Department of Molecular Medicine
 

Maria Gaczynska Maria  E. GaczynskaPh.D.

Associate Professor


Profile and Contact Information | Research | Laboratory


RESEARCH

 

Research Program

My scientific expertise spans as diverse areas as protein biochemistry and biophysics, structural biology and cell biology, as well as single-molecule and single-cell imaging. I have more than 25 years of experience with biochemistry and biophysics of membranes and enzymes, and with scanning probe microscopy (SPM) based imaging methods. I have more than 20 years of experience with biochemistry, cell biology and of structural biology of the proteasome. In short, the proteasome is a multifunctional proteolytic enzyme, a focal point of the ubiquitin-proteasome system, essential in cell cycle progression, signal transduction pathways, immune response and general “housekeeping” in the human cell. The proteasome is an established target for cancer drugs. I worked as a postdoctoral fellow in laboratory of one of founding fathers of the ubiquitin-proteasome field, Dr. A.L. Goldberg (Harvard Medical School). In the laboratories of Drs. Goldberg and Ploegh (MIT Center for Cancer Research) I took major part in discovery of immunoproteasomes and in characterization of first specific inhibitors of proteasome, respectively. As an independent investigator, together with Dr. Osmulski, I took on the vast and novel field of allosteric regulation of the proteasome. The prime interest of the laboratory is to track changes in ubiquitin-proteasome system accompanying cancer and aging, and to use small molecules to affect activity and stability of proteasomal assemblies. Our laboratory laid the groundwork for the use of atomic force microscopy to probe molecular dynamics of the proteasome and its response to drugs, and we are in the forefront of studies on the small-molecule allosteric regulators of the proteasome.
 Inhibitors of the proteasome selectively kill cancer cells. However, regulation rather than inhibition may prove beneficial to help aging cells or to attenuate effects of inflammatory diseases. Our research addresses two major questions fundamental for regulation of proteasome in health and disease.



I. How to regulate proteasome function in the most effective way? We postulate that molecular dynamics and allosteric signaling are excellent targets for small-molecule regulators capable to affect proteasome function in a truly versatile way. We created a set of small molecule compounds capable to activate or inhibit the proteasome, to change its specificity, or to synergize with competitive inhibitors.



II. How the proteasomes differ in normal, cancer or aging cells? We propose that proteasome, together with other proteases that take a part in the controlled degradation of regulatory proteins in the cell, constitute a functional entity. They form multibranched degradation pathways enabling a tight control of this irreversible process. We postulate that this web of interactions is dysfunctional in cancer or in aged organisms, creating a "proteolytic instability". Dissecting the web of interaction and aiming at its most vulnerable points would enable to manipulate the activities of the involved proteases to specifically kill tumor cells or to improve an immune response in aging tissue.





Beyond the proteasome-centered research, we are interested in cancer-relevant single cell studies. In a collaborative effort with clinical oncologists and genomics specialists we elucidate the biophysical properties of cancer cells and their environment. We are most interested in circulating tumor cells (CTCs) in prostate cancer. We are working on developing the AFM-based biophysical profiling of patient-isolated CTCs for predictive and prognostic use.

The capabilities of our laboratory include:

1. Scanning probe microscopy (SPM)/atomic force microscopy (AFM), to study dynamics of biomacromolecules and physical properties of living cells in a single-molecule and single-cell fashion. 2. Spectrofluorometry, for example used to complement the AFM studies of the dynamic structure of the proteasome; 
3. Expertise in numerous other spectroscopic methods (EPR, ENDOR, mass spectrometry);
 4. Enzymology, including advanced enzyme mechanism and molecular modeling of enzyme-ligand interactions;
 5. Development of protein purification techniques designed for giant biomacromolecules;
 6. Chemistry of peptides: design and synthesis of peptides, peptide derivatives and peptidomimetics, their purification and characterization, computer modeling of their structure and interaction with intended targets;
 7. In addition to the above specialized methods and approaches, we are using standard molecular biology methods, yeast genetics and mammalian tissue culture techniques.

 

Selected Publications

  1. Giletto MB, Osmulski PA, Jones CL, Gaczynska ME, Tepe JJ. Pipecolic esters as minimized templates for proteasome inhibition. Org Biomol Chem. 2019;17(10):2734–2746.

  2. Njomen E, Osmulski PA, Jones CL, Gaczynska M, Tepe JJ. Small Molecule Modulation of Proteasome Assembly. Biochemistry. 2018 Jul 17;57(28):4214–4224.

  3. Giżyńska M, Witkowska J, Karpowicz P, Rostankowski R, Chocron ES, Pickering AM, Osmulski P, Gaczynska M, Jankowska E. Proline- and Arginine-Rich Peptides as Flexible Allosteric Modulators of Human Proteasome Activity. J Med Chem. 2019 Jan 10;62(1):359–370.

  4. Polusani SR, Huang Y-W, Huang G, Chen C-W, Wang C-M, Lin L-L, Osmulski P, Lucio ND, Liu L, Hsu Y-T, Zhou Y, Lin C-L, Aguilera-Barrantes I, Valente PT, Kost ER, Chen C-L, Shim EY, Lee SE, Ruan J, Gaczynska ME, Yan P, Goodfellow PJ, Mutch DG, Jin VX, Nicholson BJ, Huang TH-M, Kirma NB. Adipokines deregulate cellular communication via epigenetic repression of gap junction loci in obese endometrial cancer. Cancer Res. 2019;79(1):196–208.

  5. Gaczynska M, Osmulski PA, Jiang Y, Lee J-K, Bermudez V, Hurwitz J. Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA. Proc Natl Acad Sci U S A. 2004;101(52):17952–17957.

  6. Gaczynska M, Osmulski PA. Targeting Protein–Protein Interactions in the Ubiquitin–Proteasome Pathway. In: Donev R, editor. Elsevier Inc.; 2018. p. 123–165.

  7. Karpowicz, P., Osmulski, P.A., Witkowska, J., Sikorska, E., Giżyńska, M.; Belczyk-Ciesielska, A., Gaczynska, M.(co-corresponding), Jankowska, E. (2015) Interplay between structure and charge as a key to allosteric modulation of human 20S proteasome by the basic fragment of HIV-1 Tat protein. PLoS ONE 10(11): e0143038. PMID: 26575189. PMCID: PMC4648528

  8. Osmulski, P.A., Gaczynska, M. (2015) Targeting protein-protein interactions in the proteasome super-assemblies. Curr. Topics Med. Chem. 15, 2056-2067.PMID: 25986687

  9. Witkowska, J., Karpowicz, P., Gaczynska, M., Osmulski, P.A., Jankowska, E. (2014) Dissecting a role of a charge and conformation of Tat2 peptide in allosteric regulation of 20S proteasome. J. Peptide Sci. psc.2642. PMID: 24819612

  10. Osmulski, P.A., Mahalingam, D., Gaczynska, M., Liu, J., Huang, S., Horning, A.M., Wang, C-M., Thompson, I.M., Huang, T. H-M., Chen,. C-L. (2014) Nanomechanical biomarkers of single circulating tumor cells for detection of castration resistant prostate cancer. Prostate 74, 1297-1307. PMID: 25065737, PMCID4142568

  11. Rodriguez, K.A., Osmulski, P.A., Pierce, A., Pierce, Weintraub, S.T., Gaczynska, M., Buffenstein, S. (2014) A cytosolic protein factor from the naked mole-rat activates proteasomes of other species and protects these from inhibition. Biochim. Biophys. Acta–MBD 1842/11, 2060-2072. PMID: 25018089

  12. Gaczynska, M. and Osmulski, P.A. (2014) Harnessing proteasome dynamics and allostery in drug design. Antioxidant and Redox Signaling 21/17, 2286-2301. PMID: 24410482, PMCID4241894

  13. Osmulski PA> and Gaczynska M: (2013) Rapamycin allosterically inhibits the proteasome. Mol Pharmacol. 84(1): 104-13.

  14. Edrey YE, Medina DX, Gaczynska M, Osmulski PA, Oddo S, Caccamo A, and Buffenstein R: (2013) Amyloid beta and the longest-lived rodent: the naked mole-rat as a model for natural protection from Alzheimer's disease. Neurobiol Aging. 34(10): 2352-60.

  15. Chen CL, Mahalingam D, Osmulski P, Jadhav RR, Wang CM, Leach RJ, Chang TC, Weitman SD, Kumar AP, Sun L, Gaczynska ME, Thompson IM, and Huang TH: (2013) Single-cell analysis of circulating tumor cells identifies cumulative expression patterns of EMT-related genes in metastatic prostate cancer. Prostate. 73(8): 813-26.

  16. Jankowska E, Stoj J, Karpowicz P, Osmulski PA>, and Gaczynska M: (2013) The proteasome in health and disease. Curr Pharm Des. 19(6): 1010-28.

  17. Rodriguez KA, Edrey YH, Osmulski P, Gaczynska M, and Buffenstein R: (2012) Altered composition of liver proteasome assemblies contributes to enhanced proteasome activity in the exceptionally long-lived naked mole-rat. PLoS One. 7(5): e35890.

  18. Robinson AK, Leal BZ, Chadwell LV, Wang R, Ilangovan U, Kaur Y, Junco SE, Schirf V, Osmulski PA, Gaczynska M, Hinck AP, Demeler B, McEwen DG, and Kim CA: (2012) The growth-suppressive function of the polycomb group protein polyhomeotic is mediated by polymerization of its sterile alpha motif (SAM) domain. J Biol Chem. 287(12): 8702-13.

  19. Gaczynska M and Osmulski PA: (2011) Atomic force microscopy of proteasome assemblies. In: Atomic Force Microscopy in Biomedical Research: Methods and Protocols, Ed. Braga & Ricci., ISBN: 978-1-61779-104-8, Humana Press. DOI: 10.1007/978-1-61779-105-5_9 Series: Methods in Molecular Biology, 736: 117-132.

  20. Rodriguez KA, Gaczynska M, and Osmulski PA: (2010) Molecular mechanisms of proteasome plasticity in aging. Mech Ageing Dev. 131(2): 144-55.

  21. Jankowska E, Gaczynska M, Osmulski P, Sikorska E, Rostankowski R, Madabhushi S, Tokmina-Lukaszewska M, and Kasprzykowski F: (2010) Potential allosteric modulators of the proteasome activity. Biopolymers. 93(5): 481-95.

  22. Osmulski PA, Hochstrasser M, and Gaczynska M: (2009) A tetrahedral transition state at the active sites of the 20S proteasome is coupled to opening of the alpha-ring channel. Structure. 17(8): 1137-47.

  23. Rosenzweig R, Osmulski PA, Gaczynska M, and Glickman MH: (2008) The central unit within the 19S regulatory particle of the proteasome. Nat Struct Mol Biol. 15(6): 573-80.

  24. Gaczynska M and Osmulski PA: (2008) AFM of biological complexes: what can we learn? Curr Opin Colloid Interface Sci. 13(5): 351-67.

  25. Osmulski PA, Tokmina-Lukaszewska M, Endel L, Sosnowska R, Gaczynska M: (2008) Proteasome, Chemistry of. Wiley Encyclopedia of Chemical Biology

  26. Gaczynska M, Rodriguez K, Madabhushi S, and Osmulski PA: (2006) Highbrow proteasome in high-throughput technology. Expert Rev Proteomics. 3(1): 115-27.

  27. Gaczynska M and Osmulski PA: (2005) Characterization of noncompetitive regulators of proteasome activity. In: Ubiquitin and Protein Degradation, Part A Methods Enzymol. 398: 425-38. RJ Deshaies, ed., Elsevier.

  28. Osmulski PA and Gaczynska M: (2005) Atomic force microscopy of the proteasome. In: Ubiquitin and Protein Degradation, Part A Methods Enzymol. 398: 414-25. RJ Deshaies, ed., Elsevier.

  29. Gaczynska M, Osmulski PA, Jiang Y, Lee JK, Bermudez V, and Hurwitz J: (2004) Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA. Proc Natl Acad Sci USA. 101(52): 17952-7.

  30. Yasmin R, Yeung KT, Chung RH, Gaczynska ME, Osmulski PA, and Noy N: (2004) DNA-looping by RXR tetramers permits transcriptional regulation "at a distance." J Mol Biol. 343(2): 327-38.

  31. Gaczynska M, Osmulski PA, Gao Y, Post MJ, and Simons M: (2003) Proline- and arginine-rich peptides constitute a novel class of allosteric inhibitors of proteasome activity. Biochemistry. 42(29): 8663-70. See comment: Drug Discov Today. 8(19): 866-8.

  32. Osmulski PA and Gaczynska M: (2002) Nanoenzymology of the 20S proteasome: proteasomal actions are controlled by the allosteric transition. Biochemistry. 41(22): 7047-53.

  33. Osmulski PA and Gaczynska M: (2000) Atomic force microscopy reveals two conformations of the 20S proteasome from fission yeast. J. Biol Chem. 275(18): 13171-4.

  34. Osmulski PA and Gaczynska M: (1998) A new large proteolytic complex distinct from the proteasome is present in the cytosol of fission yeast. Curr Biol. 8(18): 1023-6.


Complete list of published work.