Northwestern University Science, 6, 216-224 (2018). Research Interests

Keywords:

The Loverde laboratory utilizes all-atomistic and coarse-grained molecular dynamics simulations to investigate properties of soft and biological materials. We are also interested in characterizing the stability of macromolecular assemblies composed by proteins and/or nucleic acids. Dr. Prabodhika Mallikaratchy Selected Publications 1.Federica Moccia,Chiara Platella, Domenica Prabodhika Mallikaratchy Musumeci, Sana Batool, , Hasan Zumrut, John develops nucleic acid aptamers Bradshaw, Prabodhika Mallikaratchy*, Daniela against cellular targets to probe cell- Montesarchio* “The role of G-quadruplex structures cell interactions, receptor-ligands of LIGS-generated aptamers R1. 2 and R1. 3 in IgM interactions. Her research is highly specific recognition” : Int J Biol Macromol. 2019 ; interdisciplinary, which incorporate 133:839-849. organic chemistry, combinatorial screening, structural biology, 2.S Lingala, LU Nordstrøm, PR Mallikaratchy and biochemistry. “Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides”: Tetrahedron Letters, 2019; 60(3):211-213. Prabodhika Mallikaratchy 3.Sana Batool, Kimon V Argyropoulos, Roksana Associate Professor Azad, Precious Okeoma, Hasan Zumrut, Sanam Lehman College and the Graduate Center Bhandari, Rigzin Dekhang, Prabodhika Mallikaratchy* 250 Bedford Park Blvd. West, ” Dimerization of an aptamer generated from Bronx, NY 10468 Ligand-guided selection (LIGS) yields a high affinity [email protected] scaffold against B-cells “Biochimica et Biophysica www.mallikaratchylab.org Acta (BBA)-General Subjects, 2019; 1863 (1), 232- 240. 4.Hasan Zümrüt, Naznin Ara, Maria Fraile, George 2019- current Associate Professor Maio, Prabodhika Mallikaratchy “Ligand-guided 2012-2019 Assistant Professor selection of target-specific aptamers: A screening 2008-2012 Research fellow, Memorial Sloan Kettering technology for identifying specific aptamers cancer center against cell-surface proteins”. Nucleic Acid Ther. 2003-2008 PhD, University of Florida 2016 ;26(3):190-8.

For the current list of publications: www.https://scholar.google.com/citations?user=hCW xLbcAAAAJ&hl=en

Research Interests

Keywords: Nucleic Acid Aptamers (NAAs), Ligand-Guided Selection (LIGS), Nucleic Acid Nanotechnology Long-term goal oft this laboratory is to develop oligonucleotide aptamer based synthetic scaffolds for biological and biomedical applications. Therefore, our research program is aimed at generating new aptamers against biologically important cellular targets, and molecular engineering of multifunctional aptamer structures suitable for drug delivery, imaging and designer immunotherapeutic molecules. Dr. Louis Massa Publications Dielectric Response of High Explosives at THz Frequencies Calculated by Density Functional Theory, Lulu Huang, Andrew Shabaev, Sam Lambrakos, Noam Bernstein, Vern Jacobs, Dan Finkenstadt, Lou Massa, Journal of Materials Engineering and Performance (2012) 21(7), 1120-1132.

The Kernel Energy Method: Application to Graphene and Extended Aromatics, Lulu Huang, Hugo Bohorquez, Cherif F. Matta and Lou Hiroshi Matsui Massa, IJQC, Vol. 111, 15, 4150-4157 (2011) Professor Hunter College The Kernel Energy Method: Construction of 3 & 695 Park Avenue, 4 tuple Kernels from a List of Double Kernel Interactions, Lulu Huang, Lou Massa, Journal of New York, NY 10065 Molecular Structure: THEOCHEM, Vol. 962, [email protected] issue 1-3, 72-79 (2010) http://www.hunter.cuny.edu/chemistry/faculty/Lou/Lou Calculation of Strong and Weak Interactions in Postdoc: Brookhaven National Laboratory TDA1 and RangDP52 by Kernel Energy Method, PhD: Theoretical Molecular Physics, Georgetown Huang, L.; Massa, L.; Karle, I.; Karle, J. University Proceedings of the National Academy of Sciences, Vol. 106, No. 10, 3664-3669 (2009)

The Kernel Energy Method of Quantum Mechanical Approximation carried to Fourth Order Terms, Huang, L.; Massa, L.; and Karle, J. PNAS, Vol. 105, No. 6, 1849-1854 (2008) Research Interests

Keywords: differential equations, density matrices, density functional theory, Xray crystallography, kernel energy method, information theory,

Applications of to the electronic structure of , molecules, and solids. Dr. Sébastien Poget

Dr. Poget is interested in Publications membrane and function, with a P. Anand, A. Grigoryan, M. H. Bhuiyan, B. particular emphasis on the Ueberheide, V. Russell, J. Quinoñez, P. Moy, B. interactions between ion T. Chait, S. F. Poget, M. Holford: Sample limited channel domains and characterization of a novel disulfide-rich venom animal peptide toxins. peptide toxin from terebrid marine snail Terebra variegata. PLoS ONE 2014, 9, e94122.

Sébastien Poget S. F. Poget, M. E. Girvin: Solution NMR of Assistant Professor membrane proteins in bilayer mimics: Small is College of Staten Island, CUNY beautiful, but sometimes bigger is better. Department of Chemistry Biochim. Biophys. Acta 2007, 1768, 3098-106. 2800 Victory Blvd. S. F. Poget, S. M. Cahill, M. E. Girvin: Isotropic Staten Island, NY 10314 bicelles stabilize the functional form of a small [email protected] multidrug-resistance pump for NMR structural www.csi.cuny.edu/faculty/POGET_SEBASTIEN.html studies. J. Am. Chem. Soc. 2007, 129 2432- 2433. 2009- current Assistant Professor, College of Staten Island, CUNY 2003-2009 Postdoc, Albert Einstein College of Medicine, NY 2001-2003 Postdoc, Rockefeller University, NY 1997-2001 PhD, University of Cambridge, UK Research Interests

Keywords: Solution-state NMR, membrane protein structural biology, ion channels, toxins, electrophysiology, biophysics

The Poget lab is interested in the structural and functional study of membrane proteins through solution- state NMR and other biophysical methods. Our studies focus on better understanding the interactions of animal peptide toxins with their target ion channel domains as tools for an improved understanding of ion channel function and starting point for drug development. To carry out these studies at the cutting edge of structural biology, we are also involved in the development of new and improved methods for membrane protein studies, including development of more powerful membrane mimetics such as bicelles and optimized NMR methods. Dr. Adam A. Profit Publications

Protein-ligand interactions is Profit, A. A., Vedad, J. Saleh, M., and Desamero, the unifying theme of my R.Z.B. Aromaticity and Amyloid Formation: research interests. In Effect of p-Electron Distribution and Aryl particular, the design, Substituent Geometry on the Self-Assembly of synthesis and application of Peptides Derived from hIAPP22-29 Arch biologically relevant probe Biochem Biophys 2015, 567, 46-58. molecules to study and elucidate protein-protein and Profit, A. A., Felsen, V., Chinwong, J., Mojica, E- protein-ligand interactions R., and Desamero, R.Z.B. Evidence of p- involved in amyloid diseases stacking Interactions in the Self-assembly of and cancer. hIAPP22-29 PROTEINS: Structure, Function and Bioinformatics 2013, 81, 690-703. Adam A. Profit, Ph.D. Associate Professor York College 94-20 Guy R. Brewer Blvd Jamaica, NY 11451 [email protected] www.york.cuny.edu/portal_college/aprofit

2014- current Associate Professor of Chemistry 2004-2014 Assistant Professor of Chemistry 2000-2004 Merck Research Laboratories 1997-2000 Postdoc - Albert Einstein College of Medicine 1997 PhD - Stony Brook University Research Interests

Keywords: Amyloid, protein kinases, peptides, peptoids, enzymology, solid phase synthesis

The abnormal formation of protein aggregates, or amyloid deposits, is the hallmark of Alzheimers disease as well as type 2 diabetes. My laboratory is investigating the molecular interactions that occur between key proteins that contribute to the formation of amyloid in these diseases. Through a more detailed understanding of how these proteins self-assembly to form aggregates, we hope to design and develop small molecule and peptide mimetic inhibitors which may serve as potential therapeutic agents.

We are also developing compounds that inhibit the activity of key (kinases) which can cause tissues to grow out of control and develop into tumors. To accomplish this we are synthesizing molecules that exploit the unique molecular recognition motifs found in these enzymes to more effectively deliver inhibitory species to the active site. Dr. Susan A. Rotenberg Publications

X. Zhao, and S.A. Rotenberg. Phosphorylation of Cdc42 effector protein-4 (CEP4) by protein kinase C promotes motility of human breast Prof. Rotenberg cells. J. Biol. Chem. 2014, 289:25844-25854.

S. De, A. Tsimounis, X. Chen, and S.A. Rotenberg. "Phosphorylation of a-tubulin by protein kinase C stimulates dynamics in human breast cells." Cytoskeleton 2014, 71: 257-272.

X. Chen, X. Zhao, T. P. Abeyweera, and S. A. Susan A. Rotenberg Rotenberg. Analysis of substrates of protein Position: Professor kinase C isoforms in human breast cells by the Affiliation: Queens College traceable kinase method. Biochemistry 2012, Department of Chemistry & Biochemistry 51: 7087-7097. 65-30 Kissena Boulevard Flushing, NY 11367 X. Chen and S.A. Rotenberg. Phospho- [email protected] MARCKS drives motility of mouse melanoma cells. Cell. Signal. 2010, 22: 1097-1103. http://rotenberglab.com/ (website under construction) T.P. Abeyweera, X. Chen, and S. A. Rotenberg. Phosphorylation of a6-tubulin by protein kinase 1990 - current Professor Ca activates motility of human breast cells. J. 1985 - 1990 Postdoctoral - Rockefeller University, Biol. Chem. 2009, 284: 17648-17656. Columbia University 1980 - 1985 Ph.D. – Brown University

Research Interests

Keywords: Enzyme inhibitors; protein structure and function relationships; cell signaling pathways Dr. Kevin Ryan Publications

Dr. Ryan’s lab applies Liu, M. T.; Nagre, N. N.; Ryan, K., Structurally chemical concepts to diverse low molecular weight activators of the biological problems in two mammalian pre-mRNA 3' cleavage reaction. main areas, RNA and Bioorganic & Medicinal Chemistry 2014, 22 (2), olfactory molecular 834-41; recognition. Li, Y.; Peterlin, Z.; et al., Aldehyde Recognition and Discrimination by Mammalian Odorant Receptors via Functional Group-Specific Hydration Chemistry. ACS Chemical Biology 2014;

Kevin Ryan, Ph.D. Lama, L.; Seidl, C. I.; Ryan, K., New insights into Associate Professor, Biochemistry Division the promoterless transcription of DNA coligo Department of Chemistry and Biochemistry templates by RNA polymerase III. Transcription The City College of New York 2014, 5 (1); MR-1337, 160 Convent Ave. New York NY Seidl, C. I.; Lama, L.; Ryan, K., Circularized [email protected] synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for http://www.sci.ccny.cuny.edu/~kr107/index2/index.html small RNA generation in human cells. Nucleic 2009- current Associate Professor Acids Research 2013, 41 (4), 2552-64; 2003-2008 Assistant Professor 1996-2003 Postdoc, Columbia University (Chemistry Kurland, M. D.; Newcomer, M. B.; et al., and Biology Depts.) Discrimination of saturated aldehydes by the rat 1996 Ph.D., University of Rochester I7 olfactory receptor. Biochemistry 2010, 49 (30), 6302-4.

Research Interests

Keywords: molecular recognition, olfaction, RNA, micro RNA, RNA interference, RNA polymerase III, chemical biology, transcription

In the RNA area, we study the use of chemically synthesized transcription templates as potential information-bearing molecules for producing small therapeutic RNA in human cells. A second RNA area is the biochemistry of RNA processing reactions that occur during the biogenesis of messenger RNA in human cells. In the olfaction area, we use , organic synthesis and chemical biology to probe the biochemistry of the sense of smell. Publications Dr. Ruth E. Stark W. Huang, O. Serra, K. Dastmalchi, L. Jin, L. Yang, R.E. Stark, Comprehensive MS and Solid- Dr. Stark’s biophysics state NMR metabolomic profiling reveals research program focuses molecular variations in native periderms from on the molecular structure four Solanum tuberosum potato cultivars, J. and interactions of Agric. Food Chem., 2017, 65, 2258-2274. protective plant bio- polymers, fatty acid-binding L.Q. Jin,* Q. Cai,* W. Huang, K. Dastmalchi, J. proteins that mediate pain Rigau, M. Molinas, M. Figueras, O. Serra, R.E. and obesity, and melanin Stark, Potato native and wound periderms are pigments associated with differently affected by down-regulation of FHT, a human fungal infections. Potato Feruloyl Transferase, Phytochemistry, 2018, 147, 30-48. Ruth E. Stark Distinguished Professor Q. Wang,* S. Rizk,* C. Bernard, M.P. Lai, D. City College Dept. of Chemistry and Biochemistry Kam, J. Storch, R.E. Stark, Protocols and pitfalls CUNY Institute for Macromolecular Assemblies of obtaining fatty acid-binding proteins for CCNY CDI 1302, 85 St. Nicholas Terrace biophysical studies of ligand-protein and protein- protein interactions, Biochem. Biophys. Rep., New York, NY 10031 2017, 10, 318-324. [email protected] http://www.sci.ccny.cuny.edu/resgroup E. Camacho, C. Chrissian, R.J.B. Cordero, L. Liporagi-Lopes, R.E. Stark, A. Casadevall, N- 2007 - current CUNY Dist. Prof., CCNY acetylglucosamine supplementation affects 1985 - 2007 Assoc.-Dist. Prof., Coll. of Staten Island Cryptococcus neoformans cell wall composition 1979 - 1985 Asst. Prof., Amherst College and melanin architecture, , 2018, 1977 - 1979 Postdoctoral Fellow, M.I.T. 163, 1540-1556. 1977 PhD, Physical Chemistry, UC San Diego

Research Interests

Keywords: molecular biophysics, , bioanalytical chemistry, solid- and solution-state NMR

The Stark Laboratory uses structural biology and biophysical approaches to study plant protective polymers, lipid , and potentially pathogenic melanized fungal cells. Study of the molecular and mesoscopic architectures underlying the integrity of cuticles in natural and engineered potatoes and tomatoes is undertaken using solid- and solution-state nuclear magnetic resonance (NMR), , and . Ligand recognition and peroxisome proliferator-activated receptor interactions of fatty acid-binding proteins are under investigation by solution-state NMR and fluorescence spectroscopy. The molecular structure and development of melanin pigments within fungal cells are probed using (bio)chemical synthesis and solid-state NMR. Dr. Maria C. Tamargo Publications V. Deligiannakis, S. Dhomkar, M. S. Claro, I. L. Kuskovsky, M. C. Tamargo, Interface Modification in Type-II Maria C. Tamargo is ZnCdSe/Zn(Cd)Te QDs for High Professor of Chemistry at Efficiency Intermediate Band Solar Cells, the City College of New J. Crystal Growth 512, 203-207 (2019). York. Her research is in semiconductor materials M. S. Claro, I. Levy, A. Gangopadhyay, and nanostructures design, D. J. Smith, M. C. Tamargo, Self-

growth by epitaxial growth assembled Bismuth Selenide (Bi2Se3) techniques, characterization quantum dots grown by molecular beam methods, and applications. epitaxy, Scientific Reports 9, 3370 (2019). Maria C. Tamargo Professor and Former Executive Officer I. Levy, T. A. Garcia, S. Shafique and M. The City College of New York C. Tamargo, Reduced twinning and Department of Chemistry surface roughness of Bi2Se3 and Bi2Te 3 160 Convent Avenue layers grown by molecular beam epitaxy New York NY 10031 on sapphire substrates, J. Vac. Sci. [email protected] Technol. B 36, 02D107-1 (2018). https://www.ccny.cuny.edu/profiles/maria-tamargo https://www.idealscrest.org Y. Kaya, A. Ravikumar, G. Chen, M. C. Tamargo, A. Shen, and C. Gmachl, Two- band ZnCdSe/ZnCdMgSe quantum well 1993 - present The City College of New York and photodetector, AIP Adv. 8, The Graduate Center - CUNY 075105 (2018) 1984-1992 Bellcore 1978-1984 AT&T Bell Labs T. A. Garcia, V. Deligiannakis, C. 1972-1978 PhD (Johns Hopkins University) Forrester, I. Levy and M. C. Tamargo, 1968-1972 BS (University of Puerto Rico) Bi2Se3 van der Waals Virtual Substrates for II–VI Heterostructures, phys. status solidi b 254, 1700275 (2017). Research Interests

Keywords: Molecular Beam Epitaxy, compound semiconductors, II-VI semiconductors, photonic devices, nanomaterials, topological insulators. Materials growth, properties and applications of semiconductor multi-layered structures grown by molecular beam epitaxy (MBE). Areas of research activity include III-V compounds, strained-layer and short-period superlattices, surface and interface chemistry, visible light emitters, optoelectronic devices, wide bandgap II-VI compounds, II-VI/III-V heteroepitaxy, low dimensional nanostructures, selective area epitaxy, intersubband devices, quantum cascade lasers, VECSELs, topological insulators. Dr. Mariana Torrente Publications

Dr. Torrente is interested in Torrente, M.P., L.M. Castellano, and J. Shorter. the molecular mechanisms Suramin inhibits Hsp104 ATPase and disaggregase underlying neurodegenerative activity. PLoS ONE. 9(10): e110115. (2014) and psychiatric disease. Torrente, M.P., and J. Shorter. The metazoan protein disaggregase and amyloid depolymerase system: Hsp110, Hsp70, Hsp40, and small heat shock proteins. Prion. 7(6): 457-463. (2013) Torrente, M.P, Gelenberg, A.J., and Vrana, K.V. Boosting serotonin in the brain: is it time to revamp the treatment of depression? J Psychopharmacol. 26(5), 629-35. (2012) Torrente, M.P., Zee, B.M.; Young, N.L.; Baliban, Mariana Torrente R.C; Leroy, G.; Floudas, C.A.; Hake, S.B.; Garcia Assistant Professor B.A., Proteomic Interrogation of Human Chromatin. PLoS One, 6, (9), e24747. (2011) Department of Chemistry 2900 Bedford Avenue Plazas-Mayorca, M.D. and Vrana, K.E. Proteomic Ingersoll Hall Extension 343/345 investigation of in neuropsychiatric Brooklyn NY disorders: A missing link between and behavior? Journal of Proteome Research, 10 (1), [email protected] 58-65. (2011)

2015- current Assistant Professor, Brooklyn College; NIH Career Transition Award Fellow 2012-2015 IRACDA PENN-PORT Postdoctoral Fellow, University of Pennsylvania 2010-2012 NIH NRSA Postdoctoral Fellow, Penn State University College of Medicine 2010 Ph.D. in Chemistry, Princeton University

Research Interests

Keywords: We seek to understand the role of epigenetic mechanisms and protein folding in the etiology of neurodegenerative and neuropsychiatric disease. The central hypothesis of our research is that posttranslational modification (PTM) of histones and protein misfolding play a key role in linking genetic predisposition to cellular toxicity in neurodegenerative disease. Epigenetics and protein aggregation may reveal alternative mechanisms behind the occurrence of disease, serving as the missing link between genetic and environmental factors.