Cell Signalling and Metabolism

Park Group, Lake Simcoe, Ontario, December 2011
Group Site: 
Group Leader: 

Hee-Won Park

Group Info

Research Areas

Dr. Park's laboratory studies the structural aspects of intracellular protein and membrane trafficking pathways. Functional vesicular trafficking is central to normal cellular physiology. Ras-like proteins from rat brains (Rabs) and ADP ribosylation factors (Arfs) are regulators of trafficking of proteins and membranes by acting as docking sites for an assembly of effecter molecules. Mutations in Rabs, Arfs and their associated regulatory proteins or effectors are implicated in causing numerous human diseases.

Rab and Arf GTPases function as molecular switches, cycling between the switched-on state (GTP-bound) and the switched-off state (GDP-bound). The GTPase-activating proteins (GAPs) stimulate GTP-hydrolysis activity and thus keep Rabs and Arfs in the switched-off state, whereas the guanine nucleotide exchange factors (GEFs) exchange GDP for GTP and thus activate Rabs and Arfs to the switched-on state. The Arf and Rab structures and their complexes with GAPs and GEFs are essential for a better understanding of the structural dynamics of intracellular trafficking. Furthermore, these structural analyses will provide unique therapeutic opportunities in developing strategies that target Rab and Arf GTPases and their regulatory proteins.

We are also interested in understanding kinesin molecular motor function. Kinesins play diverse roles in organelle transport, cell division, and cell movement. Kinesins use the chemical energy derived from ATP hydrolysis to generate force for movement along the microtubule. The mechanism by which kinesins capture the energy from ATP hydrolysis and convert it to force is unknown. The structural elements that undergo movement and the force-producing conformational changes of the kinesin motor must be identified in order to elucidate this mechanism. We solve the structures of human kinesins to understand these motor functions. Knowledge of the kinesin structures will allow the rational design of small molecules and the development of specific inhibitors of human kinesin motor family.

Finally, we study structure/function relationships of non-protein kinases that catalyze the phosphorylation of non-protein substrates. Mutations of the non-protein kinases have been implicated in many different human disease. Many human genes encode the non-protein kinases. The sequences between the non-protein kinases share no obvious sequence similarity although the cores of the available structures resemble the nucleotide-binding fold. We perform the structural analysis of each and every non-protein kinases to understand their structure/functional relationships. The resulting structures will provide an explanation for pathogenic mutations that are present in patients with non-protein kinase-defective diseases.

Group Members
Hee-Won Park, Ph.D

Principal Investigator,

also an Associate professor at the Department of Pharmacology and Toxicology, University of Toronto

Bum-Soo Hong, Ph.D

Research Associate, 2010 - present

Postdoc 2005 - 2009

Natallia Strushkevich, Ph.D

Postdoc, Jul.2007 - present,

Postdoc at SGC from 2005

Youngpil Kim, Ph.D

Postdoc, Oct. 2011 - present

Wolfram Tempel, Ph.D.

Crystallographer

Xinyu (Johnny) Guan, M.Sc.

Technician

Scott Hughes, Ph.D candidate

PhD. student, Sep.2011 - present

Negar Nosrati, Ph.D candidate

PhD. student, Sep.2011 - present

Han Youl Lee, M.Sc. student

M.Sc. student, Sep.2009 - present

Buren Li, M.Sc. student

M.Sc. student, Sep.2010 - present,

B.Sc. student, May.2009 - Aug.2010

Katayoun (Kathy) Motaghi, M.Sc. student

M.Sc. student, Sep.2010 - present

Kyung-Phil (Cathy) Kim
Kyung-Phil (Cathy) Kim, undergraduate student

B.Sc. student, Apr.2010 - present

Structures

Lastest structures are now updated http://www.thesgc.com/structures/index.php?terms=park on the SGC main page

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List of solved structures by Dr. Park's group till Jul. 2009

Sorted by release date.


GNBP: ARL8

GNBP: ARL5

GNBP: ARF4

GNBP: ARL10B

NPK: AK3L1

NPK: PKM2

Reductase:GAPDH

NPK: NME3

GNBP: RAB2B

GNBP: RAB14

NPK: PDXK

GNBP: ARL10C

NPK: PAPSS2

GAP: UPLC1

GNBP: ARF5

GNBP: RAB30

GNBP: RAB27B

GNBP: RAB31

GNBP: RAB1A

NPK: RBKS

Kinesin: KIF1C

GNBP: RAB26

GNBP: SARA1

NPK: CKMT2

GNBP: RAB3D

Kinesin: KIF2

GNBP: ARL10B

GNBP: ARL5

GNBP: ARL5

Kinesin: KIFC3

GNBP: RAB5B

Kinesin: KIF2C

GNBP: ARL6

NPK: KHK

GNBP: RAB43

NPK: PANK3

NPK: CHKA

NPK: CHKB

GNBP:LOC201475

GAP: LOC64744

Kinesin: KIF9

NPK: HK2

GNBP: RAB4B

NPK: PANK2

NPK: PANK3

GNBP: RAB9B

GNBP: RAB25

CYP: CYP2R1

GAP: HRB

GAP: CHN1

GAP: ZNF289

GNBP: RASEF

NPK: C9orf95

GNBP: RASEF

GNBP: KRASB

GNBP: RRAGD

GAP: C22orf4

GNBP: NEDD5

GAP: TBC1D14

NPK: C9orf95

NPK: C9orf95

NPK: C9orf95

NPK: C9orf95

GAP: PLXNB1

Kinesin: KIFC1

Kinesin: KIF3B

Kinesin: KIF3C

Complex:PLXNB1+RND1

Kinesin: KIF22

ElongationFactor:EIF4A2

ElongationFactor:EIF3J

GNBP: RASL12

GNBP: GRLF1

CYP: CYP2R1

GNBP: REM2

GNBP: NRAS

ElongationFactor:EIF5A1

GAP: Full length CHN1

GAP: ARFGAP1

GNBP: Rab3B

GAP: TBC1D22B
Publications

Search Pubmed for publications of Dr. Park.

Reference List:

Strushkevich N, Usanov SA, Plotnikov AN, Jones G, Park HW: Structural analysis of CYP2R1 in complex with vitamin D3. J.Mol.Biol. 2008, 380:95-106.

Senisterra GA, Soo HB, Park HW, Vedadi M: Application of high-throughput isothermal denaturation to assess protein stability and screen for ligands. J.Biomol.Screen. 2008, 13:337-342.

Tempel W, Tong Y, Dimov S, Bochkarev A, Park H: First crystallographic models of human TBC domains in the context of a family-wide structural analysis. Proteins 2008, 71:497-502.

Park HW: Structure determination of the motor domain of yeast kinesin kar3 by x-ray crystallography. Methods Mol.Biol. 2007, 392:199-211.

Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M: Binding of Rac1, Rnd1, and RhoD to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J.Biol.Chem. 2007, 282:37215-37224.

Tempel W, Rabeh WM, Bogan KL, Belenky P, Wojcik M, Seidle HF, Nedyalkova L, Yang T, Sauve AA, Park HW, Brenner C: Nicotinamide riboside kinase structures reveal new pathways to NAD+. PLoS.Biol. 2007, 5:e263.

Hong BS, Senisterra G, Rabeh WM, Vedadi M, Leonardi R, Zhang YM, Rock CO, Jackowski S, Park HW: Crystal structures of human pantothenate kinases. Insights into allosteric regulation and mutations linked to a neurodegeneration disorder. J.Biol.Chem. 2007, 282:27984-27993.

Shanmuganatham KK, Ravichandran M, Howe MM, Park HW: Crystallization and preliminary X-ray analysis of phage Mu activator protein C in a complex with promoter DNA. Acta Crystallogr.Sect.F.Struct.Biol.Cryst.Commun. 2007, 63:620-623.

Hong BS, Yun MK, Zhang YM, Chohnan S, Rock CO, White SW, Jackowski S, Park HW, Leonardi R: Prokaryotic type II and type III pantothenate kinases: The same monomer fold creates dimers with distinct catalytic properties. Structure. 2006, 14: 1251-1261.

Virga KG, Zhang YM, Leonardi R, Ivey RA, Hevener K, Park HW, Jackowski S, Rock CO, Lee RE: Structure-activity relationships and enzyme inhibition of pantothenamide-type pantothenate kinase inhibitors. Bioorg.Med.Chem. 2006, 14:1007-1020.

Chu HM, Yun M, Anderson DE, Sage H, Park HW, Endow SA: Kar3 interaction with Cik1 alters motor structure and function. EMBO J. 2005, 24:3214-3223.

Ismail SA, Park HW: Structural analysis of human liver glyceraldehyde-3-phosphate dehydrogenase. Acta Crystallogr.D.Biol.Crystallogr. 2005, 61:1508-1513.

Aziz RK, Ismail SA, Park HW, Kotb M: Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenes. Mol.Microbiol. 2004, 54:184-197.

Brown VM, Krynetski EY, Krynetskaia NF, Grieger D, Mukatira ST, Murti KG, Slaughter CA, Park HW, Evans WE: A novel CRM1-mediated nuclear export signal governs nuclear accumulation of glyceraldehyde-3-phosphate dehydrogenase following genotoxic stress. J.Biol.Chem. 2004, 279:5984-5992.

Higuchi H, Bronner CE, Park HW, Endow SA: Rapid double 8-nm steps by a kinesin mutant. EMBO J. 2004, 23:2993-2999.

Ivey RA, Zhang YM, Virga KG, Hevener K, Lee RE, Rock CO, Jackowski S, Park HW: The structure of the pantothenate kinase.ADP.pantothenate ternary complex reveals the relationship between the binding sites for substrate, allosteric regulator, and antimetabolites. J.Biol.Chem. 2004, 279:35622-35629.

Kumaraswami M, Howe MM, Park HW: Crystal structure of the Mor protein of bacteriophage Mu, a member of the Mor/C family of transcription activators. J.Biol.Chem. 2004, 279:16581-16590.

Rock CO, Park HW, Jackowski S: Role of feedback regulation of pantothenate kinase (CoaA) in control of coenzyme A levels in Escherichia coli. J.Bacteriol. 2003, 185:3410-3415.

Yun M, Bronner CE, Park CG, Cha SS, Park HW, Endow SA: Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd. EMBO J. 2003, 22:5382-5389.

Yun M, Keshvara L, Park CG, Zhang YM, Dickerson JB, Zheng J, Rock CO, Curran T, Park HW: Crystal structures of the Dab homology domains of mouse disabled 1 and 2. J.Biol.Chem. 2003, 278:36572-36581.

Kwak BY, Zhang YM, Yun M, Heath RJ, Rock CO, Jackowski S, Park HW: Structure and mechanism of CTP:phosphocholine cytidylyltransferase (LicC) from Streptococcus pneumoniae. J.Biol.Chem. 2002, 277:4343-4350.

Rock CO, Heath RJ, Park HW, Jackowski S: The licC gene of Streptococcus pneumoniae encodes a CTP:phosphocholine cytidylyltransferase. J.Bacteriol. 2001, 183:4927-4931.

Yun M, Zhang X, Park CG, Park HW, Endow SA: A structural pathway for activation of the kinesin motor ATPase. EMBO J. 2001, 20:2611-2618.

Rodriguez AC, Park HW, Mao C, Beese LS: Crystal structure of a pol alpha family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N-7. J.Mol.Biol. 2000, 299:447-462.

Yun M, Park CG, Kim JY, Rock CO, Jackowski S, Park HW: Structural basis for the feedback regulation of Escherichia coli pantothenate kinase by coenzyme A. J.Biol.Chem. 2000, 275:28093-28099.

Yun M, Park CG, Kim JY, Park HW: Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes. Biochemistry 2000, 39:10702-10710.

Park HW, Beese LS: Protein farnesyltransferase. Curr.Opin.Struct.Biol. 1997, 7: 873-880.

Park HW, Boduluri SR, Moomaw JF, Casey PJ, Beese LS: Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution. Science 1997, 275:1800-1804.

Park HW, Kim ST, Sancar A, Deisenhofer J: Crystal structure of DNA photolyase from Escherichia coli. Science 1995, 268:1866-1872.

Park HW, Sancar A, Deisenhofer J: Crystallization and preliminary crystallographic analysis of Escherichia coli DNA photolyase. J.Mol.Biol. 1993, 231:1122-1125.

Contact

Hee-Won Park, Ph.D.

Principal Investigator, Structural Genomics Consortium

Associate Professor, Department of Pharmacology, University of Toronto

E-mail: heewon [dot] park[at]utoronto [dot] ca

Tel: 416-946-3867

Fax: 416-946-0588

Alumni

Technicians

Limin shen
Technician, from 2005 - Oct. 2011
Lyudmila (Lucy) Nedyalkova Technician, from 2005 - Jun.2011
Slav Dimov Technician, from 2005 - Jun.2011
Yang Shen Technician, from 2005-2010.06

Postdoctoral

Yufeng Tong Postdoc, Aug. 2006 - Jun. 2011
Nan Zhong Postdoc, May.2009 - Jun. 2011
Hui Wang Postdoc, Nov.2008 - Dec.2011
Deepthi Sukumar Postdoc, 2005 - Mar.2009

Current position: Senior Fellow at York University, Department of Kinesiology and Health Sciences

Haizhong Zhu Postdoc, Aug.2006 - Apr.2008
Wael Rabeh Postdoc, 2005-2007
Anelia Atanassova Postdoc, 2005-2006
Shehab Ismail Postdoc, 2005-2006
Jihong Wang Postdoc, 2005-2006

Graduate Students

Peter Khoury 2008 - 2009

Co-op Students

Trang Vu Co-op student 2006 spring - summer
Jagdeep Singh Jassi Co-op student 2007 spring - summer
Chinar Co-op student 2007 summer
Bo Gong, aka. Sarah Co-op student 2007 fall - 2008 summer
Sandy Hong Co-op student 2008.08 - 2008.12
Joyce Lau Co-op student from 2009.01-2009.04

Undergraduate Students

Sarah Kwan Undergraduate student 2009 spring
Catherine Ng Undergraduate student 2009 summer

Volunteers

Xing Sun Volunteer 2008 spring
Nayan Kruti Volunteer 2008 spring