Center of Biomedical Research Excellence (COBRE) in Protein Struc- Ture and Function Is Hosted in the Department of Medicinal Chemistry at the University of Kansas

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Participating Institutions The Center of Biomedical Research Excellence (COBRE) in Protein Struc- ture and Function is hosted in the Department of Medicinal Chemistry at The University of Kansas. The KU Higuchi Biosciences Center provides the Center with its administrative support. Other participating institutions are Kansas State University, Wichita State University and The University of Kansas Medical Center. Center of Biomedical Research Excellence (COBRE) in Protein Structure and Function

Wichita State University The University of Kansas Wichita, Kansas Medical Center Kansas City, Kansas For more information contact: COBRE in Protein Structure and Function Robert P. Hanzlik, Program Director The University of Kansas, Department of Medicinal Chemistry 1251 Wescoe Hall Drive, 4070 Malott Lawrence, Kansas 66045 Office: (785) 864-3750; Fax: (785) 864-5326 This project is supported by grants from the National Center for Research Resources (5P20RR017708-10) and the [email protected] National Institute of General Medical Sciences http://psf.cobre.ku.edu (8 P20 GM103420-10) from the National Institutes of Health. The Center of Biomedical Research Excellence in Protein Structure Biomolecular NMR Laboratory and Function (COBRE-PSF) at The University of Kansas conducts health- Director: Asokan Anbanandam, Ph.D. related basic research in protein structure and function. The Center was estab- Office: Del Shankel Structural Biology Center, lished in 2002, and has been supported by grants from the National Center for Room 1011 Research Resources (5P20RR017708-10) and the National Institute of General Telephone: 785-864-3746; Fax: 785-864-8141 Medical Sciences (8 P20 GM103420-10) from the Email: [email protected] National Institutes of Health.

The objectives of the COBRE program are 1) to The Biomolecular NMR Laboratory maintains two high field NMR spec- strengthen an institution’s biomedical research infra- trometers in support of structural and dynamics studies of biomolecules. Its structure through establishment of a thematic multi- capabilities include determining high resolution structures, biological macro- disciplinary center, and 2) to enhance the ability of molecules, elucidation and structural mapping of protein-protein, protein- investigators to compete independently for comple- nucleic acid, protein-peptide, protein-drug interactions, and studies of the dy- mentary NIH individual research grants or other ex- namics of proteins and their complexes in solution. ternal peer-reviewed support. To meet these goals, COBRE-PSF provides research support and men- Laboratory staff provide consultation, training, assistance and service to toring to accelerate the career development of out- investigators. The staff is also responsible for implementation of new NMR standing junior faculty researchers. The Center Robert P. Hanzlik, Ph.D. pulse sequences, and assisting local and remote users with technical problems. now supports eight research investigators from six Program Director and Laboratory Capabilities and Services departments at four Kansas universities: The Univer- Professor, KU Dept. of ■ From 1D to 4D NMR data acquisition sity of Kansas, Kansas State University, Wichita State Medicinal Chemistry ■ nD-NMR data processing, analysis, and interpretation University, and The University of Kansas Medical ■ High resolution structure determination in solution Center. New investigators are added as others become independently funded. 15 15 15 ■ N-T1, N-T2, N-{1H}-NOE-NMR experiments (pico to nano Since its inception, COBRE-PSF has supported 37 junior faculty investigators second motions) by providing research support and a professional development program with ■ Micro to millisecond motion dy- mentoring by accomplished senior faculty researchers. namics studies by relaxation disper- Our investigators address significant problems in sion NMR protein structure and function from biological and ■ NMR titration measurements chemical perspectives in an integrated, multi- ■ Protein-protein, protein-DNA, pro- disciplinary way. An important feature of this plan is tein-ligand interaction studies

that biologically-oriented scientists work with chemi- The laboratory has two NMR spec- cally-oriented scientists, and vice versa, resulting in trometers capable of performing any significant cross-disciplinary broadening of junior advanced bio-NMR experiments: faculty early in their careers. ■ Bruker Avance 800 MHz with TCI The Center also supports three professionally- cryoprobe ■ Bruker Avance III 600 MHz with staffed Core Laboratories that are available to re- Anbanandam loading sample into the Mary L. Michaelis, Ph.D. gional researchers. These laboratories are dedicated TXI-RT probe Bruker Avance III 600 MHz. Associate Director and to protein purification, protein X-ray crystallography, Professor, KU Dept. of and biomolecular NMR spectroscopy. They comple- Pharmacology and Cover: The structures featured on the brochure cover were determined in the KU Protein Struc- Toxicology ment other core laboratories at KU and other Kansas ture Laboratory. They depict the Luciferase/PTC-124 Complex and bacterioferritin B complex Board of Regents universities. containing 24 monomers and 96 iron atoms. Protein Structure Laboratory COBRE Investigators Director: Scott Lovell, Ph.D. Faculty selected to become COBRE investigators are early in their careers Del Shankel Structural Biology Center, Room 1015 and are establishing research programs with significant emphasis on protein Lawrence, KS 66047 structure and function. Investigators receive research support and mentoring Tel: (785) 864-3772, Fax: (785) 864-8141 by a senior faculty advisor. They are expected to set specific goals for devel- Email: [email protected] oping and submitting proposals for independent external research support.

Moriah Beck (2011-present) The mission of the Protein Structure Laboratory (PSL) is to provide investi- Assistant Professor, Chemistry, Wichita State University gators with state-of-the-art instrumentation, facilities, and expertise for protein Palladin and Regulation of Actin Dynamics crystallization, X-ray data collection, data analysis, and structure solution and refinement from an à la carte menu.

Laboratory staff provide advice and consultation, training, access to facilities for experienced crystallographers, and a range of services from crystal John Karanicolas (2011-present) growth to full structure solution and refinement. The PSL staff will perform or Assistant Professor, Molecular Biosciences assist investigators with any of these functions: University of Kansas Structure-based Chemical Rescue of Enzyme Activity In-house and Synchrotron X-ray Data Collection ■ Screen crystals for diffraction and collect data for structure solution ■ Rigaku rotating anode generator, R-axis IV++ image plate detector and X-stream 2000 cryostream Alexander Moise (2011-present) ■ Collaboration with Advanced Photon Source (APS) IMCA-CAT, Assistant Professor, Pharmacology and Toxicology Sector 17 for synchrotron data collection University of Kansas ■ Ship samples, data collected and returned; processed data provided via ftp site Structure-function Studies of Adipose Phospholipase ■ Model building and refinement of structures deduced from diffraction data ■ Phase determination (experimentally or through molecular replacement) Jeroen Roelofs (2010-present) High Throughput Crystallization Screening Assistant Professor, Biology ■ High throughput crystallography with protein-ligand complexes Kansas State University ■ 96-well screen setup in five to 10 minutes, using 50mL of concentrated Mechanism of Chaperone-assisted Assembly of Proteasome protein per 96-well screen Regulatory Particle ■ Greater number of screens setup with less sample

Structure Solution and Refinement ■ Molecular replacement, MIR and SAD/MAD phasing methods Emeritus Investigators

■ Structure refinement and model building James Bann (2008-2011) Associate Professor, Chemistry, Wichita State University Structural Characterization of the Anthrax Toxin Protective An- tigen

Emeritus Investigators, Cont. Protein Production Group Director: Fei Philip Gao, Ph.D. Brian Blagg (2002-2005) Research Associate: Na Zhang, Ph.D. Professor, Medicinal Chemistry, University of Kansas Del Shankel Structural Biology Center, Room 1095 Identification of Hsp90 Cochaperones, Immunophilins, and Lawrence, KS 66047 Client Proteins Tel: (785) 864-1825; Fax: (785) 864-8141

Email: [email protected]; [email protected]

Roberto De Guzman (2005-2008) The COBRE Protein Production Group (PPG) focuses on the cloning, ex- Associate Professor, Molecular Biosciences, University of Kansas pression and purification of prokaryotic and eukaryotic proteins. The labora- Structure and Dynamics of Bacterial Needle Proteins tory maintains a variety of equipment to support the production of properly folded proteins in quantities suitable for structural studies (X-ray and NMR), functional studies (catalytic or biological), label-free binding studies (SPR) Heather Desaire (2002-2005) and/or high throughput (HTP) screening studies. The PPG employs both E. Associate Professor, Chemistry, University of Kansas coli and insect cell expression systems. It is equally at home with routine pro- Structural Characterization of Glycoproteins using Mass cedures of any complexity, with scouting and method optimization. The PPG Spectrometry also provides advice and consultation, training, access to equipment, and cus- tom services in many aspects of protein production, starting with cloning. The laboratory offers the following services: Susan Egan (2002-2005) Professor, Molecular Biosciences, University of Kansas Activities in the Protein Production Laboratory Protein-Protein Interactions Required for Transcription ■ Construct design ■ Protein characterization and analysis Activation by RhaR ■ Isotope-labeled proteins ■ Cloning, expression & solubility testing ■ Scale-up purification ■ Protein expression in insect cells ■ Label-free binding studies ■ Large scale protein expression in E. coli Christopher Fischer (2008-2011) ■ Protein refolding and reconstitution

Associate Professor, Astronomy and Physics High Throughput Cloning University of Kansas ■ Ligation independent cloning used to clone genes into a pET vector without Remodeler Translocation Along DNA restriction enzyme digestion and ligation

■ Targeted gene can be cloned in ~one day with low background ■ Protein can be purified using one-step affinity chromatography P. Scott Hefty (2008-2010) Assistant Professor, Molecular Biosciences, University of Kansas Expression of Challenging Proteins Mechanism and Role of a Novel Chlamydial Transcriptional Various fusion proteins are used to increase the expression level, solubility Regulator, CHXR and/or stability of the protein, or to drive the protein into inclusion bodies. The same PCR product can be inserted into all the fusion vectors. All tags and fusion proteins are cleavable. Todd Holyoak (2008-2012) Major Equipment Associate Professor, Biochemistry and Molecular Biology, ■ ÅKTAxpress, ÅKTA purifier and FPLC systems University of Kansas Medical Center (associate professor, ■ Biacore 3000 ■ Shaker incubators and fermentors biology, University of Waterloo, Waterloo, Canada) ■ High capacity centrifuges ■ Hydraulic cell disruptors, thermocyclers The Role of Dynamics in PEPCK Mediated Catalysis Emeritus Pilot Project Directors, cont. Emeritus Investigators, cont.

Emily Scott (2010-2012) Audrey Lamb (2004-2007) Associate Professor, Medicinal Chemistry, University of Kansas Associate Professor, Molecular Biosciences, University of Kansas Structure and Function of CYP17A1, a Critical Enzyme in Structural Biology of Pyoverdin Biosynthesis Human Androgen Biosynthesis

Irina Smirnova (2005-2007) Assistant Professor, Physical Therapy/Rehabilitation Sciences, Jennifer Laurence (2005-2007) University of Kansas Medical Center, Associate Professor, Pharmaceutical Chemistry and Role of Posttranslational Protein Modifications in Diabetic Chemical & Petroleum Engineering, University of Kansas Cardiomyopathy Redox Effects on Structure and Dynamics of PRL-1

Liang Tang (2008-2010, 2010-2012) Assistant Professor, Molecular Biosciences, University of Kansas Julian Limburg (2004-2007; deceased) Mechanisms of Genome Packaging in DNA Viruses Assistant Professor, Chemistry, University of Kansas Structure and Function of Bacterial Prolyl-4-hydroxylase

Qize Wei (2005-2007)

Assistant Professor, Biochemistry, Kansas State University William Picking (2002-2005) Roles of MyoGEF and its Interacting Partners in Cell Division Professor, Molecular Biosciences and Cell Signaling University of Kansas (professor and chair, Microbiology and Mo- Kandatege Wimalasena (2009-present) lecular Genetics, Oklahoma State University, Stillwater, OK) Professor, Chemistry, Wichita State University Subversion of Eukaryotic Cell Function by Shigella Structure-Activity Relationship Studies of Dopamine beta-Monooxygenase Emily Scott (2004-2007) Associate Professor, Medicinal Chemistry, Asma Zaidi (2004-2007) University of Kansas Res. Assistant Professor, Pharmacology & Toxicology, University of Structure-Function of Mammalian Cytochromes P450 Kansas (professor, biochemistry, Kansas City University of Medicine and Biosciences, MO) 2+ Jeffrey Staudinger (2002-2005) Trafficking of Plasma Membrane Ca -ATPase to Rafts Associate Professor, Pharmacology & Toxicology Core Laboratories University of Kansas The COBRE Center supports three Core Laboratories, each directed by a Crystallization of Pregnane X Receptor Splice Variants

highly experienced Ph.D. scientist. These fee- Liskin Swint-Kruse (2004-2007) for-service facilities are available to qualified Associate Professor, Biochemistry and Molecular Biology researchers in academia, not-for-profit, and University of Kansas Medical Center industry. Staff provide consultation in experi- Elucidating Structural Elements that Fine-tune the Function of mental design, assistance preparing grant Members in a Genetic Regulatory Protein applications and manuscripts, training in spe- cialized research techniques, access to state-of- Anna Zolkiewska (2002-2004) the-art research equipment (for experienced Associate Professor, Biochemistry, Kansas State University users), and a menu of research services. The Structure and Function of Cell Adhesion Domain of ADAM12 Del Shankel Structural Biology Center laboratories are in the Structural Biology Center (SBC), a facility devoted to advancing biomedical and bioscience research. Emeritus Pilot Project Directors (cont.) Pilot Project Directors Pilot project grants are awarded to junior faculty, COBRE graduates or other David Eichhorn (2004-2007) faculty making a significant effort to address aspects of protein structure and function. Professor and Chair, Chemistry, Wichita State University Synthesis of Model Complexes for Nitrile Hydratase Katsura Asano (2012-present) Associate Professor, Biology, Kansas State University Molecular basis of control of translational initiation in eukaryotes Weijun Huang (2004-2007) Director, Protein Structure Laboratory, University of Kansas Revathi Govind (2012-present) Structural and Functional Studies on D52 Tumor Proteins from Assistant Professor, Biology, Kansas State University Human Tissue Structure-function studies on Clostridium difficile anti-sigma factor TcdC Wonpil Im (2008-2010) Associate Professor, Molecular Biosciences, University of Kansas P. Scott Hefty (2012-present) NMR and Computational Studies of Protein Translocation in Bac- Assistant Professor, Molecular Biosciences, University of Kansas terial Needles Structural and functional genomics for Chlamydial hypothetical proteins John Karanicolas (2009-2011; ARRA) Assistant Professor, Molecular Biosciences, University of Kansas Ping Li (2012-present) Towards Novel Inhibitors of OX40L-OX40: A Dominant Assistant Professor, Chemistry, Kansas State University Negative Approach Expression and purification of an obesity-important enzyme Shiguang Liu (2004-2007) hGOAT in E. coli Research Assistant Professor, The Kidney Institute, Mario Rivera (2008, 2010-2012, 2012-present) University of Kansas Medical Center Professor, Chemistry, University of Kansas Identification of Inhibitors and Substrates of Phex

Probes to disrupt iron homeostasis in Pseudomonas aeruginosa Kristin Michel (2009-2011; ARRA) Assistant Professor, Biology, Kansas State University

Structure and Target Protease of Anopheles SRPN6, an Inhibitor Emeritus Pilot Project Directors of Malaria Parasite Infection James Bann (2005-2007) Alexander Moise (2009-2011; ARRA) Assistant Professor, Chemistry, Wichita State University Assistant Professor, Pharmacology and Toxicology Structure and Mechanism of CS1 Pilus Assembly University of Kansas Structural Characterization of Lecithin:Retinol Acyltransferase

Xue-Wen Chen (2004-2007) Silvia Mora (2004-2006) Assistant Professor, Electrical Engineering and ComputerSciences, Assistant Professor, Biology, Kansas State University (currently University of Kansas researcher, Molecular Physiology, University of Liverpool, UK) Computational Proteomics: Protein Interaction Prediction Protein Interactions that Regulate Leptin Secretion

Roberto De Guzman (2008-2010) Robert R.R. Rowland (2004-2006) Associate Professor, Molecular Biosciences Professor, Diagnostic Medicine and Pathobiology University of Kansas Kansas State University Interactions of Salmonella Needle and Tip Proteins Structure/Nucleolar Function of SARS N Protein