department of pharmacology

Untitled Page

Nathan Alexander

Nathan Alexander, Ph.D., Postdoctoral Fellow
Contact: 330-564-7648
Research Interest: Computational clustering; software engineering; high resolution protein structure determination
Field of study: Structural biology
Selected recent publications:
  • Alexander, N. S.; Bortolus, M.; Al-Mestarihi, A.; Mchaourab, H.; Meilerl, J., De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure 2008, 16, (2), 181-195.
  • Alexander, N. S.; Woetzel, N.; Meiler, J., Bcl::Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System, In Computational Advances in Bio and Medical Sciences (ICCABS), 2011 IEEE 1st International Conference on, 3-5 Feb. 2011, pp 13-18.
  • Van Eps, N. ; Preininger, A. M. ; Alexander, N. S. ; Kaya, A. I.; Meier, S.; Meiler, J.; Hamm, H. E.; Hubbell, W. L., Interaction of a G protein with an activated receptor opens the interdomain interface in the alpha subunit.Proceedings of the National Academy of Sciences 108, (23), 9420-9424.

  • Elliot Choi

    Elliot Choi, , MSTP Graduate Student
    Contact: (216)-368-5294
    Research Interest:
    Field of study: Molecular Biology and Biochemistry
    Selected recent publications:
  • Wang T, Lee MH, Choi E, Pardo-Villamizar CA, Lee SB, Yang IH, Calabresi PA, Nath A. Granzyme neurotoxicity is mediated via activation of PAR-1 receptor and Kv1.3 channel. PLoS One. 2012;7(8)
  • Wang T, Choi E, Monaco MC, Campanac E, Medynets M, Do T, Rao P, Johnson KR, Elkahloun AG, Von Geldern G, Johnson T, Subramaniam S, Hoffman D, Major E, Nath A. Derivation of neural stem cells from human adult peripheral CD34+ cells for an autologous model of neuroinflammation. PLoS One. 2013;8(11)
  • Wang T, Choi E, Monaco MC, Major EO, Medynets M, Nath A. Direct induction of human neural stem cells from peripheral blood hematopoietic progenitor cells. J Vis Exp. 2015 Jan

  • Zhiqian Dong

    Zhiqian Dong, M.D., Ph. D., , Research Scientist
    Contact: (216) 368 3714
    Research Interest: Neurodegenerative diseases and neuropathology
    Field of study:
    Selected recent publications:
  • Xiao X*, Cali I*, Dong Z* (equal contribution*), Puoti G, Yuan J, Qing L, Wang H, Kong Q, Gambetti P, Zou W. Protease-sensitive prions with 144-bp insertion mutations. Aging (Albany NY) 2013; 5(3): 155-73
  • Maeda T, Dong Z, Jin H, Savada O, Palczewska G, Palczewski K. QLT091001, a 9-cis-retinal analog, is well tolerated by retinas of mice with impaired visual cycles. Invest Ophth Vis Sci 2013, Jan; 54(1):455-66
  • Gambetti P, Dong Z, Yuan J, Xiao X, Zheng M, Alshekhlee A, Castellani R, Cohen M, Barria MA, Gonzalez-Romero D, Belay ED, Schonberger LB, Marder K, Harris C, Burke JR, Montine T, Wisniewski T, Dickson DW, Soto C, Hulette CM, Mastrianni JA, Kong Q, Zou WQ. A novel human disease with abnormal prion protein sensitive to protease. Ann Neurol. 2008, 63: 697-708
  • Dong Z, Pang JS, Ng MH, Poon WS, Zhou L, Ng HK. Identification of two contiguous minimally deleted regions on chromosome 1p36.31-p36.32 in oligodendroglial tumours. Br J Cancer. 2004, 91: 1105-11
  • Dong Z, Pang JC, Tong CY, Zhou LF, Ng HK. Clonality of oligoastrocytomas. Hum Pathol. 2002; 33(5): 528-535

  • Tamar Getter

    Tamar Getter, , Postdoctoral Scholar
    Contact: NA
    Research Interest: Biochemistry and Pharmacology
    Field of study: Search for all-trans-retinal quenchers, Opsin non retinoid ligands, ligands for rhodopsin dimerization disruption and high end fluorophores.
    Selected recent publications:
  • Getter T, Zaks I, Barhum Y, Ben-Zur T, Böselt S, Gregoire S, Viskind O, Shani T, Gottlieb H, Green O, Shubely M, Senderowitz H, Israelson A, Kwon I, Petri S, Offen D, Gruzman A.
  • Zaks I, Getter T, Gruzman A. Future Med Chem. 2014 Jul;6(11):1325-53. doi: 10.4155/fmc.14.74. Review.
  • Meltzer-Mats E, Babai-Shani G, Pasternak L, Uritsky N, Getter T, Viskind O, Eckel J, Cerasi E, Senderowitz H, Sasson S, Gruzman A. J Med Chem. 2013 Jul 11;56(13):5335-50. doi: 10.1021/jm4001488. Epub 2013 Jun 26.

  • Sahil Gulati

    Sahil Gulati, , Graduate Student
    Contact: (216) 368-5294
    Research Interest: Retinoid biochemistry, X-ray crystallography, Pharmacology, Electron Microscopy
    Field of study: Structural biology
    Selected recent publications:
  • R. Sreejith, Jyoti Rana, Sahil Gulati, Amita Gupta, Sanjay Gupta, Predicting the host protein interactors of Chandipura virus using a structure similarity based approach. FEMS Pathogens and Disease, Vol. 69[1], pp 29–35, 2013.
  • R. Sreejith, Sahil Gulati, Sanjay Gupta, Interfacial Interactions involved in the Biological Assembly of Chandipura virus Nucleocapsid protein. Virus Genes, Vol. 46[3], pp 535-537, 2013.
  • urangna Jain, Sanjay Gupta, Deciphering the Host-Pathogen Protein Interface in Chikungunya Virus Mediated Sickness. Archives of Virology, Vol. 158[6], pp 1159-1172, 2013.

  • Shirin Kahremany

    Shirin Kahremany, , Postdoctoral Scholar
    Contact: NA
    Research Interest: Biochemistry and Pharmacology
    Field of study: Search for Opsin non retinoid ligands and drug delivery studies.
    Selected recent publications:
  • Kahremany S, Livne A, Gruzman A, Senderowitz H, Sasson S. Br J Pharmacol. 2015 Feb;172(3):754-70. doi: 10.1111/bph.12950. Epub 2014 Dec 15. Review.
  • Weintraub S, Yarnitzky T, Kahremany S, Barrera I, Viskind O, Rosenblum K, Niv MY, Gruzman A. Mol Divers. 2016 Nov;20(4):805-819. Epub 2016 Aug 1.
  • Munder A, Israel LL, Kahremany S, Ben-Shabat-Binyamini R, Zhang C, Kolitz-Domb M, Viskind O, Levine A, Senderowitz H, Chessler S, Lellouche JP, Gruzman A. ACS Appl Mater Interfaces. 2017 Jan 18;9(2):1189-1206. doi: 10.1021/acsami.6b10568. Epub 2017 Jan 3.

  • Les Kallestad

    Les Kallestad, ,
    Contact: NA
    Research Interest: Regulation of Genetic Expression
    Field of study: Epigenetics
    Selected recent publications:
  • Kallestad L, Christensen K, Woods E, and Milavetz B, Transcriptional Repression is Epigenetically Marked by H3K9 Methylation during SV40 Replication - Clin Epigenetics. 2014 Oct 27;6(1):21. doi: 10.1186/1868-7083-6-21. eCollection 2014.
  • Kallestad L, Woods E, Christensen K, Gefroh A, Balakrishnan L, Milavetz B, Transcription and replication result in distinct epigenetic marks following repression of early gene expression, Front Genet. 2013 Jul 30;4:140. doi: 10.3389/fgene.2013.00140. ECollection 2013.
  • Milavetz B, Kallestad L, Gefroh A, Adams N, Woods E, Balakrishnan L, Virion-mediated transfer of SV40 epigenetic information, Epigenetics. 2012 Jun 1;7(6):528-34. doi: 10.4161/epi.20057. Epub 2012 Jun 1.

  • Henri Leinonen

    Henri Leinonen, , Ph.D. (pharm.), Postdoctoral Scholar
    Contact: 973.970.8008
    Research Interest: Pharmacology, Visual Neuroscience
    Field of study: Systems Pharmacology
    Selected recent publications:
  • Leinonen H, Rossi M, Salo AM, Tiainen P, Hyvärinen J, Pitkänen M, Sormunen R, Miinalainen I, Zhang C, Soininen R, Kivirikko KI, Koskelainen A, Tanila H, Myllyharju J, Koivunen P. Lack of P4H-TM in mice results in age-related retinal and renal alterations. Hum Mol Genet. 2016 Jul 27. pii: ddw228.
  • Leinonen H, Lipponen A, Gurevicius K, Tanila H. Normal Amplitude of Electroretinography and Visual Evoked Potential Responses in AβPP/PS1 Mice. J Alzheimers Dis. 2016;51(1):21-6.
  • Ragauskas S*, Leinonen H*, Puranen J, Rönkkö S, Nymark S, Gurevicius K, Lipponen A, Kontkanen O, Puoliväli J, Tanila H, Kalesnykas G. Early retinal function deficit without prominent morphological changes in the R6/2 mouse model of Huntington's disease. PLoS One. 2014 Dec 3;9(12):e113317. *equal contribution
  • Koivisto H*, Leinonen H*, Puurula M, Hafez HS, Barrera GA, Stridh MH, Waagepetersen HS, Tiainen M, Soininen P, Zilberter Y, Tanila H. Chronic Pyruvate Supplementation Increases Exploratory Activity and Brain Energy Reserves in Young and Middle-Aged Mice. Front Aging Neurosci. 2016 Mar 16;8:41. doi: 10.3389 *equal contribution

  • Dominik Lewandowski

    Dominik Lewandowski, Ph.D., Postdoctoral Fellow
    Contact: NA
    Research Interest: Structure of the key proteins engaged in the phototransduction cycle/ high-throughput drug screening/ L-ORMD
    Field of study: Structural and molecular biology, pharmacology
    Selected recent publications:
  • Urbanowicz A, Lewandowski D, Jodynis-Liebert J, Sadowski C, Figlerowicz M. Functional insights into recombinant TROSPA protein from Ixodes ricinus. PLoS ONE 8(10): e76848. doi:10.1371/journal.pone.0076848
  • Lewandowski D, Urbanowicz A, Figlerowicz M. Molecular interactions between Borrelia burgdorferi ticks and mammals. Advances in Microbiology, 2013, vol. 52(1)
  • Lewandowski D, Urbanowicz A, Figlerowicz M. The fruitful coexistence of Borrelia burgdorferi and Ixodes ticks. BioTechnologia, 2013, vol. 94(1)
  • Urbanowicz A, Lewandowski D, Figlerowicz M. Oral Lyme disease vaccine. BioTechnologia, 2014, vol. 95(4)
  • Urbanowicz A*, Lewandowski D*, Szpotkowski K, Figlerowicz M. Tick receptor for outer surface protein A from Ixodes ricinus - the first intrinsically disordered protein involved in vector-microbe recognition. Scientific Reports. 2016 Apr 26;6:25205. doi: 10.1038/srep25205 (* equal contributions)

  • Timothy S. Owen

    Timothy S. Owen, , Postdoc
    Contact: NA
    Research Interest: Biochemistry and Pharmacology
    Field of study: Biochemistry and Structural Biology
    Selected recent publications:
  • Owen, T. S. et al. Active Site Targeting of Hedgehog Precursor Protein with Phenylarsine Oxide, ChemBioChem, 2015, 16, 55-58
  • Xie. J., Owen, T. et al. Zinc inhibits Hedgehog Autoprocessing: Linking Zinc Deficiency with Hedgehog Activation, J. Biol. Chem. 2015, 290, 11591-600 **One of JBC’s Top 5 Most Viewed Articles in 2015**
  • Xie, J., Owen, T. et al. A Single Aspartate Coordinates Two Catalytic Steps in Hedgehog Autoprocessing, JACS. Accepted: DOI: 10.1021/jacs.6b06928
  • Owen, T. S. et al. Förster Resonance Energy Transfer-based Cholesterolysis Assay Identifies a Novel Hedgehog Inhibitor, Anal. Biochem. 2015, 488, 1-5

  • David Peck

    David Peck, , Lab Manager
    Contact: (216)-368-5294
    Research Interest:
    Field of study:
    Selected recent publications:
  • Moise AR, Lobo GP, Erokwu B, Wilson DL, Peck D, Alvarez S, Domínguez M, Alvarez R, Flask CA, de Lera AR, von Lintig J, Palczewski K. Increased adiposity in the retinol saturase-knockout mouse. FASEB J. 2010, 24:1261-70

  • Daniel Ruminski

    Daniel Ruminski, , Postdoctoral Scholar
    Contact: 216-368-0411
    Research Interest: Optical Coherence Tomography (morphology, angiography, Doppler), Microperimetry
    Field of study: Biophysics, Ophthalmology
    Selected recent publications:
  • D. Ruminski, B. L. Sikorski, D. Bukowska, M. Szkulmowski, K. Krawiec, J. Włodarczyk, G. Malukiewicz, L. Bieganowski, M. Wojtkowski, OCT angiography based on absolute intensity difference analysis, Biomed. Opt. Express 6(8), 2015.
  • D. Bukowska, D. Ruminski, D. Szlag, I. Grulkowski, J. Włodarczyk, M. Szkulmowski, G. Wilczyński, I. Gorczynska, M. Wojtkowski, Multi-parametric imaging of murine brain using spectral and time domain optical coherence tomography, J. Biomed. Opt. 17 (10), 2012.

  • Sanae Sakami

    Sanae Sakami, Ph. D., Research Associate
    Contact: (216) 368-3657
    Research Interest: Retinal Degeneration
    Field of study: Retinal Degeneration
    Selected recent publications:
  • Sakami S, Hisatomi O, Sakakibara S, Liu J, Reh TA, Tokunaga F. Downregulation of Otx2 in the dedifferentiated RPE cells of regenerating newt retina. Brain Res Dev Brain Res. 2005; (155) 49-59.
  • Sakami S, Etter P, Reh TA. Activin signaling limits the competence for retinal regeneration from the pigmented epithelium. Mechanisms of Development. 2007, 125 (1-2):106-16.
  • Sakami S, Maeda T, Bereta G, Okano K, Golczak M, Sumaroka A, Roman AJ, Cideciyan AV, Jacobson SG, Palczewski K. Probing mechanisms of photoreceptor degeneration in a new mouse model of the common form of autosomal dominant retinitis pigmentosa due to P23H opsin mutations. J Biol Chem. 2011 Jan 11.
  • Sakami S, Kolesnikov AV, Kefalov VJ, Palczewski K. P23H opsin knock-in mice reveal a novel step in retinal rod disc morphogenesis. Hum Mol Genet. 2014 Apr1;23(7):1723-41. Epub 2013 Nov 7.
  • Chiang WC, Kroeger H, Sakami S, Messah C, Yasumura D, Matthes MT, Coppinger JA, Palczewski K, LaVail MM, Lin JH. Robust Endoplasmic Reticulum-Associated Degradation of Rhodopsin Precedes Retinal Degeneration. Mol Neurobiol. 2015, 52(1):679-95.
  • Comitato A, Di Salvo MT, Turchiano G, Montanari M, Sakami S, Palczewski K, Marigo V. Dominant and recessive mutations in rhodopsin activate different cell death pathways. Hum Mol Genet. 2016 May 5. pii: ddw137. [Epub ahead of print] PubMed PMID: 27149983.
  • Athanasiou D, M. Aguila, C. A. Opefi, K. South, J. Bellingham, D. Bevilacqua, P. M. Munro, N. Kanuga1, F. E. Mackenzie, A. M. Dubis, A. Georgiadis, A.B. Graca, R. A. Pearson1, R. R. Ali, S. Sakami, K. Palczewski, M. Y. Sherman, P. J. Reeves, M. E. Cheetham. Rescue of mutant rhodopsin traffic by metformin-induced AMPK activation accelerates photoreceptor degeneration. Hum. Mol. Genetics 2016 (in press).

  • David Salom

    David Salom, Ph.D., Sr. Research Associate
    Contact: (216) 658-4528
    Research Interest: Structure-activity relationship of membrane proteins in general, and GPCRs in particular
    Field of study: Biophysics and structural biology of membrane proteins
    Selected recent publications:
  • Salom D , Hill BR, Lear JD, DeGrado WF. pH-Dependent tetramerization and amantadine binding of the transmembrane helix of M2 from influenza A virus. Biochemistry 2000, 39:14160-14170.
  • Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K. Crystal structure of a photoactivated deprotonated intermediate of rhodopsin. Proc Natl Acad. Sci. USA 2006, 103:16123-16128.
  • Stouffer AL*, Acharya R*, Salom D*, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. Structural basis for the function and inhibition of an influenza virus proton channel. Nature. 2008 Jan 31;451(7178):596-9.
  • Salom D, Wu N, Sun W, Dong Z, Palczewski K, Jordan S, Salon JA. Heterologous expression and purification of the serotonin type 4 receptor from transgenic mouse retina. Biochemistry. 2008 Dec 16;47(50):13296-307
  • Padayatti P, Palczewska G, Sun W, Palczewski K, Salom D. "Imaging of protein crystals with two-photon microscopy". Biochemistry 2012;51(8):1625-37
  • Stouffer* AL, Acharya* R, Salom* D, Levine AS, Di Costanzo L, Soto CS, Tereshko V, Nanda V, Stayrook S, DeGrado WF. "Structural basis for the function and inhibition of an influenza virus proton channel". Nature 2008;451(7178):596-9.
  • Salom D, Lodowski DT, Stenkamp RE, Le Trong I, Golczak M, Jastrzebska B, Harris T, Ballesteros JA, Palczewski K. "Crystal structure of a photoactivated deprotonated intermediate of rhodopsin". Proc. Natl. Acad. Sci. USA. 2006;103(44):16123-8.
  • Salom D, Cao P, Sun W, Kramp K, Jastrzebska B, Jin H, Feng Z, Palczewski K. "Heterologous expression of functional G-protein-coupled receptors in Caenorhabditis elegans". FASEB J. 2012;26(2):492-502

  • Avery Sears

    Avery Sears, , MSTP graduate student
    Contact: (216)368-3063
    Research Interest: Retinoid metabolism and inherited retinal disease
    Field of study: Structural biology and pharmacology
    Selected recent publications:
  • Golczak M., Kiser P.D., Sears A.E., Lodowski D.T., Blaner W.S., Palczewski, K. Structural basis for the acyltransferase activity of lecithin:retinol acyltransferase-like proteins. J Biol Chem. 2012; 287(28):23790-807
  • Golczak M. Sears A.E., Kiser P.D., Palczewski K. LRAT-specific domain facilitates vitamin A metabolism by domain swapping in HRASLS3. Nature Chem Biol. 2015; 11(1):26-32

  • Susie Suh

    Susie Suh, , MSTP Graduate Student
    Contact: (216) 368-5294
    Research Interest:
    Field of study: Molecular Biology and Biochemistry
    Selected recent publications:
  • R.P. Hickerson, W.C. Wey, D.L. Rimm, T. Speaker, S. Suh, M.A. Flores, E. Gonzalez-Gonzalez, D. Leake, C.H. Contag, R.L. Kaspar, Gene silencing in skin after deposition of self-delivery siRNA with a motorized microneedle array device. Molecular Therapy. Nucleic Acids 2 (2013) e129.

  • Wendy Sun

    Wendy Sun, M.D., Ph.D., Scientist
    Contact: (216)-368-3714
    Research Interest: Molecular genetics techniques
    Field of study: Molecular biology
    Selected recent publications:
  • Sun W, Gerth C, Maeda A, Lodowski DT, van der Kraak L, Saperstein DA, Heon E, Palczewski K. Novel RDH12 mutations associated with Leber Congenital Amaurosis and Cone-Rod Dysthrophy: Biochemical and Clinical Evaluations. Vision Res. 2007, 47:2055-66.
  • Maeda A, Maeda T, Sun W, Zhang H, Baehr W, Palczewski K. Redundant and unique roles of retinol dehydrogenases in the mouse retina. Proc Natl Acad Sci U S A 2007, 104:19565-70.
  • Chen Y, Guo X, Deng FM, Liang FX, Sun W, Ren M, Izumi T, Sabatini DD, Sun TT, Kreibich G. Rab27b is associated with fusiform vesicles and may be involved in targeting uroplakins to urothelial apical membranes. Proc Natl Acad Sci U S A 2003, 100:14012-14017.
  • Sun W, Liu S, Brindley PJ, Mcmanus DP. Bacterial expression and characterization of functional recombinant triosephosphate isomerase from Schistosoma japonicum. Protein Expr Purif. 1999, 17:410-3.

  • Aleksander Tworak

    Aleksander Tworak, , Postdoctoral Fellow
    Contact: NA
    Research Interest: Structural and functional biology
    Field of study: Phagocytosis of photoreceptor outer segments
    Selected recent publications:
  • Tworak A, Urbanowicz A, Podkowinski J, Kurzynska-Kokorniak A, Koralewska N, Figlerowicz M.
  • Kurzynska-Kokorniak A, Koralewska N, Pokornowska M, Urbanowicz A, Tworak A, Mickiewicz A, Figlerowicz M.

  • Jianye Zhang

    Jianye Zhang, Ph.D., Postdoctoral fellow
    Contact: (216)-368-6187
    Research Interest: Retinoid metabolism
    Field of study: Medicinal Chemistry
    Selected recent publications:
  • Fan X, Sell DR, Zhang J, Nemet I, Theves M, Lu J, et al. Anaerobic vs aerobic pathways of carbonyl and oxidant stress in human lens and skin during aging and in diabetes: A comparative analysis. Free radical biology & medicine. 2010;49(5):847-56; PMCID: PMC2910832
  • Zhu X, Tang X, Zhang J, Tochtrop GP, Anderson VE, Sayre LM. Mass spectrometric evidence for the existence of distinct modifications of different proteins by 2(E),4(E)-decadienal. Chemical research in toxicology. 2010;23(3):467-73; PMCID: PMC2838956.
  • Collard F, Fagan RL, Zhang J, Nemet I, Palfey BA, Monnier VM. The cation-pi interaction between Lys53 and the flavin of fructosamine oxidase (FAOX-II) is critical for activity. Biochemistry. 2011;50(37):7977-86; PMCID: PMC2556003.