Faculty Profile

Professional Summary:

The Malkowski Laboratory is focused on understanding the structure and function of integral membrane enzymes involved in the conversion of lipid precursors into potent bioactive signaling molecules. We utilize a myriad of methods and techniques to characterize these enzymes, including X-ray crystallography, electron spin resonance spectroscopy, protein chemistry, biochemistry, molecular biology, cell biology, and kinetics.

Education and Training:

PhD, Biochemistry, Wayne State University (1997)
BS, Chemistry, University of Detroit, Magna Cum Laude (1991)

Employment:

Professor, Structural Biology, SUNY at Buffalo (2014-present)
Principal Research Scientist, Hauptman-Woodward Medical Research Institute (2012-present)
Assistant Professor, Structural Biology, SUNY at Buffalo (2002–2014)
Senior Research Scientist, Hauptman-Woodward Medical Research Institute (2007–2012)
Research Scientist, Hauptman-Woodward Medical Research Institute (2001–2007)
NIH Postdoctoral Fellow, Biochemistry, Michigan State University (1997–2001)

Awards and Honors:

Eicosanoid Research Foundation Young Investigator Award (2011)
Arthritis Investigator Award, Arthritis Foundation (2005)
NRSA Individual Postdoctoral Fellowship, National Institutes of Health (1999)
NIH Predoctoral Training Fellowship, Wayne State University (1993)
Merck Index Award, Outstanding Chemistry Student, University of Detroit (1991)
Presidential Scholarship, University of Detroit, Detroit, MI (1987)

Research Expertise:

Fatty Acid Metabolism: Interested in membrane associated enzymes involved in the (di)oxygenation of fatty acid substrates. Current systems being studied in the lab include 1) cyclooxygenase-1 and -2 (COX-1 and COX-2); and 2) pathogen-inducible oxygenase (PIOX).
Protein Expression and Purification: Extensive technical expertise in: 1) the expression of prokaryotic and eukaryotic proteins in E. coli, S. cerevisiae, and insect cell expression hosts; 2) purification of soluble and membrane proteins using various modes of column chromatography.
Structural Biology of Membrane Proteins: Expertise in structure-function studies of membrane proteins, including 1) expression in insect cells, E. coli, and S. cerevisiae; 2) detergent solubilization; 3) purification; 4) pre-crystallization screening of protein-detergent complexes; and 5) high-throughput crystallization screening and optimization.
X-ray Crystallography: Expertise in all aspects of structure determination using x-ray crystallographic methods, including: 1) high-throughput crystallization screening and optimization; 2) cryopreservation; 3) in-house and synchrotron data collection; 4) phasing (MIR and MAD); and 5) refinement and model building.

UB 2020 Strategic Strengths:

Molecular Recognition in Biological Systems and Bioinformatics

Grants and Sponsored Research:

August 2015–July 2019
Structure and Dynamics of Cyclooxygenase Catalysis and Inhibition
NIH/NIGMS
Role: Principal Investigator
April 2013–March 2018
Characterization of Treponema pallidum Rare Outer Membrane Proteins
National Institutes of Health/NIAID
Role: Co-Investigator
July 2010–June 2015
Multi-Level Optimization of Membrane Proteins for Crystallography
NIGMS
Role: Principal Investigator
September 2011–May 2015
Catalysis by Prostaglandin Endoperoxide H Synthases
NIGMS
Role: Co-Investigator
February 2007–January 2012
Structure Biology of Oxylipin Biosynthesis
NIH/NIGMS
Role: Principal Investigator

Journal Articles:

Malkowski MG, Ginell SL, Smith WL, Garavito RM. The productive conformation of arachidonic acid bound to prostaglandin synthase. Science. 2000; 289(5486).
Dong L, Yuan C, Orlando BJ, Malkowski MG, Smith WL. Fatty Acid Binding to the Allosteric Subunit of Cyclooxygenase-2 Relieves a Tonic Inhibition of the Catalytic Subunit. J Biol Chem. 2016; 291(49).
Orlando BJ, Malkowski MG. Crystal structure of rofecoxib bound to human cyclooxygenase-2. Acta Crystallogr F Struct Biol Commun. 2016; 72(Pt 10).
Murphy TF, Kirkham C, Johnson A, Brauer AL, Koszelak-Rosenblum M, Malkowski MG. Sulfate-binding protein, CysP, is a candidate vaccine antigen of Moraxella catarrhalis. Vaccine. 2016; 34(33).
Orlando BJ, Malkowski MG. Substrate-selective Inhibition of Cyclooxygeanse-2 by Fenamic Acid Derivatives Is Dependent on Peroxide Tone. J Biol Chem. 2016; 291(29).
Lucido MJ, Orlando BJ, Vecchio AJ, Malkowski MG. Crystal Structure of Aspirin-Acetylated Human Cyclooxygenase-2: Insight into the Formation of Products with Reversed Stereochemistry. Biochemistry. 2016; 55(8).
Otsuka T, Kirkham C, Brauer A, Koszelak-Rosenblum M, Malkowski MG, Murphy TF. The Vaccine Candidate Substrate Binding Protein SBP2 Plays a Key Role in Arginine Uptake, Which Is Required for Growth of Moraxella catarrhalis. Infect Immun. 2016; 84(2).
Orlando BJ, Borbat PP, Georgieva ER, Freed JH, Malkowski MG. Pulsed Dipolar Spectroscopy Reveals That Tyrosyl Radicals Are Generated in Both Monomers of the Cyclooxygenase-2 Dimer. Biochemistry. 2015.
Otsuka T, Kirkham C, Brauer A, Koszelak-Rosenblum M, Malkowski MG, Murphy TF. The Vaccine Candidate, Substrate Binding Protein SBP2, Plays a Key Role in Arginine Uptake, which is Required for Growth of Moraxella catarrhalis. Infect Immun. 2015.
Zhu G, Koszelak-Rosenblum M, Connelly SM, Dumont ME, Malkowski MG. The crystal structure of an integral membrane fatty acid a-hydroxylase. J Biol Chem. 2015.
Bauer WJ, Luthra A, Zhu G, Radolf JD, Malkowski MG, Caimano MJ. Structural characterization and modeling of the Borrelia burgdorferi hybrid histidine kinase Hk1 periplasmic sensor: A system for sensing small molecules associated with tick feeding. J Struct Biol. 2015; 192(1).
Anand A, LeDoyt M, Karanian C, Luthra A, Koszelak-Rosenblum M, Malkowski MG, Puthenveetil R, Vinogradova O, Radolf JD. Bipartite Topology of Treponema pallidum Repeat Proteins C/D and I: OUTER MEMBRANE INSERTION, TRIMERIZATION, AND PORIN FUNCTION REQUIRE A C-TERMINAL ß-BARREL DOMAIN. J Biol Chem. 2015; 290(19).
Orlando BJ, Lucido MJ, Malkowski MG. The structure of ibuprofen bound to cyclooxygenase-2. J Struct Biol. 2015; 189(1).
Jones MM, Johnson A, Koszelak-Rosenblum M, Kirkham C, Brauer AL, Malkowski MG, Murphy TF. Role of the oligopeptide permease ABC Transporter of Moraxella catarrhalis in nutrient acquisition and persistence in the respiratory tract. Infect Immun. 2014; 82(11).
Orlando BJ, McDougle DR, Lucido MJ, Eng ET, Graham LA, Schneider C, Stokes DL, Das A, Malkowski MG. Cyclooxygenase-2 catalysis and inhibition in lipid bilayer nanodiscs. Arch Biochem Biophys. 2014; 546.
Zhu G, Koszelak-Rosenblum M, Malkowski MG. Crystal structures of a-dioxygenase from Oryza sativa: insights into substrate binding and activation by hydrogen peroxide. Protein Sci. 2013; 22(10).
Murphy TF, Brauer AL, Kirkham C, Johnson A, Koszelak-Rosenblum M, Malkowski MG. Role of the Zinc Uptake ABC Transporter of Moraxella catarrhalis in Persistence in the Respiratory Tract. Infect Immun. 2013; 81(9).
Pryor EE, Horanyi PS, Clark KM, Fedoriw N, Connelly SM, Koszelak-Rosenblum M, Zhu G, Malkowski MG, Wiener MC, Dumont ME. Structure of the integral membrane protein CAAX protease Ste24p. Science. 2013; 339(6127).
Goulah CC, Zhu G, Koszelak-Rosenblum M, Malkowski MG. The Crystal Structure of a-Dioxygenase Provides Insight into Diversity in the Cyclooxygenase-Peroxidase Superfamily. Biochemistry. 2013; 52(8).
Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A. Coordinating the impact of structural genomics on the human a-helical transmembrane proteome. Nat Struct Mol Biol. 2013; 20(2).
Vecchio AJ, Orlando BJ, Nandagiri R, Malkowski MG. Investigating substrate promiscuity in cyclooxygenase-2: the role of Arg-120 and residues lining the hydrophobic groove. J Biol Chem. 2012; 287(29).
Luthra A, Zhu G, Desrosiers DC, Eggers CH, Mulay V, Anand A, McArthur FA, Romano FB, Caimano MJ, Heuck AP, Malkowski MG, Radolf JD. The transition from closed to open conformation of Treponema pallidum outer membrane-associated lipoprotein TP0453 involves membrane sensing and integration by two amphipathic helices. J Biol Chem. 2011; 286(48).
Vecchio AJ, Malkowski MG. The structure of NS-398 bound to cyclooxygenase-2. J Struct Biol. 2011; 176(2).
Vecchio AJ, Malkowski MG. The structural basis of endocannabinoid oxygenation by cyclooxygenase-2. J Biol Chem. 2011; 286(23).
Dong L, Vecchio AJ, Sharma NP, Jurban BJ, Malkowski MG, Smith WL. Human cyclooxygenase-2 is a sequence homodimer that functions as a conformational heterodimer. J Biol Chem. 2011; 286(21).
Vecchio AJ, Simmons DM, Malkowski MG. Structural basis of fatty acid substrate binding to cyclooxygenase-2. J Biol Chem. 2010; 285(29).
Calamini B, Ratia K, Malkowski MG, Cuendet M, Pezzuto JM, Santarsiero BD, Mesecar AD. Pleiotropic mechanisms facilitated by resveratrol and its metabolites. Biochem J. 2010; 429(2).
Clark KM, Fedoriw N, Robinson K, Connelly SM, Randles J, Malkowski MG, Detitta GT, Dumont ME. Purification of transmembrane proteins from Saccharomyces cerevisiae for X-ray crystallography. Protein Expr Purif. 2010; 71(2).
Koszelak-Rosenblum M, Krol A, Mozumdar N, Wunsch K, Ferin A, Cook E, Veatch CK, Nagel R, Luft JR, Detitta GT, Malkowski MG. Determination and application of empirically derived detergent phase boundaries to effectively crystallize membrane proteins. Protein Sci. 2009; 18(9).
Snell EH, Luft JR, Potter SA, Lauricella AM, Gulde SM, Malkowski MG, Koszelak-Rosenblum M, Said MI, Smith JL, Veatch CK, Collins RJ, Franks G, Thayer M, Cumbaa C, Jurisica I, Detitta GT. Establishing a training set through the visual analysis of crystallization trials. Part I: approximately 150,000 images. Acta Crystallogr D Biol Crystallogr. 2008; 64(Pt 11).
Snell EH, Lauricella AM, Potter SA, Luft JR, Gulde SM, Collins RJ, Franks G, Malkowski MG, Cumbaa C, Jurisica I, DeTitta GT. Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples. Acta Crystallogr D Biol Crystallogr. 2008; 64(Pt 11).
Koszelak-Rosenblum M, Krol AC, Simmons DM, Goulah CC, Wroblewski L, Malkowski MG. His-311 and Arg-559 are key residues involved in fatty acid oxygenation in pathogen-inducible oxygenase. J Biol Chem. 2008; 283(36).
Fox BG, Goulding C, Malkowski MG, Stewart L, Deacon A. Structural genomics: from genes to structures with valuable materials and many questions in between. Nat Methods. 2008; 5(2).
Malkowski MG, Quartley E, Friedman AE, Babulski J, Kon Y, Wolfley J, Said M, Luft JR, Phizicky EM, DeTitta GT, Grayhack EJ. Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing. Proc Natl Acad Sci U S A. 2007; 104(16).
Luft JR, Wolfley JR, Said MI, Nagel RM, Lauricella AM, Smith JL, Thayer MH, Veatch CK, Snell EH, Malkowski MG, Detitta GT. Efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature. Protein Sci. 2007; 16(4).
Garavito RM, Malkowski MG, DeWitt DL. The structures of prostaglandin endoperoxide H synthases-1 and -2. Prostaglandins Other Lipid Mediat. 2002; 68-69.
Malkowski MG, Thuresson ED, Lakkides KM, Rieke CJ, Micielli R, Smith WL, Garavito RM. Structure of eicosapentaenoic and linoleic acids in the cyclooxygenase site of prostaglandin endoperoxide H synthase-1. J Biol Chem. 2001; 276(40).
Thuresson ED, Malkowski MG, Lakkides KM, Rieke CJ, Mulichak AM, Ginell SL, Garavito RM, Smith WL. Mutational and X-ray crystallographic analysis of the interaction of dihomo-gamma -linolenic acid with prostaglandin endoperoxide H synthases. J Biol Chem. 2001; 276(13).
Thuresson ED, Lakkides KM, Rieke CJ, Sun Y, Wingerd BA, Micielli R, Mulichak AM, Malkowski MG, Garavito RM, Smith WL. Prostaglandin endoperoxide H synthase-1: the functions of cyclooxygenase active site residues in the binding, positioning, and oxygenation of arachidonic acid. J Biol Chem. 2001; 276(13).
Malkowski MG, Theisen MJ, Scharmen A, Garavito RM. The formation of stable fatty acid substrate complexes in prostaglandin H(2) synthase-1. Arch Biochem Biophys. 2000; 380(1).
Martin PD, Malkowski MG, Box J, Esmon CT, Edwards BF. New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK. Structure. 1997; 5(12).
Malkowski MG, Martin PD, Lord ST, Edwards BF. Crystal structure of fibrinogen-Aalpha peptide 1-23 (F8Y) bound to bovine thrombin explains why the mutation of Phe-8 to tyrosine strongly inhibits normal cleavage at Arg-16. Biochem J. 1997; 326 (.
Malkowski MG, Martin PD, Guzik JC, Edwards BF. The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding. Protein Sci. 1997; 6(7).
Malkowski MG, Lazar JB, Johnson PH, Edwards BF. The amino-terminal residues in the crystal structure of connective tissue activating peptide-III (des10) block the ELR chemotactic sequence. J Mol Biol. 1997; 266(2).
Martin PD, Malkowski MG, DiMaio J, Konishi Y, Ni F, Edwards BF. Bovine thrombin complexed with an uncleavable analog of residues 7-19 of fibrinogen A alpha: geometry of the catalytic triad and interactions of the P1‘, P2‘, and P3‘ substrate residues. Biochemistry. 1996; 35(40).
Vitali J, Martin PD, Malkowski MG, Olsen CM, Johnson PH, Edwards BF. Structure of a bovine thrombin-hirudin51-65 complex determined by a combination of molecular replacement and graphics. Incorporation of known structural information in molecular replacement. Acta Crystallogr D Biol Crystallogr. 1996; 52(Pt 3).
Malkowski MG, Wu JY, Lazar JB, Johnson PH, Edwards BF. The crystal structure of recombinant human neutrophil-activating peptide-2 (M6L) at 1.9-A resolution. J Biol Chem. 1995; 270(13).
Vitali J, Martin PD, Malkowski MG, Robertson WD, Lazar JB, Winant RC, Johnson PH, Edwards BF. The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8-A resolution. J Biol Chem. 1992; 267(25).

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Professional Memberships:

American Society for Biochemistry and Molecular Biology (2009–present)

Presentations:

"New Insights into Cyclooxygenase Catalysis and Inhibition" Seminar Series, University of Connecticut, Department of Molecular Biology and Biochemistry (2016)
"New Perspectives in Cyclooxygenase Structure, Function, and Dynamics" Seminar Series, SUNY at Buffalo, Department of Oral Biology (2014)
"Investigating Cyclooxygenase-2 Catalysis and Inhibition in a Lipid Bilayer" Bioactive Lipids in Cancer, Inflammation, and Related Disease 13th International Conference, Eicosanoid Research Foundation (2013)
"Monotopic Membrane Enzymes: Structural Features that Govern Catalysis at the Membrane Interface" Advanced Photon Source User's Meeting, Argonne National Laboratory (2013)
"Do Plants Have COX? Structural Studies of a Cyclooxygenase-like alpha-dioxygenase from Arabidopsis" , Hospital for Sick Kids, Department of Molecular and Structural Function (2012)
"Flexibility Drives Substrate Promiscuity in Cyclooxygenase-2" CHESS User's Meeting, Cornell University (2012)
"Insights into the Oxygenation of Substrates by COX-2" , SUNY-IT, Department of Chemistry (2012)
"Molecular Features that Govern the Oxygenation of Substrates by COX-2" 14th Winter Eicosanoid Conference (2012)
"The Structure of alpha-Dioxygenase: a Case Study in the Use of Detergent Phase Boundaries to Crystallize Membrane Proteins" , Michigan State University, Department of Biochemistry (2011)
"The Who, What, and Why of Structural Biology" , University of Detroit-Mercy, Department of Chemistry (2011)
"Substrate Binding to Cyclooxygenase-2: Insight into Specificity and Catalysis" Bioactive Lipids in Cancer, Inflammation, and related Diseases 12th International Conference, Eicosanoid Research Foundation (2011)
"High-Throughput Crystallization Screening for the Structural Biology Community" American Crystallographic Association Annual Meeting, American Crystallographic Association (2011)
"Structural Studies of Fatty Acid Oxygenation by Membrane Bound Enzymes" The Institute for Molecular Diversity and Drug Design 13th Annual Symposium, University of Louisville (2011)
"Using Experimentally Derived Detergent Phase Boundaries to Facilitate Crystallization of Membrane Proteins" 13th International Conference on the Crystallization of Biomolecules (2010)
"Multi-Level Optimization of Membrane Proteins" PSI:Biology Kickoff Meeting, National Institutes of Health, National Institute for General Medical Sciences (2010)
"Just a Phase? Using Experimentally-derived Detergent Phase Boundaries to Facilitate Crystallization of Membrane Proteins" 40th Mid-Atlantic Crystallography Meeting (2010)
"Using Experimentally-Derived Detergent Phase Boundaries to Facilitate Crystallization of Membrane Proteins" , GlaxoSmithKline (2010)
"Then and Now: Structural Biology of Cyclooxygenase-2" , Vanderbilt University, Institute of Chemical Biology (2010)
"CHTSB: Technology Development Highlights" Protein Structure Initiative Annual Meeting, National Institutes of Health, National Institute of General Medical Sciences (2009)
"Molecular Determinants Governing Oxylipin Biosynthesis in Fatty Acid Oxygenases" , Johns Hopkins University, Department of Chemistry (2009)
"Recent Advances in Membrane Protein Crystallization: Determination and Application of Empirically-Derived Detergent Phase Boundaries for Crystallization" 2009 SSRL/LCLS User's Meeting, Stanford University (2009)
"Molecular Determinants Governing Fatty Acid Oxygenation in alpha-dioxygenases" Regulatory Oxylipins: an International Symposium (2009)
"Technology Development Efforts at the Center for High-Throughput Structural Biology" Protein Structure Initiative Annual Meeting, National Institutes of Health, National Institute of General Medical Sciences (2008)
"Using Detergent Phase Boundaries to Crystallize Membrane Proteins" Protein Structure Initiative 7th Bottlenecks Workshop, National Institutes of Health, National Institute of General Medical Sciences (2008)
"Technology Developments at the CHTSB" Protein Structure Initiative Annual Meeting, National Institues of Health, National Institute of General Medical Sciences (2007)
"The Utilization of Detergent Phase Boundary Information for Crystallizing Membrane Proteins" 65th Annual Pittsburgh Diffraction Conference, Pittsburgh Diffraction Society (2007)
"The Center for High-Throughput Structural Biology: Show Me the Bottlenecks" Protein Structure Initiative's 6th Bottlenecks Workshop, National Institutes of Health, National Institute of General Medical Sciences (2007)
"Oxylipin Biosynthesis in Pathogen-Inducible Oxygenase" Biophysics and Structural Biology Retreat, University of Rochester (2007)
"Novel Oxygenations of Arachidonic Acid by Cyclooxygenases" Segal Osteoarthritis Symposium, Northwestern University (2006)
"Technology Development at the Center for High-Throughput Structural Biology" Protein Structure Initiative Annual Meeting, National Institues of Health, National Institute of General Medical Sciences (2006)
"The Center for High-Throughput Structural Biology" Protein Structure Initiative's 5th Bottlenecks Workshop, National Institutes of Health, National Institute of General Medical Sciences (2006)
"Novel Oxygenations of Polyunsaturated Fatty Acids" Upstate New York Structural Biology Day, University of Rochester (2003)
"Fatty Acid Interactions with Cyclooxygenases" , Roswell Park Cancer Institute, Department of Molecular and Cellular Biophysics (2001)
"Fatty Acid Substrate Interactions with Cyclooxygenases" 10th Buffalo-Hamilton-Toronto Crystallography Meeting (2001)
"Fatty Acid Substrate Interactions with Cyclooxygenases" 4th International Workshop on COX-2 (2001)

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Service Activities:

BioXFEL Faculty Search Committee; Committee Member (2016–present)
PPBS Admissions Commitee; Committee Member (2015–2016)
PPBS Steering Committee; Department of Structural Biology representative; Committee Member (2013–present)
IGPBS Admissions Assessment Committee; Department of Structural Biology representative; Committee Member (2008)
IGPBS Steering Committee; Department of Structural Biology representative; Committee Member (2001–2009)
IGPBS Admissions Committee; Department of Structural Biology representative; Committee Member (2001–2003)

Michael G. Malkowski PhD

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