Publications

A. Dikiy, I., Edupuganti, U.R., Abzalimov,R.R., Borbat, P.P., Srivastava, M., Freed,J.H., Gardner, K.H. Insights intohistidine kinase activation mechanismsfrom the monomeric blue light sensorEL346. Proceedings of the NationalAcademy of Sciences, USA, 2019, 116,4963-4972.

B. Ben-Shalom, I.Y., Lin, C., Kurtzman, T.,Walker, R.C., Gilson, M.K. Simulatingwater exchange to buried binding sites.Journal of Chemical Theory andComputation. 2019, 15, 2684-2691.

C. Perea, W., Schroeder, K.T., Bryant,A.N., Greenbaum, N.L. Interactionbetween the Spliceosomal Pre-mRNABranch Site and U2 snRNP Protein p14Biochemistry, 2016, 55 (4), pp. 629-632.

Research Areas

• Biophysical mechanisms of ligand binding • Protein NMR• Structural Biology • Computational biophysical chemistry• Neutron scattering • Enzymology• X-ray Crystallography • Biotechnology

Molecular Biophysics seeks to understand essential biologicalprocesses in terms of physical chemistry. CUNY has over 30faculty working in this area. Research interests include themechanisms of signal transduction in cells, protein dynamics byneutron scattering and NMR, experimental and computationalanalysis of membrane protein structure and dynamics, andprotein design. Students are encouraged to contact anindividual faculty member to explore different researchopportunities.

Molecular BiophysicsProf. Thomas Kurtzman, Subdiscipline Chairsimpleliquid@gmail.com

Name: Zimei BuPosition: ProfessorAffiliation: City College of New YorkAddress: 160 Convent AvenueAddress: Marshak Science Bldg. Room 1336New York NYzbu@ccny.cuny.edu: http://www.sci.ccny.cuny.edu/~zbu/

Publications• Controllable Activation of Nanoscale Dynamics in aDisordered Protein Alters Binding Kinetics. CallawayDJE, Matsui T, Weiss T, Stingaciu LR, Stanley CB,Heller WT, Bu Z., J Mol Biol. 2017;429(7):987-998.

• Visualizing the nanoscale: protein internal dynamicsand neutron spin echo spectroscopy. Callaway DJ, BuZ., Curr Opin Struct Biol. 2017; 42:1-5.

• Phosphatidylinositol 4,5-bisphosphate clusters thecell adhesion molecule CD44 and assembles aspecific CD44-Ezrin heterocomplex, as revealed bysmall angle neutron scattering. Chen X, Khajeh JA, JuJH, Gupta YK, Stanley CB, Do C, Heller WT,Aggarwal AK, Callaway DJ, Bu Z. J Biol Chem.2015;290(10):6639-52.

• Molecular conformation of the full-length tumorsuppressor NF2/Merlin--a small-angle neutronscattering study. Ali Khajeh J, Ju JH, Atchiba M,Allaire M, Stanley C, Heller WT, Callaway DJ, Bu Z., JMol Biol. 2014;426(15):2755-68.

• Ligand-induced dynamic changes in extended PDZdomains from NHERF1. Bhattacharya S, Ju JH,Orlova N, Khajeh JA, Cowburn D, Bu Z. J Mol Biol.2013;425(14):2509-28

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. Bu’s group studiesthe structure anddynamics of proteincomplexes in cellsignaling, using neutronand X-ray scattering

2010- current Professor, CCNY2003-2010 Faculty, Fox Chase Cancer Center1999-2002 Chemist, NIST1994-1999 Postdoc, Yale University1994 PhD, Louisiana State University

Dr. Zimei Bu

Junyong ChoiAssistant ProfessorDepartment of Chemistry and BiochemistryQueens College of the City University of New York65-30 Kissena Blvd.Queens, NYJunyong.choi@qc.cuny.eduwww.choiresearchlab.com

PublicationsJY Choi, et. al., Comparative structuralanalysis and molecular design for thedevelopment of highly potent and selectiveagents targeting Matrix Metalloproteinase13, J. Med. Chem., 2017, 60, 5816-5825

CM Calvet, JY Choi, et. al., 4-aminopyridyl-based lead compounds targeting CYP51prevent spontaneous parasite relapse in achronic model and improve cardiacpathology in an acute model ofTrypanosoma cruzi infection, PLoS Negl.Trop. Dis., 2017, 11: e0006132

JY Choi, et. al., Structure Based Design ofCYP51 Inhibitors, Curr. Top. in Med.Chem., 2017, 17, 30-39

JY Choi, et. al., Drug strategies targetingCYP51 in neglected tropical diseases, Chem.Rev., 2014, 114, 11242-11271

JY Choi, et. al., The R-Configuration of 4-aminopyridyl-based inhibitors of CYP51confers superior efficacy againstTrypanosoma cruzi, ACS Med. Chem.Lett., 2014, 5, 434-439

Research InterestsKeywords: Medicinal Chemistry, Organic Synthesis, Computer-aided Drug Design, ChemicalBiology

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, andchemical biology to discover bioactive chemical probes. We are particularly interested in discovery of smallmolecule agents with novel mechanism of action to elucidate specific functions of biological targets. Thediscovery and techniques established in my laboratory will advance the chemical science in biomedicalresearch for the development of therapeutics

Junyong Choi is asynthetic and computationalmedicinal chemist. Hisresearch focuses ondevelopment of therapeuticcandidates by applyingorganic synthesis,computer-aided drugdesign, and chemicalbiology.

2017- current Assistant Professor, Queens College2012-2017 Sr. Research Associate, Scripps Florida2009-2012 Postdoc, Scripps Florida2009 PhD, Stony Brook University

Dr. Junyong Choi

Melissa DeriAssistant ProfessorLehman College250 Bedford Park Blvd WBronx, NY 10468melissa.deri@lehman.cuny.eduhttp://www.lehman.edu/academics/chemistry/faculty.php

PublicationsDeri, M. A.; Mills, P.; McGregor, D. Structure andEvaluation of a Flipped General Chemistry Courseas a Model for both Small and Large GatewayScience Course at an Urban Public Institution.Journal of College Science Teaching: 2018; Vol. 47,pp 46-55.

Deri, M. A.; McGregor, D.; Mills, P., UsingTechnology To Flip and Structure General ChemistryCourses at a Large Public University: Our Approach,Experience, and Outcomes. In Teaching and theInternet: The Application of Web Apps, Networking,and Online Tech for Chemistry Education, AmericanChemical Society: 2017; Vol. 1270, pp 75-97.

Deri, M. A.; Ponnala, S.; Kozlowski, P.; Burton-Pye,B. P.; Cicek, H. T.; Hu, C.; Lewis, J. S.; Francesconi,L. C. p-SCN-Bn-HOPO: A Superior BifunctionalChelator for 89Zr ImmunoPET. Bioconjugate Chem2015; 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.An Alternative Chelator for 89ZrRadiopharmaceuticals: Radiolabeling and Evaluationof 3,4,3-(LI-1,2-HOPO). J Med Chem 2014;57(11):4849-4860. PMID: 24814511

Deri, M. A.; Zeglis, B.M.; Francesconi L. C.; Lewis, J.S. PET imaging with 89Zr: From radiochemistry tothe clinic. Nucl Med Biol 2013; 40:3-14. PMID:22998840Research Interests

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 • Onlinelearning tools • Flipped classroom pedagogy • Active learning strategies

The overarching goal ofthe Deri Lab is theintegration and applicationof radiochemistry towardstangible benefits to society.We focus on the intersectionof radiochemistry andbiomedical science, morespecifically in molecularimaging and radiotherapyusing radioactive metals.

2017- current Assistant Professor, Lehman College2015-2017 Postdoctoral Fellow, Lehman College2015 Postdoctoral Fellow, Memorial Sloan

Kettering Cancer Center2010-2015 PhD, Hunter College and The Graduate

Center, CUNY

Dr. Melissa A. Deri

Ruel Z. B. DesameroProfessorYork College, the Institute of MacromolecularAssembly, and the Graduate Center94-20 Guy R. Brewer Blvd.Jamaica, NY 11451rdesamero@york.cuny.eduwww.york.cuny.edu/portal_college/rdesamero

PublicationsProfit A.A, Desamero R.Z.B. (2018) “Development of Peptide-Based Inhibitors of Amylin Aggregation Employing Aromatic and Electrostatic Repulsion. In: Mavromoustakos T. Kellici T. (eds) Rational Drug Design. Methods in Molecular Biology, vol 1824. Human Press, New York, NY

Lagarias P., Elkhou Y., Vedad J., Konstantinidi A., Profit A.A., Kellici T.F., Kolocouris A., Desamero R.Z.B., Mavromoustakos T. (2018) Molecular Dynamics Simulations on the Bioactive Molecules of hIAPP22-29(NFGAILSS) and Rational Drug Design. In: Mavromoustakos T. Kellici T. (eds) Rational Drug Design. Methods in Molecular Biology, vol 1824. Human Press, New York, NY

Vedad, J., Domaradzki, M. E., Mojica, E.-R. E., Chang, E. J., Profit, A.A., Desamero, R. Z. B.. (2017) "Conformational Differentiation of alpha-cyanohydroxycinnamic acid isomers: a Raman spectroscopic study." Journal of Raman Spectroscopy. 48: 1282-1288.

Deng, H., Vedad, J., Desamero, R. Z. B., Callender R.. (2017) "Difference FTIR Studies of Substrate Distribution in Triosephosphate Isomerase." Journal of Physical Chemistry B. 121: 10036-10046.

Profit, A.A., Vedad, J. and Desamero, R.Z.B.. (2017) "Peptide Conjugates of Benzene Carboxylic Acids as Agonists and Antagonists of Amylin Aggregation." Bioconjugate Chemistry. 28: 666-677.

Research Interests

Keywords: vibrational spectroscopy; fluorescence; circular dichroism; temperature-jumptechniques; structural biology; protein biochemistry; enzymology

My research is centered on investigating the structural and dynamical aspects of protein-small moleculeinteractions using techniques such as vibrational spectroscopy and temperature-jump relaxation. One aspect ofthe work is to understand at the molecular level how protein systems work. Enzyme-substrate interactions havelong been recognized as representing an extreme expression of structural complementarities in biologicalchemistry. Basic research geared towards understanding the inner workings of an enzyme system is important ifcures for the diseases caused by a malfunctioning or deficient enzyme are to be found. We have also startedinvestigating the mechanism behind amyloid formation with the goal of synthesizing peptide inhibitors thatdiminish protein aggregation.

Dr. Desamero is aspectroscopist by trainingcurrently investigatingprotein-ligand interaction aswell as protein-proteinaggregation using varioustechniques.

2015 – present Professor, York College - CUNY2010 - 2015 Associate Professor, York College - CUNY2003 - 2010 Assistant Professor, York College - CUNY2000 - 2003 Postdoc, Albert Einstein College of Medicine1998 - 2000 Postdoc, City College - CUNY1998 PhD, University of Connecticut

Dr. Ruel Desamero

Amedee des GeorgesAssistant Professor, ASRC Structural Biology InitiativeCity College, Dept. of Chemistry and BiochemistryCUNY Advanced Science Center, Room 3.31685 St. Nicholas TerraceNew York NY 10031Amedee.desGeorges@asrc.cuny.edustructbio.asrc.cuny.edu

Publications

des Georges et al., Structure of mammalian eIF3in the context of the 43S preinitiation complex,Nature, 2015

R. Zalk, O. B. Clarke, A. des Georges et al.,Structure of a mammalian ryanodine receptor.Nature, 2014.

Y. Hashem, A. des Georges et al., Structure ofthe mammalian ribosomal 43S preinitiationcomplex bound to the scanning factor DHX29.Cell, 2013, 153, 1108-1119.

des Georges et al., Structure of the mammalianribosomal pre-termination complex associatedwith eRF1• eRF3• GDPNP, Nucleic acidsresearch, 2013, gkt1279.

Research Interests

Keywords:

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

The des Georges lab isinterested in the molecularmechanisms of cellregulation. We use cryo-electron microscopy todecipher at the atomic levelthe function of largemacromolecular complexesinvolved in calcium signalingand in the regulation ofprotein synthesis.

2015- current Assistant professor, Structural Biology Initiative, CUNY Advanced Science Research CenterAssistant professor, Department of Chemistry and Biochemistry, City College of New York

2008-2015 Postdoc – HHMI / Columbia University – (w/ Dr. Joachim Frank)2004-2008 PhD – MRC-Laboratory of Molecular Biology, Cambridge, UK – (w/ Drs. Linda Amos & Jan Lowe)

Dr. Amedee des Georges

Terry DowdAssociate ProfessorBrooklyn College2847 Old Ingersoll2900 Bedford Ave.Brooklyn, NYtdowd@Brooklyn.cuny.eduhttp://academic.brooklyn.cuny.edu/chem/howell/facultyWebPages/Dowd/Dowd_home.htm

Publications

Chan KL, Dowd TL, Gibney BR.,�Characterization of the Zn(II) binding propertiesof the human Wilms' tumor suppressor protein C-terminal zinc finger peptide. � (2014) InorgChem. 53:6309.

Malashkevich, V., Dowd, T.L., "The X-ray CrystalStructure of Bovine 3 Glu-Osteocalcin. �Biochemistry (2013) 52:8387.

B. Kalmatsky, T.L. Dowd, �Structural studies ofN-terminal mutants of connexin 32 using 1HNMR spectroscopy.� Arch. Biochem. Biophys.(2012) 526: 1-8.

A.U. Monir, T.L. Dowd, �The Effect of Lead onBone Mineral Properties From Female AdultC57/BL6 Mice.� Bone 2010 47:888-94.

B. Kalmatsky, T.L. Dowd, �Structural studies ofthe N-terminus of Connexin 32 using 1H NMRspectroscopy.� Arch. Biochim. Biophys. 2009490: 9-16.

Research Interests

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

Dr. Terry Dowd is involvedin two areas of research.One area is the alteration inbone mineral properties indisease. The second projectinvolves alterations instructure–functionrelationships in the gapjunction molecule Connexinin deafness, neuropathy andskin disease.

2014- current Associate Professor2005 Assistant Professor1992-1996 Instructor1986-1992 Postdoc1986 Ph.D.

Dr. Terry Dowd

Emilio GallicchioAssistant ProfessorDepartment of Chemistry, Brooklyn College2900 Bedford AvenueBrooklyn, NYegallicchio@brooklyn.cuny.edusites.google.com/site/emiliogallicchiolab

Publications

Emilio Gallicchio, et al. BEDAM Binding FreeEnergy Predictions for the SAMPL4 Octa-AcidHost Challenge. J. Comp. Aided Mol. Des. 29,315-325 (2015).

Emilio Gallicchio, et al. Virtual Screening ofIntegrase Inhibitors by Large Scale Binding FreeEnergy Calculations: the SAMPL4 Challenge. JComp Aided Mol Design, 28, 475-490 (2014).

Guohua Yi, Mauro Lapelosa, Emilio Gallicchio,Gail Ferstandig Arnold et al. ChimericRhinoviruses Displaying MPER Epitopes ElicitAnti-HIV Neutralizing Responses. PLoS ONE8(9), e72205 (2013).

Gallicchio E. Role of Ligand Reorganization andConformational Restraints on the Binding FreeEnergies of DAPY Non-Nucleoside Inhibitors toHIV Reverse Transcriptase. ComputationalMolecular Bioscience, 2, 7-22 (2012).

Research Interests

-Thermodynamics of protein-protein and protein-ligand binding- Virtual drug screening- Protein conformational equilibria- Statistical thermodynamics of protein folding and misfolding- Thermodynamics of solvation of biological macromolecules- Force field development and high resolution protein modeling- Design of high performance computational chemistry algorithms- Parallel and distributed computing

Emilio Gallicchio’s research is in the area of computational molecular biophysics. He uses advanced computational models to investigate the dynamics and thermodynamics of biological systems.

2013- current Asst. Professor, Dept. Chemistry, Brooklyn College2012-2013 Research Professor, Dept. Chemistry, Rutgers University2001-2012 Associate Director, BioMaPS Institute, Rutgers University1997-2000 Postdoctoral, Rutgers University1991-1996 PhD Columbia University, Chemical Physics

Dr. Emilio Gallicchio

Kevin H. GardnerDirector, Structural Biology InitiativeCUNY Advanced Science Center, Room 3.32285 St. Nicholas TerraceNew York, NY 10031Kevin.Gardner@asrc.cuny.edustructbio.asrc.cuny.edu • kglab.org

PublicationsY. Guo et al., Coiled-coil coactivators play astructural role mediating interactions in hypoxiainducible factor heterodimerization. J. Biol.Chem., 2015, online now.

V. Ocasio et al., Ligand-induced folding of a twocomponent signaling receiver domain.Biochemistry, 54, 1353-1363.

G. Rivera-Cancel et al., Full-length structure of amonomeric histidine kinase reveals basis forsensory regulation, Proc. Natl. Acad. Sci USA,2014, 111, 17839-17844.

L.B. Motta-Mena et al., An optogenetic geneexpression system with rapid activation anddeactivation kinetics. Nat. Chem. Biol., 2014,10, 196-202.

T.H. Scheuermann et al., Allosteric inhibition ofHypoxia Inducible Factor 2 with small molecules.Nat. Chem. Biol., 9, 271-276.

Research Interests

Keywords: environmental sensing • protein/protein interactions • ligand binding • allostery • NMRspectroscopy • X-ray diffraction • biochemistry • photosensors • cancer • protein engineering

The Gardner lab studieshow cells perceive andrespond to changes in theenvironment around them.Such information providesinsights into fundamentalprinciples of proteinstructure and signaling,guides the engineering ofnew protein-based tools,and lays the foundation fornew therapeutic strategies.

2014- current Director, Structural Biology Initiative, CUNY Advanced Science Research CenterEinstein Professor of Chemistry, City College of New York

1998-2014 Professor of Biophysics and Biochemistry, UT Southwestern Medical Center1995-1998 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)

Dr. Kevin H. Gardner

PublicationsAlexandratos, S.D. et al. “Sustaining WaterResources: Environmental and EconomicImpact” ACS Sustainable Chemistry &Engineering, 2019, 7, 2879-2888.

Gibney, B.R. “Equilibrium Studies of DesignedMetalloproteins” Methods in Enzymology,Peptide, Protein and Enzyme Design, Pecoraro,V.L. Ed., 2016, 580. 417-438.

Assignargues, C. et al. “Structure and Functionof a Bacterial Microcompartment Shell ProteinEngineered to Bind a [4Fe-4S] Cluster”, J. Am.Chem. Soc. . 2016, 138, 5262-5270.

Reddi A.R. et al. “Evaluation of the Intrinsic Zn(II)Affinity of a Cys3His1 Site in the Absence ofProtein Folding Effects”, Inorg. Chem. 2015, 54,5942-5948.

Chan, K.L. et al. Characterization of the Zn(II)Binding Properties of the Wilms’ TumorSuppressor Protein C-Terminal Zinc FingerPeptide”, Inorg. Chem. 2014, 53, 6309-6320.

Gibney, B.R. Metallopeptides as Tools toUnderstand Metalloprotein Folding and Stabilityin Protein Folding and Metal Ions – Mechanisms,Biology and Disease, Gomes, C and Wittung-Stafshede, P. Eds. 2011, 227-245.Research Interests

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 coordinationchemistry and biophysical perspective. We are currently investigating the role of zinc in controlling geneexpressions in human cancer, and the role of heme proteins in cardiovascular disease.

The Gibney Lab usesmetalloprotein design toinvestigate the fundamentalengineering of biologicalsystems. These studiesprovide insight into metal-induced protein folding,heme electrochemistry, andthe role of chemicallymodified hemes in biology.

2008- current Associate Professor Brooklyn College2005-2008 Associate Professor Columbia University2000-2005 Assistant Professor Columbia University1995-2000 NIH Postdoc University of Pennsylvania1990-1995 PhD University of Michigan1986-1990 BS (ACS Certified) Florida State University

Dr. Brian R. Gibney

Brian R. GibneyAssociate ProfessorBrooklyn College2900 Bedford AvenueBrooklyn, NY 11210bgibney@broklyn.cuny.eduhttp://www.biochemistry.nyc

Dr. Dixie GossHunter College Chemistry Dept.695 Park AveNew York, NY 10065dgoss@hunter.cuny.eduhttp://www.hunter.cuny.edu/chemistry/faculty/Dixie/goss-group-1/resume

PublicationsRecruitment of 40S Ribosome to the 3'Untranslated Region (UTR) of a Viral mRNA, viathe eIF4F Complex, Facilitates Cap-independentTranslation.Das Sharma S, Kraft JJ, Miller WA, Goss DJ.J Biol Chem. 2015 Mar 19.

Pokeweed antiviral protein, a ribosome inactivatingprotein: activity, inhibition and prospects.Domashevskiy AV, Goss DJ.Toxins (Basel). 2015 Jan 28;7(2):274-98.

Rapid kinetics of iron responsive element (IRE)RNA/iron regulatory protein 1 and IRE-RNA/eIF4Fcomplexes respond differently to metal ions.Khan MA, Ma J, Walden WE, Merrick WC, TheilEC, Goss DJ.Nucleic Acids Res. 2014 Jun;42(10):6567-77.

Eukaryotic initiation factor (eIF) 4F binding to barleyyellow dwarf virus (BYDV) 3'-untranslated regioncorrelates with translation efficiency.Banerjee B, Goss DJ.J Biol Chem. 2014 Feb 14;289(7):4286-94.

Poly(A) binding proteins: are they all createdequal?Goss DJ, Kleiman FE.Wiley Interdiscip Rev RNA. 2013 Mar-Apr;4(2):167-79.

Research InterestsKeywords: protein synthesis, virus, protein-nucleic acid 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 areinterested in how unique structures in viral RNA allow viruses to take over host cell protein synthesis.

Prof. Goss is a professor ofChemistry and Biochemistryand Elion Endowed Scholar

1990- current Professor of Chemistry1989-1990 Associate Professor of Chemistry1984-1989 Assistant Professor

Post-Doc. U. of Nebraska and U. ofGeorgia

1975 Ph.D U. of Nebraska

Dr. Dixie J. Goss

Michael E GreenProfessorCity College of New YorkDept. of Chemistry160 Convent AveNew York NY 10031green@sci.ccny.cuny.eduhttp://forum.sci.ccny.cuny.edu/people/science-division-directory/b009

PublicationsA. M. Kariev and M. E. Green, "Caution is required in interpretation of mutations in the voltage sensing domain of voltage gated channels as evidence for gating mechanisms.," Int'l J. Molec. Sci. (2015) 16, 1627-1643.

A. M. Kariev and M. E. Green, "Quantum Effects in a Simple Ring with Hydrogen Bonds " J. Phys. Chem. B (2015)119,5962-5969

A. M. Kariev, P. Njau, and M. E. Green, "The Open Gate of the Kv1.2 Channel: Quantum Calculations Show The Key Role Of Hydration," Biophys J. (2014). 106, 548-555

A. M. Kariev and M. E. Green, "Voltage Gated Ion Channel Function: Gating, Conduction, and the Role of Water and Protons," Int'l J. Molec. Sci. (2012) 13, 1680-1709

S. Liao and M. E. Green, "Quantum calculations on salt bridges with water: Potentials, structure, and properties," Comput. Theo. Chem. (2011) 963, 207-214.

Dr. Green is acomputational chemist, witha principal interest inbiophysical problems,especially related to a classof proteins, ion channels,responsible for the nerveimpulse, among other things.

Dr. Green has been a faculty member inChemistry at CCNY since Sept 1966.

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. Michael Green

ProfessorHunter College of CUNYDept. of Chemistry & Biochemistry695 Park AvenueNew York NY 10065ngreenba.hunter@cuny.eduwww.cuny.edu/chemistry/faculty/nancy/greenbaum

PublicationsRiskowski, R.A., Armstrong, R.E., Greenbaum,N.L, and Strouse, G.F. (2016) TriangulatingNucleic Acid Conformations Using MulticolorSurface Energy Transfer (McSET) ACS Nano10:1926-1938.

Zhao, C, Devany, M, Greenbaum, NL (2014)Measurement of Chemical Exchange betweenRNA Conformers by 19F NMR. Biochem.Biophys. Res. Comm. 453,692-695.

Popović, M, Greenbaum, NL (2014) Role ofhelical constraints of the EBS1-IBS1 duplex of agroup II intron on demarcation of the 5′ splicesite. RNA 20, 24-35.

Zhao, C*, Bachu, R*, Popović, M, Devany, M,Brenowitz, M, Schlatterer, JC, Greenbaum, NL(2013) Conformational heterogeneity of theprotein-free human spliceosomal U2-U6 snRNAcomplex. RNA 19, 561-573. *these authorscontributed equally to the work.

Popović, M, Nelson, JD, Schroeder, KT,Greenbaum, NL (2012) Impact of base pairidentity 5¢ to the spliceosomal branch siteadenosine on branch site conformation. RNA18, 2093-2103.Research Interests

Keywords: RNA, spliceosome, 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 introns, 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.

Prof. Greenbaum is astructural biologist whoseresearch addresses the roleof biomolecular structure andfunction in biochemicalactivity of noncoding RNAmolecules. We incorporatesolution NMR, fluorescencetechniques, and biochemicalapproaches in our studies.

2007- current Professor, Hunter College2004-2007 Associate Professor, Florida State Univ.1997-2004 Assistant Professor, Florida State Univ.1992-1996 Postdoc, Columbia University1985-1989 Postdoc, Rockefeller University1981-1984 PhD, University of Pennsylvania

Dr. Nancy Greenbaum

Rupal GuptaAssistant ProfessorDepartment of ChemistryCollege of Staten Island2800 Victory Blvd.Staten Island NYRupal.Gupta@csi.cuny.edu

Publications

Rupal Gupta, et al.: “Dynamic Nuclear PolarizationEnhanced MAS NMR Spectroscopy for StructuralAnalysis of HIV-1 Protein Assemblies”, The Journal ofPhysical Chemistry B, 2016, 120, 329-339.Rupal Gupta, Taketo Taguchi, Benedikt Lassalle-Kaiser, Emile Bominaar, Junko Yano, Michael P.Hendrich, A. S. Borovik: “High-Spin Mn-OxoComplexes and their Relevance to the Oxygen-Evolving Complex within Photosystem II”,Proceedings of the National Academy of Science ofthe United States of America, 2015, 112, 5319-5324.Rupal Gupta, Guangjin Hou, Rokus Renirie, TatyanaPolenova: “51V NMR Crystallography of VanadiumChloroperoxidase and its Directed EvolutionP395D/L241V/T343A Mutant: ProtonationEnvironment of the Active Site”, Journal of theAmerican Chemical Society, 2015, 137, 5618-5628.Rupal Gupta, David C. Lacy, Emile Bominaar, A. S.Borovik, and Michael P. Hendrich: “ElectronParamagnetic Resonance and MössbauerSpectroscopy and Density Functional TheoryAnalysis of a High-Spin FeIV-oxo Complex”, Journal ofthe American Chemical Society, 2012, 134, 9775–9784.Rupal Gupta, Rong Fu, Aimin Liu and Michael P.Hendrich: “EPR and Mössbauer Spectroscopy ShowInequivalent Hemes in Tryptophan Dioxygenase”,Journal of the American Chemical Society, 2010, 132,1098–1109.Research Interests

Keywords: Bioinorganic Chemistry, Spectroscopy, Biophysical Chemistry, Magnetic Resonance,Quantum Chemical Calculations

Transition metal homeostasis is one of mechanisms through which the human body combats microbialattack. We are investigating both the processes undertaken by pathogens during invasion of a host celland the responses executed by the host cell during such an attack. The research projects aim to study themechanisms 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 interfaceof chemistry and biology will provide atomic-level understanding of fundamental processes in the humanbody during microbial invasion, which will have significant implications for human health and in the designof efficient therapeutics.

Elucidation of transition metal-mediated processesundertaken by pathogens andthe corresponding immuneresponse by the human bodyduring infection usingbioinorganic, biophysical andcomputational methodologies

2017- current Assistant Professor2013-2016 Postdoc, University of Delaware2006-2012 PhD, Carnegie Mellon University

Dr. Rupal Gupta

David JeruzalmiProfessor of Chemistry Marshak 1219 • City College of New York • Graduate Center of the City University of New York160 Convent Avenue New York, NY 10031dj@ccny.cuny.edu

Publications

Lu, M., Yang, J., Ren, Z., Sabui, S., Espejo, A.,Bedford, M. T., et al. (2009). Crystal structure ofthe three tandem FF domains of thetranscription elongation regulator CA150.Journal of Molecular Biology, 393(2), 397–408.

Pakotiprapha, D., & Jeruzalmi, D. (2013).Small-angle X-ray scattering revealsarchitecture and A(2) B(2) stoichiometry of theUvrA-UvrB DNA damage sensor. Proteins:Structure, Function, and Bioinformatics, 81(1),132–139.

Pakotiprapha, D., Liu, Y., Verdine, G. L., &Jeruzalmi, D. (2009). A structural model for thedamage-sensing complex in bacterialnucleotide excision repair. The Journal ofBiological Chemistry, 284(19), 12837–12844.

Pakotiprapha, D., Samuels, M., Shen, K., Hu, J.H., & Jeruzalmi, D. (2012). Structure andmechanism of the UvrA–UvrB DNA damagesensor. Nature Structural & MolecularBiology, 1–9.

Samuels, M., Gulati, G., Shin, J.-H., Opara, R.,McSweeney, E., Sekedat, M., et al. (2009). Abiochemically active MCM-like helicase inBacillus cereus. Nucleic Acids Research,37(13), 4441–4452.Research Interests

The faithful transmission of gene1c information is an important biological imperative. To carry out thisfunction, organisms have evolved processes to replicate their genomes and defend them from attack. Westudy important mechanisms associated with the processes of DNA replica1on and repair. The centralchallenge in understanding these processes stems from the large size of the involved multi-protein DNAcomplexes; these entities also populate many conformational states. Together, these complications placelimits on insights that can be revealed by static crystallographic structures or solution methods alone; bothsources of information are essential for defining underlying mechanisms.To this end, my group applies X-ray crystallography, supplemented withelectron microscopy, to understand these long-standing problems in DNAbiology. We also use biochemical studies to inform these approaches andfollow up on the resulting insights.

2012- current Professor of Chemistry, CCNY2002-2012 Molecular and Cellular Biology, Harvard1996-2002 The Rockefeller University1994 Ph.D., Yale University

Dr. David JeruzalmiJeruzalmi’s group appliesX-ray crystallography,supplemented with electronmicroscopy, to understandthese long-standing problemsin DNA biology. We also usebiochemical studies to informthese approaches and followup on the resulting insights.

Daniel A. KeedyAssistant ProfessorCity College of New York, Chemistry & BiochemistryAdvanced Science Research Center, Structural Biology85 St. Nicholas TerraceRoom 3.314New York, NY 10031daniel.keedy@asrc.cuny.eduwww.keedylab.org

Publications

DA Keedy*, ZB Hill*, et al. “An expandedallosteric network in PTP1B by multitemperaturecrystallography, fragment screening, andcovalent tethering.” eLife (2018).

DA Keedy*, LR Kenner*, M Warkentin*, RAWoldeyes*, et al. "Mapping Energy Landscapesof Dynamic Proteins by Multitemperature andXFEL Crystallography." eLife (2015).

DA Keedy, JS Fraser, H van den Bedem.“Improved automated modeling of alternativeprotein backbone conformations in X-raycrystallography.” PLoS Comp Biol (2015).

DA Keedy. “Conformational and connotationalheterogeneity: A surprising relationship betweenprotein structural flexibility and puns.” Proteins:Struct Funct Bioinf (2015).

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 towardspecific conformations that underlie functions such as allostery, ligand binding, and catalysis. Our workreveals new opportunities to modulate the activities of therapeutic targets such as tyrosine phosphataseswith small molecules and protein engineering, and also offers insights into more general evolutionaryprocesses that led to functional diversity in the human genome.

The Keedy Lab isinterested in how atomicmotions imbue proteinmolecules with biologicalfunctions. We use novel X-ray experiments pluscomputational modeling toexplore dynamic processeslike ligand binding andallostery in proteins.

2018-current Assistant Professor, CUNY Advanced Science Research Center , Structural Biology InitiativeAssistant 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)

Dr. Daniel A. Keedy

Reza KhayatAssistant ProfessorCity College of New YorkCenter for Discovery and Innovation85 Saint Nicholas Terrace; 12316New York, NY 10031rkhayat@ccny.cuny.eduwww.khayatlab.org

Publications

Veesler D, Khayat R, Architecture of a dsDNAviral capsid in complex with its maturationprotease. Structure 2014 Feb 4 (22): 1-8

Khayat R, Lee JH, Structural characterization ofcleaved, soluble human immunodeficiency virustype-1 envelope glycoprotein trimers. J. Virology,2013 Sep;87(17):9865-72

Pejchal R, Khayat R, A potent and broadneutralizing antibody recognizes and penetratesthe HIV glycan shield, Science 2011 Nov.25:334(6059):1097-103

Khayat R, Brunn N, The 2.3-angstrom structureof porcine circovirus 2, 2011 J. Virology Aug;85(15):7856-62

Khayat R, Lander GC, An automated procedurefor detecting protein folds from sub-nanometerresolution electron density, 2010 J. Struct. Bio.Jun; 170(3); 513-21

Research Interests

Keywords: cryo-electron microscopy, X-ray crystallography, biophysics, biochemistry, cellularbiologyWe seek to understand the structural and chemical mechanism by which pathogens hijack the cellularmachinery of their host for infection and replication. We use a combination of techniques to understandthis mechanism at the atomic resolution to relate how chemistry drives biology, and a number oftechniques to understand how biology feeds back into chemistry for new pathways to be exploited by thepathogen for infection and replication. We are also interested in developing computational methods tofurther combine X-ray crystallography with cryo-electron microscopy.

Khayat group studies thestructure and function ofproteins encoded for andutilized by pathogens toinfect and replicate. We usea combination of X-raycrystallography, cryo-electron microscopy,biophysics, biochemistry,and cellular biology tocomplete these studies.

2012- current Current position2008-2012 Sr. Research Associate, TSRI2003-2008 Research Associate, The Scripps

Research Institute1998-2003 PhD, Columbia University

Dr. Reza Khayat

Thomas KurtzmanAssistant ProfessorLehman College250 Bedford Park Boulevard WestBronx,10468 NYhttp://www.lehman.edu/faculty/tkurtzman/

Publications

Wickstrom, L. et al. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. J. Mol. Recognit. (Accepted Journal of Molecular Recognition)

Nguyen, C. N., Cruz, A., Gilson, M. K. &Kurtzman, T. Thermodynamics of Water in anEnzyme Active Site: Grid-Based HydrationAnalysis of Coagulation Factor Xa. J. Chem.Theory Comput. (2014). doi:10.1021/ct401110x

Armaiz-Pena, G. N. et al. Src activation by β-adrenoreceptors is a key switch for tumourmetastasis. Nat. Commun. 4, 1403 (2013).

Nguyen, C. N., Kurtzman Young, T. & Gilson, M. K. Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril. J. Chem. Phys.137, 044101–044101–17 (2012)*Young, T., Abel, R., Kim, B., Berne, B. J. & Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding. Proc. Natl. Acad. Sci. 104, 808 –813 (2007).

*Formerly published as T. Young

Research Interests

Keywords: Solvation Thermodynamics, Statistical Mechanics, Computer Aided Drug DesignResearch in the Kurtzman lab focuses on the development of computational tools that can aidin the discovery and rational design of new drugs. His approach applies statistical mechanicaltheory and computer simulations to better understand the physical principles that govern themolecular recognition between proteins and small molecule ligands (drugs). A particularemphasis is placed on the role that water plays in the molecular recognition process. Aprincipal goal of this research is to help design and discover drugs that bind with high affinityand selectivity to given protein targets

The Kurtzman group focuses on the development of methodologies to characterize the structure and thermodynamics of water on the surface of proteins and the exploitation of solvation properties for the discovery and design of new drugs.

2010- Present Assistant Professor, Lehman College-CUNY2008-2010 AsssistantProfessor, San José State Univ.2007-2008 Visiting Professor, Yeshiva University2004-2007 Postdoctoral Fellow, Columbia University2002 Doctorate, Stanford University

Dr. Tom Kurtzman

Themis LazaridisProfessorCity College of New YorkDept of Chemistry and Biochemistry160 Convent AveNew York NYtlazaridis@ccny.cuny.eduhttp://www.sci.ccny.cuny.edu/~themis/

Publications

Brice A., Lazaridis T. "Structure and Dynamics ofa Fusion Peptide Helical Hairpin on theMembrane Surface: Comparison of MolecularSimulations and NMR", J. Phys. Chem. B,118:4461-70 (2014)

Lazaridis T., Versace R. "The treatment ofsolvent in multiscale biophysical modeling", Isr.J. Chem., 54:1074-83 (2014)

Lazaridis T., Leveritt JM, PeBenito L. "Implicitmembrane treatment of buried charged groups.Application to peptide translocation across lipidbilayers", BBA Biomembranes, 1838:2149-59(2014)

Prieto L., He Y., Lazaridis T. "Protein arcs mayform stable pores in membranes", Biophys J,106:154-161 (2014)

Rahaman A., Lazaridis, T. "A thermodynamicapproach to alamethicin pore formation", BBABiomembranes 1838:98 (2014)

Research Interests

My research is in the area of Theoretical and Computational Biophysical Chemistry, which aims tounderstand how biological systems work in terms of the fundamental laws of Physics and Chemistry.Biomolecules, such as proteins and nucleic acids, have well defined conformations which often change inthe course of their function. Our goal is to understand the forces that operate within and betweenbiomolecules and develop quantitative mathematical models for their energy as a function ofconformation. Such models are useful in many ways, such as predicting the three-dimensional structurefrom sequence, characterizing conformational changes involved in biological function, or predicting thebinding affinity between two biomolecules.

The Lazaridis lab works inthe area of theoretical andcomputational Biophysics. Inthe past few years we haveworked on the interaction ofproteins with biologicalmembranes. We areespecially interested in theprocess of pore formation byantimicrobial peptides andother toxins.

1998- City College1992-1998 Postdoc, Harvard University1987-1992 PhD, University of Delaware

Dr. Themis Lazaridis

Prof. Sharon LoverdeAssociate ProfessorCollege of Staten IslandStaten Island NYsharon.loverde@csi.cuny.eduh"ps://sites.google.com/site/loverdelaboratory/

Publications1. "Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome ReposiDoning," Kaushik Chakraborty, Myungshim Kang, and Sharon M. Loverde, Journal of Physical Chemistry B, 122, 11827-11840 (2018). 2. "Molecular Dynamics SimulaDons of Supramolecular AnDcancer Nanotubes," Myungshim Kang, Kaushik Chakraborty, and Sharon M. Loverde, Journal of Chemical Informa6on and Modeling, 56, 1164-1168 (2018). 3. "NucleoDde State Effect on the ProtofilamentConformaDon of Tubulin Octamers," AnjelaManandhar, Myungshim Kang, Kaushik Chakraborty, and Sharon M. Loverde, Journal of Physical Chemistry B, 122, 6164-6178, (2018). 4. "Glassy Worm-Like Micelles in Solvent and Shear-Mediated Shape TransiDons," Kaushik Chakraborty, Kandaswamy Vijayan, Andre Brown, Dennis E. Discher, Sharon M. Loverde,SoG MaHer, 2018, DOI: 10.1039/C8SM00080H. 5."Isomeric Control of the Mechanical ProperDes of Supramolecular Filament Hydrogels," Yi-An Lin,Myungshim Kang, Wei-Chiang Chen,Yu-Chuan Ou, Andrew G. Cheetham, Pei-Hsun Wu, Denis Wirtz, Sharon M. Loverde and Honggang Cui, Biomaterials Science, 6, 216-224 (2018).

Research InterestsKeywords:

The Loverde laboratory utilizes all-atomistic and coarse-grained moleculardynamics simulations to investigate properties of soft and biological materials.We are also interested in characterizing the stability of macromolecularassemblies composed by proteins and/or nucleic acids.

Dr. Sharon Loverde is anAssociate Professor ofChemistry at College ofStaten Island. Herresearch group isinterested in the area ofsoft and biologicalmaterials.

2018- current Associate Professor, College of StaetnIsland2012-2018 Assistant Professor, College of StatenIsland2007-2012 NIH NRSA Postdoctoral Fellow, UPenn2001-2007 PhD, Materials Science and Engineering,Northwestern University

Dr. Sharon Loverde

Prabodhika MallikaratchyAssociate ProfessorLehman College and the Graduate Center250 Bedford Park Blvd. West,Bronx, NY 10468Prabodhika.mallikaratchy@lehman.cuny.eduwww.mallikaratchylab.org

Selected Publications1.Federica Moccia,Chiara Platella, DomenicaMusumeci, Sana Batool, , Hasan Zumrut, JohnBradshaw, Prabodhika Mallikaratchy*, DanielaMontesarchio* “The role of G-quadruplex structuresof LIGS-generated aptamers R1. 2 and R1. 3 in IgMspecific recognition” : Int J Biol Macromol. 2019 ;133:839-849.2.S Lingala, LU Nordstrøm, PR Mallikaratchy“Synthesis of stable azide and alkyne functionalizedphosphoramidite nucleosides”: Tetrahedron Letters,2019; 60(3):211-213.

3.Sana Batool, Kimon V Argyropoulos, RoksanaAzad, Precious Okeoma, Hasan Zumrut, SanamBhandari, Rigzin Dekhang, Prabodhika Mallikaratchy*” Dimerization of an aptamer generated fromLigand-guided selection (LIGS) yields a high affinityscaffold against B-cells “Biochimica et BiophysicaActa (BBA)-General Subjects, 2019; 1863 (1), 232-240.4.Hasan Zümrüt, Naznin Ara, Maria Fraile, GeorgeMaio, Prabodhika Mallikaratchy “Ligand-guidedselection of target-specific aptamers: A screeningtechnology for identifying specific aptamersagainst cell-surface proteins”. Nucleic Acid Ther.2016 ;26(3):190-8.

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

Research Interests

Keywords: Nucleic Acid Aptamers (NAAs), Ligand-Guided Selection (LIGS), Nucleic Acid NanotechnologyLong-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.

Prabodhika Mallikaratchydevelops nucleic acid aptamersagainst cellular targets to probe cell-cell interactions, receptor-ligandsinteractions. Her research is highlyinterdisciplinary, which incorporateorganic chemistry, combinatorialscreening, structural biology,immunology and biochemistry.

2019- current Associate Professor2012-2019 Assistant Professor2008-2012 Research fellow, Memorial Sloan Kettering

cancer center2003-2008 PhD, University of Florida

Dr. Prabodhika Mallikaratchy

Hiroshi MatsuiProfessorHunter College695 Park Avenue,New York, NY 10065lmassa@hunter.cuny.eduhttp://www.hunter.cuny.edu/chemistry/faculty/Lou/Lou

Publications

Dielectric Response of High Explosives at THzFrequencies Calculated by Density FunctionalTheory, Lulu Huang, Andrew Shabaev, SamLambrakos, Noam Bernstein, Vern Jacobs, DanFinkenstadt, Lou Massa, Journal of MaterialsEngineering and Performance (2012) 21(7),1120-1132.

The Kernel Energy Method: Application toGraphene and Extended Aromatics, Lulu Huang,Hugo Bohorquez, Cherif F. Matta and LouMassa, IJQC, Vol. 111, 15, 4150-4157 (2011)

The Kernel Energy Method: Construction of 3 &4 tuple Kernels from a List of Double KernelInteractions, Lulu Huang, Lou Massa, Journal ofMolecular Structure: THEOCHEM, Vol. 962,issue 1-3, 72-79 (2010)

Calculation of Strong and Weak Interactions inTDA1 and RangDP52 by Kernel Energy Method,Huang, L.; Massa, L.; Karle, I.; Karle, J.Proceedings of the National Academy ofSciences, Vol. 106, No. 10, 3664-3669 (2009)

The Kernel Energy Method of QuantumMechanical Approximation carried to FourthOrder 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, Xraycrystallography, kernel energy method, information theory,

Applications of Quantum Mechanics to the electronic structure of atoms, molecules, and solids.

Postdoc: Brookhaven National LaboratoryPhD: Theoretical Molecular Physics, Georgetown University

Dr. Louis Massa

Sébastien PogetAssistant ProfessorCollege of Staten Island, CUNYDepartment of Chemistry2800 Victory Blvd.Staten Island, NY 10314sebastien.poget@csi.cuny.eduwww.csi.cuny.edu/faculty/POGET_SEBASTIEN.html

PublicationsP. Anand, A. Grigoryan, M. H. Bhuiyan, B.Ueberheide, V. Russell, J. Quinoñez, P. Moy, B.T. Chait, S. F. Poget, M. Holford: Sample limitedcharacterization of a novel disulfide-rich venompeptide toxin from terebrid marine snail Terebravariegata. PLoS ONE 2014, 9, e94122.

S. F. Poget, M. E. Girvin: Solution NMR ofmembrane proteins in bilayer mimics: Small isbeautiful, but sometimes bigger is better.Biochim. Biophys. Acta 2007, 1768, 3098-106.

S. F. Poget, S. M. Cahill, M. E. Girvin: Isotropicbicelles stabilize the functional form of a smallmultidrug-resistance pump for NMR structuralstudies. J. Am. Chem. Soc. 2007, 129 2432-2433.

Research InterestsKeywords: 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 ofanimal peptide toxins with their target ion channel domains as tools for an improved understanding of ionchannel function and starting point for drug development. To carry out these studies at the cutting edge ofstructural biology, we are also involved in the development of new and improved methods for membraneprotein studies, including development of more powerful membrane mimetics such as bicelles and optimizedNMR methods.

Dr. Poget is interested inmembrane protein structureand function, with aparticular emphasis on theinteractions between ionchannel domains andanimal peptide toxins.

2009- current Assistant Professor, College of Staten Island, CUNY

2003-2009 Postdoc, Albert Einstein College of Medicine, NY

2001-2003 Postdoc, Rockefeller University, NY1997-2001 PhD, University of Cambridge, UK

Dr. Sébastien Poget

Adam A. Profit, Ph.D.Associate ProfessorYork College94-20 Guy R. Brewer BlvdJamaica, NY 11451Email.aprofit@york.cuny.eduwww.york.cuny.edu/portal_college/aprofit

Publications

Profit, A. A., Vedad, J. Saleh, M., and Desamero,R.Z.B. �Aromaticity and Amyloid Formation:Effect of p-Electron Distribution and ArylSubstituent Geometry on the Self-Assembly ofPeptides Derived from hIAPP22-29� ArchBiochem Biophys 2015, 567, 46-58.

Profit, A. A., Felsen, V., Chinwong, J., Mojica, E-R., and Desamero, R.Z.B. �Evidence of p-stacking Interactions in the Self-assembly ofhIAPP22-29� PROTEINS: Structure, Function andBioinformatics 2013, 81, 690-703.

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 Alzheimer�s disease as wellas type 2 diabetes. My laboratory is investigating the molecular interactions that occur between key proteins thatcontribute to the formation of amyloid in these diseases. Through a more detailed understanding of how theseproteins self-assembly to form aggregates, we hope to design and develop small molecule and peptide mimeticinhibitors which may serve as potential therapeutic agents.

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

Protein-ligand interactions isthe unifying theme of myresearch interests. Inparticular, the design,synthesis and application ofbiologically relevant probemolecules to study andelucidate protein-protein andprotein-ligand interactionsinvolved in amyloid diseasesand cancer.

2014- current Associate Professor of Chemistry2004-2014 Assistant Professor of Chemistry2000-2004 Merck Research Laboratories1997-2000 Postdoc - Albert Einstein College of Medicine1997 PhD - Stony Brook University

Dr. Adam A. Profit

Susan A. RotenbergPosition: ProfessorAffiliation: Queens CollegeDepartment of Chemistry & Biochemistry65-30 Kissena BoulevardFlushing, NY 11367Susan.Rotenberg@qc.cuny.eduhttp://rotenberglab.com/(website under construction)

Publications

X. Zhao, and S.A. Rotenberg. �Phosphorylationof Cdc42 effector protein-4 (CEP4) by proteinkinase C promotes motility of human breastcells.� J. Biol. Chem. 2014, 289:25844-25854.

S. De, A. Tsimounis, X. Chen, and S.A.Rotenberg. "Phosphorylation of a-tubulin byprotein kinase C stimulates microtubuledynamics in human breast cells." Cytoskeleton2014, 71: 257-272.

X. Chen, X. Zhao, T. P. Abeyweera, and S. A.Rotenberg. �Analysis of substrates of proteinkinase C isoforms in human breast cells by thetraceable kinase method.� Biochemistry 2012,51: 7087-7097.

X. Chen and S.A. Rotenberg. � Phospho-MARCKS drives motility of mouse melanomacells.� Cell. Signal. 2010, 22: 1097-1103.

T.P. Abeyweera, X. Chen, and S. A. Rotenberg.�Phosphorylation of a6-tubulin by protein kinaseCa activates motility of human breast cells.� J.Biol. Chem. 2009, 284: 17648-17656.

Research Interests

Keywords:Enzyme inhibitors; protein structure and function relationships; cell signaling pathways

Prof. Rotenberg

1990 - current Professor1985 - 1990 Postdoctoral - Rockefeller University,

Columbia University1980 - 1985 Ph.D. – Brown University

Dr. Susan A. Rotenberg

Kevin Ryan, Ph.D.Associate Professor, Biochemistry DivisionDepartment of Chemistry and BiochemistryThe City College of New YorkMR-1337, 160 Convent Ave.New York NYkr107@sci.ccny.cuny.eduhttp://www.sci.ccny.cuny.edu/~kr107/index2/index.html

Publications

Liu, M. T.; Nagre, N. N.; Ryan, K., Structurally diverse low molecular weight activators of the mammalian pre-mRNA 3' cleavage reaction. Bioorganic & Medicinal Chemistry 2014, 22 (2), 834-41;

Li, Y.; Peterlin, Z.; et al., Aldehyde Recognition and Discrimination by Mammalian Odorant Receptors via Functional Group-Specific Hydration Chemistry. ACS Chemical Biology 2014;

Lama, L.; Seidl, C. I.; Ryan, K., New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III. Transcription 2014, 5 (1);

Seidl, C. I.; Lama, L.; Ryan, K., Circularized synthetic oligodeoxynucleotides serve as promoterless RNA polymerase III templates for small RNA generation in human cells. Nucleic Acids Research 2013, 41 (4), 2552-64;

Kurland, M. D.; Newcomer, M. B.; et al., Discrimination of saturated aldehydes by the rat I7 olfactory receptor. Biochemistry 2010, 49 (30), 6302-4.

Research Interests

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

In the RNA area, we study the use of chemically synthesized transcription templates as potentialinformation-bearing molecules for producing small therapeutic RNA in human cells. A second RNA area isthe biochemistry of RNA processing reactions that occur during the biogenesis of messenger RNA inhuman cells. In the olfaction area, we use pharmacology, organic synthesis and chemical biology to probethe biochemistry of the sense of smell.

Dr. Ryan’s lab applieschemical concepts tobiological problems in twomain areas, RNA andolfactory molecularrecognition.

2009- current Associate Professor2003-2008 Assistant Professor1996-2003 Postdoc, Columbia University (Chemistry

and Biology Depts.) 1996 Ph.D., University of Rochester

Dr. Kevin Ryan

Ruth E. StarkDistinguished ProfessorCity College Dept. of Chemistry and BiochemistryCUNY Institute for Macromolecular AssembliesCCNY CDI 1302, 85 St. Nicholas TerraceNew York, NY 10031Email.rstark@ccny.cuny.eduhttp://www.sci.ccny.cuny.edu/resgroup

Publications

W. Huang, O. Serra, K. Dastmalchi, L. Jin, L.Yang, R.E. Stark, Comprehensive MS and Solid-state NMR metabolomic profiling revealsmolecular variations in native periderms fromfour Solanum tuberosum potato cultivars, J.Agric. Food Chem., 2017, 65, 2258-2274.

L.Q. Jin,* Q. Cai,* W. Huang, K. Dastmalchi, J.Rigau, M. Molinas, M. Figueras, O. Serra, R.E.Stark, Potato native and wound periderms aredifferently affected by down-regulation of FHT, aPotato Feruloyl Transferase, Phytochemistry,2018, 147, 30-48.

Q. Wang,* S. Rizk,* C. Bernard, M.P. Lai, D.Kam, J. Storch, R.E. Stark, Protocols and pitfallsof obtaining fatty acid-binding proteins forbiophysical studies of ligand-protein and protein-protein interactions, Biochem. Biophys. Rep.,2017, 10, 318-324.

E. Camacho, C. Chrissian, R.J.B. Cordero, L.Liporagi-Lopes, R.E. Stark, A. Casadevall, N-acetylglucosamine supplementation affectsCryptococcus neoformans cell wall compositionand melanin architecture, Microbiology, 2018,163, 1540-1556.

Research Interests

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

The Stark Laboratory uses structural biology and biophysical approaches to study plant protective polymers, lipid metabolism, 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), mass spectrometry, and atomic force microscopy. 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. Stark’s biophysicsresearch program focuseson the molecular structureand interactions ofprotective plant bio-polymers, fatty acid-bindingproteins that mediate painand obesity, and melaninpigments associated withhuman fungal infections.

2007 - current CUNY Dist. Prof., CCNY1985 - 2007 Assoc.-Dist. Prof., Coll. of Staten Island1979 - 1985 Asst. Prof., Amherst College1977 - 1979 Postdoctoral Fellow, M.I.T.1977 PhD, Physical Chemistry, UC San Diego

Dr. Ruth E. Stark

Maria C. TamargoProfessor and Former Executive OfficerThe City College of New YorkDepartment of Chemistry160 Convent AvenueNew York NY 10031mtamargo@ccny.cuny.eduhttps://www.ccny.cuny.edu/profiles/maria-tamargohttps://www.idealscrest.org

Publications

V. Deligiannakis, S. Dhomkar, M. S. Claro, I. L. Kuskovsky, M. C. Tamargo, Interface Modification in Type-II ZnCdSe/Zn(Cd)Te QDs for High Efficiency Intermediate Band Solar Cells, J. Crystal Growth 512, 203-207 (2019).

M. S. Claro, I. Levy, A. Gangopadhyay, D. J. Smith, M. C. Tamargo, Self-assembled Bismuth Selenide (Bi2Se3) quantum dots grown by molecular beam epitaxy, Scientific Reports 9, 3370 (2019).

I. Levy, T. A. Garcia, S. Shafique and M. C. Tamargo, Reduced twinning and surface roughness of Bi2Se3 and Bi2Te3

layers grown by molecular beam epitaxy on sapphire substrates, J. Vac. Sci. Technol. B 36, 02D107-1 (2018).

Y. Kaya, A. Ravikumar, G. Chen, M. C. Tamargo, A. Shen, and C. Gmachl, Two-band ZnCdSe/ZnCdMgSe quantum well infrared photodetector, AIP Adv. 8, 075105 (2018)

T. A. Garcia, V. Deligiannakis, C. Forrester, I. Levy and M. C. Tamargo, 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, photonicdevices, 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.

Maria C. Tamargo isProfessor of Chemistry atthe City College of NewYork. Her research is insemiconductor materialsand nanostructures design,growth by epitaxial growthtechniques, characterizationmethods, and applications.

1993 - present The City College of New York andThe Graduate Center - CUNY

1984-1992 Bellcore1978-1984 AT&T Bell Labs1972-1978 PhD (Johns Hopkins University)1968-1972 BS (University of Puerto Rico)

Dr. Maria C. Tamargo

Mariana TorrenteAssistant ProfessorDepartment of Chemistry2900 Bedford AvenueIngersoll Hall Extension 343/345Brooklyn NYmariana.torrente@brooklyn.cuny.edu

Publications

Torrente, M.P., L.M. Castellano, and J. Shorter.Suramin inhibits Hsp104 ATPase and disaggregaseactivity. PLoS ONE. 9(10): e110115. (2014)

Torrente, M.P., and J. Shorter. The metazoanprotein disaggregase and amyloid depolymerasesystem: Hsp110, Hsp70, Hsp40, and small heatshock 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 revampthe treatment of depression? J Psychopharmacol.26(5), 629-35. (2012)

Torrente, M.P., Zee, B.M.; Young, N.L.; Baliban,R.C; Leroy, G.; Floudas, C.A.; Hake, S.B.; GarciaB.A., Proteomic Interrogation of Human Chromatin.PLoS One, 6, (9), e24747. (2011)

Plazas-Mayorca, M.D. and Vrana, K.E. Proteomicinvestigation of epigenetics in neuropsychiatricdisorders: A missing link between genetics andbehavior? Journal of Proteome Research, 10 (1),58-65. (2011)

Research Interests

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

Dr. Torrente is interested inthe molecular mechanismsunderlying neurodegenerativeand psychiatric disease.

2015- current Assistant Professor, Brooklyn College; NIH Career Transition Award Fellow2012-2015 IRACDA PENN-PORT Postdoctoral Fellow, University of Pennsylvania2010-2012 NIH NRSA Postdoctoral Fellow, Penn State University College of Medicine2010 Ph.D. in Chemistry, Princeton University

Dr. Mariana Torrente