Jonathan Coleman
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Phone (412) 648-8077
Fax (412) 648-9008

University of Pittsburgh
1050 Biomedical Science Tower 3

 

Jonathan Coleman

 
The aim of my research is to elucidate the molecular function, architecture, and high-affinity drug binding sites of synaptic vesicle transporters in neurons by studying their function using biochemical techniques and determining their structures using single particle cryo-EM. I am particularly interested in understanding the conformational changes and mechanism associated with transport. I have developed methods for large-scale expression, stabilization by drugs, and for the production of antibodies which recognize these transporters. The use of transporter-antibody complexes is essential in order to provide mass and molecular features to assist in cryo-EM reconstructions because these transporters are small membrane proteins which are largely ensconced within membrane. Atomic structures of transporters in complex with therapeutic drugs are essential for the design of better small-molecule therapeutics with higher specificity and fewer side-effects and will also advance efforts toward understanding the function of these transporters.  

Visit Jonathan's lab website (coming soon)


Education & Training

Undergraduate

University of British Columbia
Hon. B.Sc. Biochemistry, 2002-2007

Postgraduate

Aarhus University, Department of Physiology
Visiting student in lab of Dr. Jens Peter Anderson, 2010

University of British Columbia, Department of Biochemistry and Molecular Biology
Ph.D. in lab of Dr. Robert Molday, 2007-2013

Oregon Health & Science University, Vollum Institute
Postdoctoral training in lab of Dr. Eric Gouaux, 2013-2020


Selected Awards and Honors


2018 OHSU School of Medicine Paper of the Month
2016 Finalist for OHSU Postdoctoral Paper of the Year
2014-2016 Banting Postdoctoral Fellowship


Representative Publications


Coleman, J.A.*, Navratna, V.*, Antermite D., Yang, D, Bull, J.A., Gouaux, E. (2020). Chemical and structural investigation of the paroxetine-human serotonin transporter complex. eLife, 9:e56427

 

Coleman, J.A.*, Yang, D.*, Zhao, Z., Wen, P., Yoshioka, C., Tajkhorshid, E., Gouaux, E. (2019). Serotonin transporter–ibogaine complexes illuminate mechanisms of inhibition and transport. Nature 569, 141-145.

 

Coleman, J. A., Gouaux, E. (2018). Structural basis for recognition of diverse antidepressants by the human serotonin transporter. Nat. Struct. Mol. Biol. 25, 170-175.

 

Coleman, J. A., Green, E. M., Gouaux, E. (2016). Thermostabilization, Expression, Purification, and Crystallization of the Human Serotonin Transporter Bound to S-citalopram. J. Vis. Exp., e54792, doi:10.3791/54792.

 

Coleman J.A., Green E.M., Gouaux E. (2016). X-ray structures and mechanism of the human serotonin transporter. Nature 532 (7599), 334-339.

 

Green E.M., Coleman J.A., Gouaux E. (2015). Thermostabilization of the human serotonin transporter in an antidepressant-bound conformation. PloS One 10 (12), e0145688.

 

Vestergaard A.L., Coleman J.A., Lemmin T., Mikkelsen S.A., Molday L.L., Vilsen B., Molday R.S., Dal Peraro M., Peter Andersen J. (2014). Critical roles of isoleucine-364 and adjacent residues in a hydrophobic gate control of phospholipid transport by the mammalian P4-ATPase ATP8A2. Pro. Natl. Acad. Sci. 111 (14), E1334-E1343.

 

Coleman J.A.*, Zhu X.*, Djajadi H.R., Molday L.L, Smith R.S., Libby R.T., John S.W.M., Molday R.S. (2014). Phospholipid flippase ATP8A2 is required for normal visual and auditory function and photoreceptor and spiral ganglion cell survival. J. Cell. Sci. 127 (5), 1138-1149.

 

Coleman J.A., Quazi F., Molday R.S. (2013). Mammalian P(4)-ATPases and ABC transporters and their role in phospholipid transport. Biochim. Biophys. Acta. 1831, 555-74.

 

Coleman J.A., Vestergaard A.L., Molday R.S., Vilsen B., Peter Andersen J. (2012). Critical role of a transmembrane lysine in aminophospholipid transport by mammalian photoreceptor P4-ATPase ATP8A2. Proc. Natl. Acad. Sci. 109, 1449-54.

 

Coleman J.A., Molday RS. (2011). Critical role of the beta-subunit CDC50A in the stable expression, assembly, subcellular localization, and lipid transport activity of the P4-ATPase ATP8A2. J. Biol. Chem. 286, 17205-16.

 

Coleman J.A., Kwok M.C., Molday R.S. (2009). Localization, purification, and functional reconstitution of the P4-ATPase Atp8a2, a phosphatidylserine flippase in photoreceptor disc membranes. J. Biol. Chem. 284, 32670-9. 

  

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(*equal contribution)


 


 



Rieko Ishima
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Phone (412) 648-9056
Fax (412) 648-9008

University of Pittsburgh
1037 Biomedical Science Tower 3

 

Rieko Ishima

Associate Professor


The major objective of our research has been to determine protein structure and dynamics using nuclear magnetic resonance (NMR); spectroscopy, in order to elucidate protein function particularly relating to protein-ligand interactions.



Visit Ishima lab website


Education & Training

Graduate

Kyoto University, Kyoto, Japan
Ph.D., 1992 in Chemistry, Supervisor:  Dr. Kazuyuki Akasaka

Postgraduate

Ontario Cancer Institute
Postdoctoral Fellow 1995 – 1997


Representative Publications


Webb, C., Upadhyay, A., Giuntini, F., Eggleston, I., Furutani-Seiki, M., Ishima, R. & Bagby, S. (2011) Structural features and ligand binding properties of tandem WW domains from YAP and TAZ, nuclear effectors of the Hippo pathway. Biochemistry, 50, 3300-9.

Myint, W., Cai, Y., Schiffer, C., Ishima, R. (2012) Quantitative comparison of errors in 15N transverse relaxation rates measured using various CPMG phasing schemes. J Biomol NMR, 53, 13-23.

Cai, Y., Yilmaz, N.K., Myint, W., Ishima, R., Schiffer, C. (2012) Differential Flap Dynamics in Wild-type and a Drug Resistant Variant of HIV-1 Protease Revealed by Molecular Dynamics and NMR Relaxation. J Chem Theory Comput. 8, 3452-62.

Liriano,  M.A., Varney, K.M., Wright, N.T., Hoffman, C.L.,  Toth, E.A., Ishima, R., and Weber, D.J. (2012) Target binding to S100B reduces dynamic properties and increases

Christen, M.T., Menon, L., Myshakina, N.A., Ahn, J., Parniak, M.A. & Ishima, R. (2012) Structural Basis of the Allosteric Inhibitor Interaction on the HIV-1 Reverse Transcriptase RNase H domain. Chemical Biology & Drug Design, 80, 706-16.



Active Grants


Conformational dynamics and inhibitor responses of HIV-1 RT RNase H in solution
10/01/13 – 08/31/17
National Institutes of Health
R01

Pittsburgh Center for HIV Protein Interactions (PCHPI)
09/30/12 – 07/31/17
National Institutes of Health
P50

 

 

 



Jinwoo Ahn
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Phone (412) 383-6933
Fax (412) 648-9008

University of Pittsburgh
1055 Biomedical Science Tower 3

 

JInwoo Ahn

Associate Professor


Protein-protein and protein-ligand interactions are major events in many critical biological pathways. My research focuses on investigating the molecular and structural basis of these interactions. To that end, I utilize molecular biology and protein biochemistry approaches to obtain functionally active recombinant proteins. With those, we reconstitute and monitor biological events in vitro to directly correlate protein structure-function with biological outcome.  We utilize various bioanalytical and biophysical methodology including, but not limited to, CD, fluorescence, SEC-MALS, ITC, SPR, SWAX and HPLC as well as conventional biochemistry. We are currently studying HIV virulence factor-host protein interactions, Cullin-based E3 ubiquitin ligase assembly, regulation of tumor suppressor p53 and its homologs functions by repressors and activators.


Visit Jinwoo's lab website


Education & Training

Undergraduate
Yonsei University, Seoul, Korea
B.S. 1991 in Chemistry

Graduate
The Ohio State University
Ph.D., 1997 in Chemistry

Postgraduate
Columbia University, New York
Postdoctoral Associate 1997 – 2003


Representative Publications


Zhou, X., Delucia, M., Hao, C., Hrecka, K., Monnie, C., Skowronski, J., Ahn, J. HIV-1 Vpr protein directly loads Helicase-like transcription factor (HLTF) onto the CRL4-DCAF1 E3 ubiquitin ligase. J. Biol. Chem. 292, 21117-21127 (2017)

Jang, S., Zhou, X., Ahn, J. Substrate specificity of SAMHD1 triphosphohydrolase activity is controlled by deoxyribonucleoside triphosphates and phosphorylation at Thr592. Biochemistry 55, 5635-5646 (2016)

Zhou, X., DeLucia, M., Ahn, J. SLX4/SLX1 independent downregulation of MUS81/EME1 by HIV-1 Vpr. J. Biol. Chem. 291, 16936-16947 (2016)

Wu, Y, Koharudin, L., Mehrens, J., DeLucia, M., Byeon, C.-H., Byeon, I.J., Calero, G., Ahn, J., and Gronenborn, A. M., Structural basis of clade-specific engagement of SAMHD1 restriction factors by lentiviral Vpx virulence factors.. J. Biol. Chem. 290, 17935-45 (2105)



Active Grants


University of Pittsburgh Center for HIV Protein Interactions (PCHPI), Core director and Project Leader
8/1/17 – 7/31/22
NIH P50GM082251

Structure and function relationships regulating SAMHD1’s dual enzymatic activities, Principal Investigator
7/1/15 – 6/30/20
NIH R01GM116642

The molecular basis of cardiolipin-protein interactions implicated in intrinsic apoptosis, Co-Investigator
9/1/16 – 8/31/20
NIH R01GM113908

Imaging of single HIV-1 uncoating and transport to the nucleus, Co-Investigator
3/24/17 – 2/28/22
NIH R01AI129862

 

 



James Conway
This email address is being protected from spambots. You need JavaScript enabled to view it. 
Phone (412) 383-9847
Fax (412) 648-8998

University of Pittsburgh
2047 Biomedical Science Tower 3

 

James Conway


Associate Professor
Department of Structural Biology



Study the structure and function of macromolecular complexes, such as virus capsids, using cryo-electron microscopy and combining this with subunit atomic models to extend interpretation into details of the protein folds and interfaces. Particular systems being studied include herpesviruses and dsDNA bacteriophages such as HK97, SPO1, T5 and others, These tailed phages have important structural similarities with each other and also with animal viruses such as herpesvirus, suggesting that there may be a long evolutionary connection between them. The dynamic aspects of the virus lifecycle – assembly, DNA packaging, infection and DNA delivery – are often better suited to cryoEM study than crystallography. Although current resolutions achieved for icosahedral capsids are between 10-20Å, this is steadily improving as new procedures are developed, such as automated data collection and high-speed data analysis. Lower symmetry structures, such as entire virus or phage particles, requires more data and achieve lower resolution but also benefit from these advances. Ultimately, we aim to characterize the structural and functional repertoire of a virus throughout its lifecycle, which will have benefits in understanding protein-protein and protein-DNA interactions as well as the evolution of protein structure, and in developing new targets for interfering with viral infection and replication, and technological application of the knowledge.

Visit Conway's lab website


Education & Training

Undergraduate
Massey University, Palmerstrom, North New Zealand
B.S. 1985 in Physics

Graduate
Massey University, Palmerston North New Zealand
Ph.D. 1989 in Biophysics

Postgraduate
National Institues of Health
Bethesda, MD 1990 - 1996



Awards & Honors


1986    Fibrous Proteins Merit Award, Massey University 
1997    Special Achievement Award, NIAMS/NIH, In recognition and appreciation of special achievement
1998    Group Merit Award, NIAMS/NIH, In recognition of pioneering contributions to image processing, advancing the resolution attainable in biological electron microscopy



Representative Publications


Lee H, Brendle SA, Bywaters SM, Guan J, Ashley RE, Yoder JD, Makhov AM, Conway JF, Christensen ND & Hafenstein S. A CryoEM study identifies the complete H16.V5 epitope and reveals global conformational changes initiated by binding of the neutralizing antibody fragment. J Virol 89, 1428-1438, 2015

Shingler KL, Cifuente JO, Ashley RE, Makhov AM, Conway JF & Hafenstein S. The enterovirus 71 procapsid binds neutralizing antibodies and rescues virus infection in vitro. J Virol 89, 1900-1908, 2015.

Sattar S, Bennett NJ, Wen WX, Guthrie JM, Blackwell LF, Conway JF & Rakonjac J. Ff-nano, short functionalized nanorods derived from Ff (f1, fd or M13) filamentous bacteriophage. Frontiers in Microbiology (Virology) 6, 316, 2015.

Guan J, Bywaters SM, Brendle SA, Lee H, Ashley RE, Makhov AM, Conway JF, Christensen ND & Hafenstein S. Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization. Virology 483, 253-263, 2015.

Tandon R, Mocarski ES and Conway JF. The A, B, Cs of herpesvirus capsids. Viruses 7, 899-914. 2015.


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Active Grants


Direct Electron Detecting (DED) Camer
04/01/15 – 03/31/16
National Institutes of Health
S10

Structure and Function of the Herpesvirus Capsid
08/15/11 – 07/31/20
National Institutes of Health
R01

Structural Determinants of Amelogenin Function in Regulating Enamel Formation
09/01/12 – 08/31/17
National Institutes of Health
R01

Inborn Errors of Long Chain Fat Metabolism
07/01/07 – 03/31/16
National Institutes of Health
R01

Roles of Cytomegalovirus Proteins pp150 and pUL96 in Virus Maturation
11/01/14 – 10/31/19
National Institutes of Health
R01