Lab Members

William Skach, MD Principal Investigator
Brian J. Conti, PhD Post-Doctoral Fellow
Jacob Gubbens, PhD Post-Doctoral Fellow
Devaki A. Kelkar, PhD Post-Doctoral Fellow
Amardeep Khushoo, PhD Post-Doctoral Fellow
Soo Jung Kim, PhD Post-Doctoral Fellow
Prasanna Kumar, PhD Post-Doctoral Fellow
Yoshihiro Matsumura, PhD Post-Doctoral Fellow
LeeAnn Austin Rooney, MS Senior Research Assistant
Zhongying Yang, MS Research Assistant II
Brian J. Conti

Brian J. Conti

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: contib@ohsu.edu

Education

B.S. Biochemistry, Colgate University, 1998

Ph.D. Biochemistry and Biophysics, University of North Carolina at Chapel Hill, 2005

Publications

Daniel CJ, Conti B, Johnson AE, Skach WR. Control of translocation through the Sec61 translocon by nascent polypeptide structure within the ribosome. J Biol Chem. 2008 Jul 25;283(30):20864-73. Epub 2008 May 13.

Bergstralh DT, Conti BJ, Moore CB, Brickey WJ, Taxman DJ, Ting JP. Global functional analysis of nucleophosmin in Taxol response, cancer, chromatin regulation, and ribosomal DNA transcription. Exp Cell Res. 2007 Jan 1;313(1):65-76. Epub 2006 Sep 26.

Clements CM, McNally RS, Conti BJ, Mak TW, Ting JP. DJ-1, a cancer- and Parkinson's disease-associated protein, stabilizes the antioxidant transcriptional master regulator Nrf2. Proc Natl Acad Sci U S A. 2006 Oct 10;103(41):15091-6. Epub 2006 Oct 2.

Taxman DJ, Livingstone LR, Zhang J, Conti BJ, Iocca HA, Williams KL, Lich JD, Ting JP, Reed W. Criteria for effective design, construction, and gene knockdown by shRNA vectors. BMC Biotechnol. 2006 Jan 24;6(1):7.

Conti BJ, Davis BK, Zhang J, O'Connor W Jr, Williams KL, Ting JP. CATERPILLER 16.2 (CLR16.2): A novel NBD/LRR family member that negatively regulates T cell function. J. Biol. Chem. 2005 May 6:280(18):18375–85.

Greer SF, Zika E, Conti B, Zhu XS, Ting JP. Enhancement of CIITA transcriptional function by ubiquitin. Nat. Immunol. 2003 Nov;4(11):1074-82.

Harton JA, O'Connor W Jr, Conti BJ, Linhoff MW, Ting JP. Leucine-rich repeats of the class II transactivator control its rate of nuclear accumulation. Hum. Immunol. 2002 Jul;63(7):588-601.

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Jacob Gubbens

Jacob Gubbens

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: gubbensj@ohsu.edu

Education

M.Sc. Chemistry, Utrecht University, the Netherlands 2003
Including a 5 month project at the University of Durham, UK 2002

Ph. D. Biochemistry of Membranes, Utrecht University, the Netherlands, 2008

Post-doctoral Fellow Biomolecular Mass Spectrometry, Utrecht University, the Netherlands 2008

Publications

Gubbens J, Ruijter E, de Fays LE, Damen JM, de Kruijff B, Slijper M, Rijkers DT, Liskamp RM, de Kroon AI. Photocrosslinking and click chemistry enable the specific detection of proteins interacting with phospholipids at the membrane interface. Chem Biol. 2009 Jan 30;16(1):3-14.

Gubbens J, Slijper M, de Kruijff B, de Kroon AI. Protein complexes in bacterial and yeast mitochondrial membranes differ in their sensitivity towards dissociation by SDS. Biochim Biophys Acta. 2008 Dec;1784(12):2012-8.

Gubbens J, Vader P, Damen JM, O'Flaherty MC, Slijper M, de Kruijff B, de Kroon AI. Probing the membrane interface-interacting proteome using photoactivatable lipid cross-linkers. J Proteome Res. 2007 May;6(5):1951-62.

Boumann HA, Gubbens J, Koorengevel MC, Oh CS, Martin CE, Heck AJ, Patton-Vogt J, Henry SA, de Kruijff B, de Kroon AI. Depletion of phosphatidylcholine in yeast induces shortening and increased saturation of the lipid acyl chains: evidence for regulation of intrinsic membrane curvature in a eukaryote. Mol Biol Cell. 2006 Feb;17(2):1006-17.

Dias-Gunasekara S, Gubbens J, van Lith M, Dunne C, Williams JA, Kataky R, Scoones D, Lapthorn A, Bulleid NJ, Benham AM. Tissue-specific expression and dimerization of the endoplasmic reticulum oxidoreductase Ero1beta. J Biol Chem. 2005 Sep 23;280(38):33066-75.

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Devaki A. Kelkar

Devaki A. Kelkar

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: kelkard@ohsu.edu

Education

B.Sc. Kurukshetra University, Kurukshetra, India, 1997

M.Sc. Zoology (Molecular Biology), University of Pune, India, 1999

Ph.D. Life Sciences, Jawaharlal Nehru University, New Delhi, India, 2005

Postdoctoral Fellow, Centre for Cellular and Molecular Biology, Hyderabad, India, 2005-2006

Publications

Chattopadhyay, A., Rawat, S.S., Greathouse, D.V., Kelkar D.A., Koeppe R.E. (2008) Role of tryptophan residues in gramicidin channel organization and function. Biophys. J. 95:166-175.

Kelkar, D.A., and Chattopadhyay, A. (2007) The gramicidin ion channel: a model membrane protein. Biochim. Biophys. Acta 1768:2011-2025.

Kelkar, D.A., and Chattopadhyay, A. (2007) Modulation of gramicidin conformation and organization by hydrophobic mismatch in saturated phosphatidylcholine bilayers. Biochim. Biophys. Acta 1768:1103-1113.

Kelkar, D.A., and Chattopadhyay, A. (2005) Effect of graded hydration on the organization and dynamics of an ion channel: a fluorescence approach. Biophys. J. 88:1070-1080.

Raghuraman, H., Kelkar, D.A., and Chattopadhyay, A. (2005) Novel insights into protein structure and dynamics utilizing the red edge excitation shift approach. Reviews in Fluorescence 2005. Geddes C.D., and Lakowicz, J.R. Editors. Springer, New York. pp. 199-222.

Kelkar, D.A., and Chattopadhyay, A. (2004) Depth-dependent solvent relaxation in reverse micelles: a fluorescence approach. J. Phys. Chem. B 108:12151-12158.

Rawat, S.S., Kelkar, D.A., and Chattopadhyay, A. (2004) Monitoring gramicidin conformations in membranes: a fluorescence approach. Biophys. J. 87:831-843.

Chattopadhyay, A., Rawat, S.S., Kelkar, D.A., Ray, S., and Chakrabarti, A. (2003) Organization and dynamics of tryptophan residues in erythroid spectrin: novel structural features of denatured spectrin revealed by the wavelength-selective fluorescence approach. Protein Sci. 12:2389-2403.

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Amardeep Khushoo

Amardeep Khushoo

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: khushooa@ohsu.edu

Education

B.S. Biology, Jammu University, India, 1996

M.S. Botany, Pune University, India, 1998

Ph.D. Biotechnology, Jawaharlal Nehru University, India, 2005

Post-Doctoral Fellow: Lung Physiology, Oklahoma State University, Jan 2006 - Sep 2006

Publications

Khasa YP, Khushoo A, Srivastava L, Mukherjee KJ. Kinetic studies of constitutive human granulocyte-macrophage colony stimulating factor (hGM-CSF) expression in continuous culture of Pichia pastoris. Biotechnol Lett. 2007 Dec; 29(12):1903-8.

Pal Y, Khushoo A, Mukherjee KJ. Process optimization of constitutive human granulocyte-macrophage colony-stimulating factor (hGM-CSF) expression in Pichia pastoris fed-batch culture. Appl Microbiol Biotechnol. 2006 Feb; 69(6):650-7.

Khushoo A, Pal Y, Mukherjee KJ. Optimization of extracellular production of recombinant asparaginase in Escherichia coli in shake-flask and bioreactor. Appl Microbiol Biotechnol. 2005 Aug; 68(2):189-97.

Khushoo A, Pal Y, Singh BN, Mukherjee KJ. Extracellular expression and single step purification of recombinant Escherichia coli L-asparaginase II. Protein Expr Purif. 2004 Nov; 38(1):29-36.

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Soo Jung Kim

Soo Jung Kim

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: kimsoo@ohsu.edu

Education

B.Sc. Department of Agricultural Chemistry, Seoul National University, 1992

M.Sc. Biology. Department of Agricultural Chemistry, Seoul National University, 1994

Ph.D. Molecular Cell Biology. Department of Biology, University of Warwick, U.K., 1999

Post-Doctoral Fellow, National Institute of Health, 1999 - 2002

Senior Researcher. Korea Research Institute of Bioscience and Biotechnology, 2003-2009

Publications

Dong Joon Kim, Song Chul Lee, Suk-Jin Yang, Jung Ju Lee, Eun Mi Bae, Dong Min Kim, Sang Hyun Min, Soo Jung Kim, Dong Chul Kang, Byung Chan Sang, Pyung Keun Myung, Kyung Chan Park, and Young Il Yeom. (2008) Lysyl oxidase like 4, a novel target gene of TGF-β1 signaling, can negatively regulate TGF-1-induced cell motility in PLC/PRF/5 hepatoma cells. BBRC 373: 521-527.

Dong Chul Lee, Yun Kyung Kang, Woo Ho Kim, Ye Jin Jang, Dong Joon Kim, In Young Park, Bo Hwa Sohn, Hyun Ahm Sohn, Hee Gu Lee, Jong Seok Lim, Jae Wha Kim, Eun Young Song, Dong Min Kim, Mi-Ni Lee, Goo Taeg Oh, Soo Jung Kim, Kyung Chan Park, Hyang Sook Yoo, Jong Young Choi, and Young Il Yeom. (2008) Functional and clinical evidence for NDRG2 as a novel candidate suppressor of liver cancer metastasis. Cancer Res. 68: 4210-4220.

Kyung Mi Park, Eunju Kang, Yeo-Jin Jeon, Nayoung Kim, Nam-Soon Kim, Hyang-Sook Yoo, Young Il Yeom, and Soo Jung Kim. (2007) Identification of novel regulators of apoptosis using a high-throughput cell-based screen. Mol. Cells 23: 170-174.

Sang-Wook Kang, Neena S. Rane, Soo Jung Kim, Jennifer L. Garrison, Jack Taunton, and Ramanujan S. Hegde. (2006) Substrate-specific translocational attenuation during ER stress defines a pre-emptive quality control pathway. Cell 127: 999-1013.

In Jeong Lee, Zhong Shu Li, Young Nam Lee, Xue-Jun Jin, Jeong-Hyung Lee, Seon-Young Kim, Nam-Soon Kim, Dong Chul Lee, Heun-Sik Lee, Suk-Jin Yang, Soo Jung Kim, and Young Il Yeom. (2006) Hepatocellular carcinoma model cell lines with two distinct migration modes. BBRC 346: 1217-1227. (co-corresponding author)

Kyung Mi Park, Dong Joon Kim, Sang Gi Paik, Soo Jung Kim, and Young Il Yeom. (2006) Novel role of E2F1 in endoplasmic reticulum stress signaling. Mol. Cells 21: 356-359. (co-corresponding author)

Soo Jung Kim, Kyung Mi Park, Nayoung Kim, and Young Il Yeom. (2006) Doxorubicin prevents endoplasmic reticulum stress-induced apoptosis. BBRC 339: 463-468. (co-corresponding author)

Soo Jung Kim and Ramanujan S. Hegde. (2002) Cotranslational partitioning of nascent prion protein into multiple populations at the translocation channel. Mol. Biol. Cell 13: 3775-3786.

Soo Jung Kim, Devarati Mitra, Jeffrey R. Salerno and Ramanujan S. Hegde. (2002) Signal sequences control gating of the protein translocation channel in a substrate-specific manner. Developmental Cell 2: 207-217.

Soo Jung Kim, Reza Rahbar and Ramanujan S. Hegde. (2001) Combinatorial control of prion protein biogenesis by the signal sequence and transmembrane domain. J. Biol. Chem. 276: 26132-26140.

Cheryl A. Woolhead, Alexandra Mant, Soo Jung Kim, Colin Robinson and Alison Rodgers. (2001) Conformation of a purified "spontaneously" inserting thylakoid membrane protein precursors in aqueous solvent and detergent micelles. J. Biol. Chem. 276: 14607-14613.

Stefan Jansson, Jenny Andersson, Soo Jung Kim and Grzegorz Jackowski. (2000) An Arabidopsis thaliana protein homologous to cyanobacterial high-light inducible proteins. Plant Mol. Biol. 42: 345-351.

Lan-Xin Shi, Soo Jung Kim, Alan Marchant, Colin Robinson and Wolfgang P. Schröder. (1999) Characterization of the PsbX protein from photosystem II and light regulation of its gene expression in higher plants. Plant Mol. Biol. 40: 737-744.

Soo Jung Kim, Stefan Jansson, Neil Hoffman, Colin Robinson and Alexandra Mant. (1999) Distinct 'assisted' and 'spontaneous' mechanisms for the insertion of polytopic chlorophyll-binding proteins into the thylakoid membrane. J. Biol. Chem. 274: 4715-4721.

Soo Jung Kim. (1998) Mechanisms of insertion of thylakoid membrane proteins. University of Warwick, Coventry, U.K. Ph.D. thesis.

Simon Thompson, Soo Jung Kim and Colin Robinson. (1998) Sec-independent insertion of thylakoid membrane proteins: analysis of insertion forces and identification of a loop intermediate involving the signal peptide. J. Biol. Chem. 273: 18979-18983.

Soo Jung Kim, Colin Robinson and Alexandra Mant. (1998) Sec/SRP-independent insertion of two thylakoid membrane proteins bearing cleavable signal peptides. FEBS Lett. 424/1-2: 105-108.

Soo Jung Kim, David Robinson and Colin Robinson (1996) An Arabidopsis thaliana cDNA encoding PSII-X, a 4.1 kDa component of photosystem II: a bipartite presequence mediates SecA/pH-independent targeting into thylakoids. FEBS Lett. 390: 175-178.

Soo Jung Kim, Jee Young Lee, Chung Ho Kim and Yang Do Choi (1995) Analysis of the glycinin Gy2 promoter activity in soybean protoplasts and transgenic tobacco plants. Agri. Chem. Biothech. (Korea) 38: 387-392.

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Prasanna Kumar

Prasanna Kumar

Postdoctoral Fellow

PhD

Center for Biotechnology

Jawaharlal Nehru University, New Delhi, India

 

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Yoshihiro Matsumura

Yoshihiro Matsumura

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: matsumuy@ohsu.edu

Education

B.E. Department of Biomolecular Engineering, Faculty of Engineering, Tohoku University, Sendai, Japan, 1998

M.Sci. Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan, 2001

Ph.D. Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan, 2004

Postdoctoral Fellow, Department of Physiology, Akita University of Medicine, Akita, Japan, 2004-2008

Publications

Pitonzo D, Yang Z, Matsumura Y, Johnson AE, Skach WR. Sequence-specific retention and regulated integration of a nascent membrane protein by the ER Sec61 translocon. Mol. Biol. Cell, 2009, 20: 685-698.

Matsumura Y, Ban N, Inagaki N. Aberrant catalytic cycle and impaired lipid transport into intracellular vesicles in ABCA3 mutants associated with nonfatal pediatric interstitial lung disease. Am. J. Physiol. Lung Cell. Mol. Physiol., 2008, 295: L698-L707.

*Yokota T, *Matsumura Y, Ban N, Matsubayashi T, Inagaki N. Heterozygous ABCA3 mutation associate with non fatal evolution of respiratory distress. Eur. J. Pediatr., 2008, 167: 691-693. (*Equally contributed.)

Kodaira Y, Kusumoto T, Takahashi T, Matsumura Y, Miyagi Y, Okamoto K, Shidoji Y, Sagami H. Formation of lipid droplets induced by 2,3-dihydrogeranylgeranoic acid distinct from aeranylgeranoic acid. Acta Biochim. Pol., 2007, 54: 777-782.

Matsumura Y, Kidokoro T, Miyagi Y, Marilingaiah NR, Sagami H. The carboxyl-terminal region of the geranylgeranyl diphosphate synthase is indispensable for the stabilization of the region involved in substrate binding and catalysis. J. Biochem. (Tokyo), 2007, 142: 533-537.

Miyagi Y, Matsumura Y, Sagami H. Human Geranylgeranyl diphosphate synthase is an octamer in solution. J. Biochem. (Tokyo), 2007, 142: 377-381.

Matsumura Y, Sakai H, Sasaki M, Ban N, Inagaki N. ABCA3-mediated choline-phospholipids uptake into intracellular vesicles in A549 cells. FEBS Lett., 2007, 581: 3139-3144.

Sakai H, Tanaka Y, Tanaka M, Ban N, Yamada K, Matsumura Y, Watanabe D, Sasaki M, Kita T, Inagaki N. ABCA2 deficiency results in abnormal sphingolipid metabolism in mouse brain. J. Biol. Chem., 2007, 282: 19692-19699.

Ban N, Matsumura Y, Sakai H, Takanezawa Y, Sasaki M, Arai H, Inagaki N. ABCA3 as a lipid transporter in pulmonary surfactant biogenesis. J. Biol. Chem., 2007, 282: 9628-9634.

Matsumura Y, Ban N, Ueda K, Inagaki N. Characterization and classification of ATP-binding cassette transporter ABCA3 mutants in fatal surfactant deficiency. J. Biol. Chem., 2006, 281: 34503-34514.

Matsumura Y, Kuzuguchi T, Sagami H. Relationship between intron 4b splicing of the rat geranylgeranyl diphosphate synthase gene and the active enzyme expression level. J. Biochem. (Tokyo), 2004, 136: 301-312.

Szabo CM, Matsumura Y, Fukura S, Martin MB, Sanders JM, Sengupta S, Cieslak JA, Loftus TC, Lea CR, Lee HJ, Koohang A, Coates RM, Sagami H, Oldfield E. Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates and diphosphates. J. Med. Chem., 2002, 45: 2185-2196.

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LeeAnn Austin Rooney

LeaAnn Austin Rooney

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: rooneyl@ohsu.edu

Education

B.S. Biochemistry, State University of New York at Stony Brook, 1984

M.S. Chemistry, State University of New York at Stony Brook, 1989
Thesis Advisor: Prof. Steven Rokita, rokita@umd.edu University of Maryland.

Publications

Sobolevsky A.I., Rooney L., Wollmuth L.P. (2002) Staggering of subunits in NMDAR channels, Biophys. J. 83(6), 3304-14.

Brown J.K., Jones C.A., Rooney L.A., Caughey G.H., Hall I.P. (2002) Tryptase’s potent mitogenic effects in human airway smooth muscle cells are via nonproteolytic actions. Am. J. Physiol, Lung Cell Mol. Physiol. 282(2), L197-206.

Brown J.K., Jones C.A., Rooney L.A., Caughey G.H. (2001) Mast cell tryptase activates extracellular-regulated kinases (p44/p42) in airway smooth–muscle cells: importance of proteolytic events, time course, and role in mediating mitogenesis. Am. J. Respir. Cell Mol. Biol., 24(2), 146-54.

Clary D.O., Weskamp G., Austin L.R., Reichardt L.F. (1998) Antibodies that mimic actions of neurotrophins. US Patent Number 5,753,225.

Clary D.O., Weskamp G., Austin L.R., Reichardt L.F. (1994) TrkA cross-linking mimics neuronal responses to nerve growth factor. Molecular Biology of the Cell, 5, 549-563.

El-Maghrabi M.R., Gidh-Jian M., Austin L.R., Pilkis S.J. (1993) Isolation of a human liver fructose-1,6-bisphosphatase cDNA and expression of the protein in E. coli., role of ASP-118 and ASP-121 in catalysis. J. Biol. Chem., 268, 9466-9472.

Austin L.R., Rice S.J., Baldo G.J., Lange A.J., Haspel H.C. and Mathias R.T. (1993) The cDNA sequence encoding the major intrinsic protein of frog lens. Gene, 124, 303-304.

El-Maghrabi M.R., Austin L.R., Correia J.J., Pilkis S.J. (1992) Lysine 274 is essential for fructose 2,6-bisphosphate inhibition of fructose-1,6-bisphosphatase. J. Biol. Chem., 267, 6526-6530.

Pasquale L.R., Mathias R.T., Austin L.R., Brink P.R., Ciunga M. (1990) Electrostatic properties of fiber cell membranes from the frog lens. Biophys. J., 58, 939-945.

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Zhongying Yang

Zhongying Yang

Department of Biochemistry and Molecular Biology
Oregon Health & Science University
3181 SW Sam Jackson Park Road
Portland, Oregon 97239
Phone: 503-494-7315
Fax: 503-494-8393
Email: yangz@ohsu.edu

Education

B.S. Applied Chemmistry, Nanjing University of Technology, China, 1985

M.S. Applied Chemistry, Nanjing University of Techonogy, China, 1989

Publications

Pitonzo, D., Yang, Z., Matsumura, Y., Johnson, A., Skach, W. Sequence-Specific Retention and regulated integration of a nascent membrane protein by the endoplasmic reticulum Sec61 translocon. Mol. Biol. Cell, 20:685-698, 2009.

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